[galaxy-dev] Re: (null):// header in visualisation links (IGV etc.)

[Martin Čech]

I don't know your setup but maybe you could serve Galaxy on a different
port without Apache/ssl to test.
M.

On Wed, Apr 14, 2021 at 11:58 AM  wrote:

> Uff, I'll try that, though it will take some time since I have to figure
> out what in my apache config belongs to the proxying and what to the
> standard ssl virtualhost config...
>
> Lubos
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[galaxy-dev] Re: (null):// header in visualisation links (IGV etc.)

[Martin Čech]

Lubos, do you have an opportunity to disable the proxy for a bit? So we can
narrow down the suspects.
Martin

On Wed, Apr 14, 2021 at 11:22 AM Lubos Klucar  wrote:

> Dear Helena,
>
> thanks a lot, but I'm afraid this is not the case - 'RequestHeader' is
> set as described.
>
> It should be probably some trivial mistake hidden somewhere in the
> config files, which enable/disable a proper construction of URL text
> string. I was looking everywhere, but still no luck.
>
> best
>
> Lubos
>
> On 14/04/2021 10:40, Helena Rasche wrote:
> > Your proxy might not be forwarding the protocol if that's the issue
> > you're seeing.
> >
> > e.g. for apache,
> https://docs.galaxyproject.org/en/master/admin/apache.html
> >
> >  # Galaxy needs to know that this is https for generating URLs
> >  RequestHeader  set X-URL-SCHEME"%{REQUEST_SCHEME}e" Hope that
> helps, Ciao
> >
> > On 14/04/2021 10:38, klu...@embnet.sk wrote:
> >> When clicking dataset visualisation links (UCSC, IGV, IGB, bam.iobio
> bam.iobio.io ...) on my galaxy installation [20.09] I'm always getting
> error:
> >>
> >> Error: (null)://
> mygalaxy.mydomain.org/display_application/3d954174ae8d
> >>
> >> When manually changing the link from "(null)://" to "https://; the
> link is fully functional.
> >>
> >> Other links from galaxy interface (download icon for any dataset) works
> without any problems.
> >>
> >> Any help would be highly appreciated!
> >>
> >> best
> >>
> >> Lubos
> >> ___
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>
> --
>
>  Lubos Klucar
>
>  Institute of Molecular Biology
>  Slovak Academy of Science
>  Dubravska cesta 21
>  845 51  Bratislava 45
>  Slovakia
>
>  Tel.: +421 2 5930 7413
>  Fax.: +421 2 5930 7416
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[galaxy-dev] Re: To implement a one-click test for a Galaxy tool.

[Martin Čech]

Hi Jin,

Galaxy has a functionality to generate tool tours using the tool's own
test data. See 
https://github.com/galaxyproject/galaxy/tree/dev/config/plugins/webhooks/demo/tour_generator

This functionality is enabled e.g. on usegalaxy.eu so you might want
to check it out and see if it fits your use case.

More related discussion here:
https://github.com/galaxyproject/galaxy/issues/7351

Cheers,
Martin

On Thu, Jul 2, 2020 at 1:17 AM Jin Li  wrote:
>
> Hi all,
>
> We have a tool in Galaxy at https://usegalaxy.eu/root?tool_id=moabs.
> We want to implement a one-click test using small data so that users
> can quickly understand how to use the interface. There are two
> difficulties in implementing the one-click test.
>
> 1. How to store small test data so that every new user can access it?
> 2. How to configure program settings automatically for the test data?
> so that the test data is automatically uploaded, and other parameters
> are pre-configured.
>
> Please help suggest any possible solution to a one-click test. Thank you.
>
> Best regards,
> Jin
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[galaxy-dev] Re: Problem with uploading data

[Martin Čech]

Hi Rodrigo,

I am not aware of any known issues with the rule based uploader that you
seem to be using. Please provide details about what Galaxy you are trying
this on and what error(s) you are getting.

Thanks,
Martin

On Fri, Nov 22, 2019 at 1:58 PM Rodrigo Machado via galaxy-dev <
galaxy-dev@lists.galaxyproject.org> wrote:

> Hello and to whom it may concern.
> As I point out in the matter, I am having trouble uploading information,
> particularly a BIOPROJECT that has already uploaded.
> I am taking exactly the same steps that I previously used to load this
> database. I don't understand if Galaxy is not working properly today or
> what it can be.
> I am loading it from: Download from web or upload from disk / Upload data
> as: Collection (s) / Load tabular data from: (pasted table).
> Thank you in advance and sorry for the inconvenience
>
>
>
> Lic. Rodrigo Machado
> JTP Introducción a la Biología, TGG - UNER
> Becario Doctoral
> EEA INTA Concordia
> Estación Yuquerí - Ruta 22 y vías FFCC - CC 34
> Concordia - Entre Ríos - Argentina
> Tel. +54-345-429 (int. 162)
>
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[galaxy-dev] Re: Error when installing from toolshed

[Martin Čech]

This might have something to do with the client build. Could you try
running 'make client` from Galaxy root folder?

Also what version of Galaxy are you experiencing this on, just 19.01 or did
you use different locally? And how are you starting Galaxy?

Martin

On Wed, Jul 31, 2019 at 1:16 PM Nancy Ide  wrote:

> I very much appreciate the offer, but unfortunately I have to leave now. I
> am at a conference in Florence and tomorrow is our demo at a workshop, so I
> would be unable to do it tomorrow either, but anytime Friday would work if
> that is possible.
>
> We are now having the same problem on the jetstream instance, but earlier
> we were able to install with the beta installer although not the regular
> one. However, just now on my local instance I tried to use the installer
> again, but I can’t get even to the repository (there is a message that the
> repository queue was loaded and has 0 elements). When I click on the
> “Galaxy Main Toolshed” button I can select one of the options but nothing
> happens. This is also true now on our jetstream instance.
>
>
> On Jul 31, 2019, at 7:02 PM, Martin Čech  wrote:
>
> Would you like to come to the admin channel so we can troubleshoot this
> interactively? https://gitter.im/galaxyproject/admins
>
> Martin
>
> On Wed, Jul 31, 2019 at 12:56 PM Nancy Ide  wrote:
>
>> Please look at jetstream.lappsgrid.org — this is the development version
>> I was using.
>>
>> When I tried to pull from github it complained that some of my”untracked”
>> files would be overwritten. I did a git stash but 3 files still were said
>> to be overwritten, and I simply deleted those. The pull then went on
>> uneventfully.
>>
>> On Jul 31, 2019, at 6:53 PM, Martin Čech  wrote:
>>
>> I see version 18.09 at http://galaxy.lappsgrid.org/ - are you trying to
>> update this instance to 19.01? Do you have any local changes or issues when
>> pulling new version?
>>
>> On Wed, Jul 31, 2019 at 12:36 PM Nancy Ide  wrote:
>>
>>> Hello
>>>
>>> Cookies were enabled—also I was updating from our galaxy instance for
>>> the LAPPS Grid, which is using version 19.01.
>>>
>>> On Jul 31, 2019, at 6:34 PM, Martin Čech  wrote:
>>>
>>> Hi Nancy,
>>>
>>> what versions of Galaxy did you update from and to? Please check if you
>>> have cookies enabled in your browser.
>>>
>>> Martin
>>>
>>> On Wed, Jul 31, 2019 at 9:45 AM Nancy Ide  wrote:
>>>
>>>> Hello
>>>>
>>>> I am suddenly (after pulling a new version of galaxy) unable to install
>>>> from the toolshed. The error is: Repository installation is not possible
>>>> due to an invalid Galaxy URL: None. You may need to enable
>>>> third-party cookies in your browser.
>>>>
>>>> Any idea how I can fix this?
>>>>
>>>>
>>>> -
>>>>
>>>> Nancy Ide
>>>> Professor of Computer Science
>>>>
>>>> Department of Computer Science
>>>> Vassar College
>>>> Poughkeepsie, New York 12604-0520
>>>> USA
>>>>
>>>> tel: (+1 845) 437 5988
>>>> fax: (+1 845) 437 7498
>>>> email: i...@cs.vassar.edu
>>>> http://www.cs.vassar.edu/~ide
>>>>
>>>> -
>>>>
>>>>
>>>>
>>>>
>>>> ___
>>>> Please keep all replies on the list by using "reply all"
>>>> in your mail client.  To manage your subscriptions to this
>>>> and other Galaxy lists, please use the interface at:
>>>>   %(web_page_url)s
>>>>
>>>> To search Galaxy mailing lists use the unified search at:
>>>>   http://galaxyproject.org/search/
>>>>
>>>
>>> -
>>>
>>> Nancy Ide
>>> Professor of Computer Science
>>>
>>> Department of Computer Science
>>> Vassar College
>>> Poughkeepsie, New York 12604-0520
>>> USA
>>>
>>> tel: (+1 845) 437 5988
>>> fax: (+1 845) 437 7498
>>> email: i...@cs.vassar.edu 
>>> http://www.cs.vassar.edu/~ide
>>>
>>> -
>>>
>>>
>>>
>>>
>>>
>> -

[galaxy-dev] Re: Error when installing from toolshed

[Martin Čech]

Would you like to come to the admin channel so we can troubleshoot this
interactively? https://gitter.im/galaxyproject/admins

Martin

On Wed, Jul 31, 2019 at 12:56 PM Nancy Ide  wrote:

> Please look at jetstream.lappsgrid.org — this is the development version
> I was using.
>
> When I tried to pull from github it complained that some of my”untracked”
> files would be overwritten. I did a git stash but 3 files still were said
> to be overwritten, and I simply deleted those. The pull then went on
> uneventfully.
>
> On Jul 31, 2019, at 6:53 PM, Martin Čech  wrote:
>
> I see version 18.09 at http://galaxy.lappsgrid.org/ - are you trying to
> update this instance to 19.01? Do you have any local changes or issues when
> pulling new version?
>
> On Wed, Jul 31, 2019 at 12:36 PM Nancy Ide  wrote:
>
>> Hello
>>
>> Cookies were enabled—also I was updating from our galaxy instance for the
>> LAPPS Grid, which is using version 19.01.
>>
>> On Jul 31, 2019, at 6:34 PM, Martin Čech  wrote:
>>
>> Hi Nancy,
>>
>> what versions of Galaxy did you update from and to? Please check if you
>> have cookies enabled in your browser.
>>
>> Martin
>>
>> On Wed, Jul 31, 2019 at 9:45 AM Nancy Ide  wrote:
>>
>>> Hello
>>>
>>> I am suddenly (after pulling a new version of galaxy) unable to install
>>> from the toolshed. The error is: Repository installation is not possible
>>> due to an invalid Galaxy URL: None. You may need to enable
>>> third-party cookies in your browser.
>>>
>>> Any idea how I can fix this?
>>>
>>>
>>> -
>>>
>>> Nancy Ide
>>> Professor of Computer Science
>>>
>>> Department of Computer Science
>>> Vassar College
>>> Poughkeepsie, New York 12604-0520
>>> USA
>>>
>>> tel: (+1 845) 437 5988
>>> fax: (+1 845) 437 7498
>>> email: i...@cs.vassar.edu
>>> http://www.cs.vassar.edu/~ide
>>>
>>> -
>>>
>>>
>>>
>>>
>>> ___
>>> Please keep all replies on the list by using "reply all"
>>> in your mail client.  To manage your subscriptions to this
>>> and other Galaxy lists, please use the interface at:
>>>   %(web_page_url)s
>>>
>>> To search Galaxy mailing lists use the unified search at:
>>>   http://galaxyproject.org/search/
>>>
>>
>> -
>>
>> Nancy Ide
>> Professor of Computer Science
>>
>> Department of Computer Science
>> Vassar College
>> Poughkeepsie, New York 12604-0520
>> USA
>>
>> tel: (+1 845) 437 5988
>> fax: (+1 845) 437 7498
>> email: i...@cs.vassar.edu 
>> http://www.cs.vassar.edu/~ide
>>
>> -
>>
>>
>>
>>
>>
> -
>
> Nancy Ide
> Professor of Computer Science
>
> Department of Computer Science
> Vassar College
> Poughkeepsie, New York 12604-0520
> USA
>
> tel: (+1 845) 437 5988
> fax: (+1 845) 437 7498
> email: i...@cs.vassar.edu 
> http://www.cs.vassar.edu/~ide
>
> -
>
>
>
>
>
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[galaxy-dev] Re: Error when installing from toolshed

[Martin Čech]

I see version 18.09 at http://galaxy.lappsgrid.org/ - are you trying to
update this instance to 19.01? Do you have any local changes or issues when
pulling new version?

On Wed, Jul 31, 2019 at 12:36 PM Nancy Ide  wrote:

> Hello
>
> Cookies were enabled—also I was updating from our galaxy instance for the
> LAPPS Grid, which is using version 19.01.
>
> On Jul 31, 2019, at 6:34 PM, Martin Čech  wrote:
>
> Hi Nancy,
>
> what versions of Galaxy did you update from and to? Please check if you
> have cookies enabled in your browser.
>
> Martin
>
> On Wed, Jul 31, 2019 at 9:45 AM Nancy Ide  wrote:
>
>> Hello
>>
>> I am suddenly (after pulling a new version of galaxy) unable to install
>> from the toolshed. The error is: Repository installation is not possible
>> due to an invalid Galaxy URL: None. You may need to enable
>> third-party cookies in your browser.
>>
>> Any idea how I can fix this?
>>
>>
>> -
>>
>> Nancy Ide
>> Professor of Computer Science
>>
>> Department of Computer Science
>> Vassar College
>> Poughkeepsie, New York 12604-0520
>> USA
>>
>> tel: (+1 845) 437 5988
>> fax: (+1 845) 437 7498
>> email: i...@cs.vassar.edu
>> http://www.cs.vassar.edu/~ide
>>
>> -
>>
>>
>>
>>
>> ___
>> Please keep all replies on the list by using "reply all"
>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>   %(web_page_url)s
>>
>> To search Galaxy mailing lists use the unified search at:
>>   http://galaxyproject.org/search/
>>
>
> -
>
> Nancy Ide
> Professor of Computer Science
>
> Department of Computer Science
> Vassar College
> Poughkeepsie, New York 12604-0520
> USA
>
> tel: (+1 845) 437 5988
> fax: (+1 845) 437 7498
> email: i...@cs.vassar.edu 
> http://www.cs.vassar.edu/~ide
>
> -
>
>
>
>
>
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[galaxy-dev] Re: Error when installing from toolshed

[Martin Čech]

Hi Nancy,

what versions of Galaxy did you update from and to? Please check if you
have cookies enabled in your browser.

Martin

On Wed, Jul 31, 2019 at 9:45 AM Nancy Ide  wrote:

> Hello
>
> I am suddenly (after pulling a new version of galaxy) unable to install
> from the toolshed. The error is: Repository installation is not possible
> due to an invalid Galaxy URL: None. You may need to enable
> third-party cookies in your browser.
>
> Any idea how I can fix this?
>
>
> -
>
> Nancy Ide
> Professor of Computer Science
>
> Department of Computer Science
> Vassar College
> Poughkeepsie, New York 12604-0520
> USA
>
> tel: (+1 845) 437 5988
> fax: (+1 845) 437 7498
> email: i...@cs.vassar.edu
> http://www.cs.vassar.edu/~ide
>
> -
>
>
>
>
> ___
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> and other Galaxy lists, please use the interface at:
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>
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[galaxy-dev] Re: samtools_slice_bam/2.0.1 no options available

[Martin Čech]

Eric: I recommend https://help.galaxyproject.org/ for your question, it
might reach a better audience there.

Paula: I believe you can unsubscribe here:
https://lists.galaxyproject.org/lists/galaxy-dev.lists.galaxyproject.org/

Regards,

Martin

On Wed, May 22, 2019 at 12:49 PM Paula Berrutti 
wrote:

> Please,
>
> Remove my email fro the list
>
> Thank you,
>
> Paula
>
> Obter o Outlook para Android
>
> 
> From: Eric Kuyt 
> Sent: Wednesday, May 22, 2019 9:33:57 AM
> To: galaxy-dev@lists.galaxyproject.org
> Subject: [galaxy-dev] Re: samtools_slice_bam/2.0.1 no options available
>
> Is this the right spot for this question? Or is it better to ask elsewhere?
>
> On Mon, 13 May 2019 at 09:50, Eric Kuyt  wrote:
>
> > Hey all,
> >
> > I have a question about the samtools_slice_bam tool in the samtools
> suite.
> >
> > It seems the references variable remains empty after re-detecting
> > metadata. I now tried sorting the bam in galaxy and manually in samtools,
> > but no references coming up.
> >
> > I also ran a breakpoint in the binary.Bam.set_meta but it doesn't seem to
> > be catched.
> >
> > Any ideas? Thx.
> >
> > Eric
> >
> >
> >
> >
> >
> ___
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[galaxy-dev] Re: Nginx+Shibboleth+UCSC

[Martin Čech]

Hi Martin,

I am sorry you did not get any responses on the list, the reason for it is
most probably the lack of our experience with Shibboleth, which seemed to
be the main cause of the issues you were facing.

To answer your last question: the `display_as` is the path to put on the
proxy allow list because that is the url on which is UCSC going to request
the datasets. The method serving them is defined in
https://github.com/galaxyproject/galaxy/blob/release_19.01/lib/galaxy/webapps/galaxy/controllers/root.py#L230
and
is being called from
https://github.com/galaxyproject/galaxy/blob/release_19.01/lib/galaxy/web/framework/webapp.py#L536
.

Regards,

Martin

On Fri, Nov 2, 2018 at 7:04 PM Martin Demko <325...@mail.muni.cz> wrote:

> Dear list,
>
> I have been trying to manage an access to UCSC genome browser from our
> Galaxy
> instance which uses Nginx as a proxy with external authentication via
> Shibboleth and IdP service.
>
> Not even the configuration of nginx+shibboleth was quite complicated to
> achieve (but I succeeded after a week or so) but now during a testing
> phase, we
> have found out that a cooperation with external UCSC servers is forbidden
> due
> to our auth. configuration.
>
> I have found a way how to do that but only for Apache (
> https://docs.galaxyproject.org/en/master/admin/special_topics/apache.html#display-sites)
> so I tried to do something similar in Nginx but only with IP addresses as
> Nginx doesn't support using of named domains and defined a location:
>
> location /display_as {
>   satisfy any;
>   deny all;
>   allow 128.114.119.131;
>   allow 128.114.119.132;
>   allow 128.114.119.133;
>   allow 128.114.119.134;
>   allow 128.114.119.135;
>   allow 128.114.119.136;
> }
>
> Used IP addresses should be the right ones for UCSC servers according to
> few
> sources such as (
> https://genome.soe.ucsc.narkive.com/sll2JSk2/ucsc-ip-address):
>
> hgw1.cse.ucsc.edu
> hgw2.cse.ucsc.edu
> hgw3.cse.ucsc.edu
> hgw4.cse.ucsc.edu
> hgw5.cse.ucsc.edu
> hgw6.cse.ucsc.edu
>
> I tried to change the location also to "/display_application" but didn't
> help
> (actually, I don't know why in the documentation there is used as the
> location
> that "/display_as" as I have never encountered such location in Galaxy
> which is
> my first question). In galaxy.ini I set:
>
> display_servers = hgw1.cse.ucsc.edu,hgw2.cse.ucsc.edu,hgw3.cse.ucsc.edu,
> hgw4.cse.ucsc.edu,hgw5.cse.ucsc.edu,hgw6.cse.ucsc.edu,hgw7.cse.ucsc.edu,
> hgw8.cse.ucsc.edu,lowepub.cse.ucsc.edu
> ,128.114.119.131,128.114.119.132,128.114.119.133,128.114.119.134,128.114.119.135,128.114.119.136
>
> Just for case I used both, the domains and also IP addresses. Also I have
> tried to use only the domains or only the addresses but nothing helped.
>
> Then I found out after reading of the following (
> https://www.switch.ch/aai/guides/sp/access-rules/) that the main obstacle
> should be actually shibboleth so I defined in
> /etc/shibboleth/shibboleth2.xml an unrestricted path:
>
> 
>   
>authType="shibboleth"
>   requireSession="true"
>   redirectToSSL="443" >
>redirectToSSL="443" />
>   
> 
>   
> 
>
> Again, I have tried to use both locations "display_as" and
> "display_application", but it
> haven't solved my problem entirely. I moved forward I suppose because now
> the
> requests
> should be going around the authentication but UCSC stil warns me that:
>
> Expected 200
> https://our.galaxy.something/display_application/e1304269a2f56a52/ucsc_bigwig/main/867c307aa7fe349f/param/track:
> 403 Forbidden
>
> Before that it was a different message containing the address of our idp
> server so I believe I'am on the right way here. The presence of attribute
> 'authType="shibboleth"' seams to be useless as 'requireSession="false"' is
> used.
>
> Then I tried to teach Nginx to use also the domain names with the using of
> 3rd
> party nginx-http-rdns module from (
> https://github.com/flant/nginx-http-rdns),
> so my nginx.conf looked like:
>
> only the part of nginx.conf
> ## Shibboleth authentication conf #
>
> # FastCGI authorizer for Shibboleth Auth Request module
> location = /shibauthorizer {
> internal;
> include fastcgi_params;
> fastcgi_pass unix:/var/run/shibboleth/shibauthorizer.sock;
> }
>
> # FastCGI responder for SSO
> location /Shibboleth.sso {
> include fastcgi_params;
> fastcgi_pass unix:/var/run/shibboleth/shibresponder.sock;
> }
>
> ### Entry point for Galaxy ###
> # Location secured by Shibboleth
> location / {
> shib_request /shibauthorizer;
> more_clear_input_headers 'Variable-*' 'Shib-*' 'Remote-User' 'REMOTE_USER'
> 'Auth-Type' 'AUTH_TYPE' 'GX_SECRET';
> include uwsgi_params;
> shib_request_set $shib_id $upstream_http_variable_eppn;
> uwsgi_param HTTP_REMOTE_USER $shib_id;
> uwsgi_param HTTP_GX_SECRET $our_secret;
> uwsgi_pass 127.0.0.1:4001;
>
> # resolver $correct_resolver_acc_to_resolv.conf;
> # rdns on;
> # satisfy 

Re: [galaxy-dev] [External] Copying files to FTP upload directory

[Martin Čech]

Hi Keith,

your message is not bouncing, it shows here:
http://dev.list.galaxyproject.org/

Your setup seems correct to me, does Galaxy have permission to read files
in the given folders?

Also Galaxy will auto-create folders if set the `user_library_import_dir`
to be the same as ftp and use `#user_library_import_dir_auto_creation:
false`

M.

On Fri, Jan 25, 2019 at 4:58 PM Keith Suderman 
wrote:

> I have been creating directories for the users, but putting files in (for
> example) /home/galaxy/database/ftp/u...@example.com does not make them
> available for the u...@example.com user in Galaxy.
>
> Also for the list admins... I never did see my message appear on the list
> and the message Cicada replied to appears to be from
> galaxy-dev-boun...@lists.galaxyproject.org.  Any ideas why my message(s)
> appear to be bouncing.  I am pretty sure I am sending from the correct
> address.
>
> Cheers,
> Keith
>
> On Jan 25, 2019, at 4:36 PM, Dennis, H. E. Cicada Brokaw 
> wrote:
>
> I think you have to create the user's directories under
> /home/galaxy/database/ftp. I don't think Galaxy will create them if they
> are not there.
> Cicada
>
> 
> From: galaxy-dev  on behalf
> of Keith Suderman 
> Sent: Friday, January 25, 2019 4:01 PM
> To: Galaxy Dev List
> Subject: [External] [galaxy-dev] Copying files to FTP upload directory
>
>
>
> Hello,
>
> I am trying to (ab)use the FTP file upload functionality to get data from
> an external service into Galaxy.  From my reading of the docs I simply need
> to configure the ftp_upload_dir and ftp_upload_site in my galaxy.ini
> (haven't migrated to yaml yet) and Galaxy will expect to find
> subdirectories named after the user's account (email) in the ftp_upload_dir.
>
> I have configured the ftp_upload_dir (/home/galaxy/database/ftp in our
> case) and the "Choose FTP File" button is now available in the Upload
> dialog, however regardless of where I put files, or what I name them,
> Galaxy always reports that "Your FTP directory does not contain any files."
>  For example, if I have the user account u...@example.org I would expect
> to be able to place files in /home/galaxy/database/ftp/u...@example.org
> and they will be available in the Upload dialog for the u...@example.org
> user.  However, this is not working; am I missing something?
>
> Thanks,
> Keith
>
>
> ___
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Re: [galaxy-dev] Search box in tools menu / uncomplete wrappers list

[Martin Čech]

Hi Sarah,

toolpanel search in Galaxy is configurable. Due to limited space the
default number of results shown is 20 so if there are more you are not
going to see them. You can also change weights of various search attributes
or use ngram search. Please see the config options explained in the sample
here:
https://github.com/galaxyproject/galaxy/blob/dev/config/galaxy.yml.sample#L1147

Please, let us know if you have more questions.

Thanks,

Martin

On Fri, Nov 9, 2018 at 12:04 PM Sarah Maman  wrote:

>
> Hello,
>
>
> When I’m searching a keyword in the « search » box in left « tools » menu,
> results are sometimes false because the wrappers' list generated by the
> query thanks to a keyword is not full, some tools are missing. In fact,
> some wrappers are not listed even if the keyword is in the tool name and/or
> the tool description.
>
> Could you please help us to understand why ?
>
>
> Thanks,
>
> Sarah Maman
>
>
>
>
>
> *_ **Sarah* *Maman*
>
> Bioinformatique/Bioinformatics
>
> INRA | SIGENAE | GenPhySE
>
>
> *Centre Inra Occitanie-Toulouse *Tél. : +33(0)5.61.28.57.08
> <+33%205%2061%2028%2057%2008>
>
> *_*
>
> Chemin de Borde Rouge CS 52627
> 31326 Castanet Tolosan cedex
>
> *www.toulouse.inra.fr* 
>
> *Suivez-nous sur Twitter !*
> ___
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Re: [galaxy-dev] Get Data and 'xlsx'

[Martin Čech]

Hi all,

I can confirm this file is sniffed as `format: blastxml` on usegalaxy.org,
which is surely wrong.

I created an issue for it here:
https://github.com/galaxyproject/galaxy/issues/6849

M.



On Wed, Oct 10, 2018 at 2:11 PM D K  wrote:

> Sure, I've attached a sample xlsx file and my datatypes_conf.xml file
>
> Thanks!
>
> On Tue, Oct 9, 2018 at 11:52 PM Peter Cock 
> wrote:
>
>> That sounds very strange - could you share the test file (ideally
>> publicly, but at least by private email)? Modern MS files do use XML but I
>> don't understand how it would be recognised as BLAST XML...
>>
>> It may also be useful to see your Galaxy data types configuration file.
>>
>> Peter
>>
>
>> On Wed, 10 Oct 2018 at 01:39, D K  wrote:
>>
>>> It looks like uploading 'xlsx' data through 'Get Data' is not working.
>>> When I try this on my local Galaxy (v18.05) and on usegalaxy.org it
>>> gets automatically converted to 'BLAST xml' when using Automatic Detection.
>>> If I select 'xlsx' during uploading I get the error message ( Warning:
>>> The file 'Type' was set to 'xlsx' but the file does not appear to be of
>>> that type  )
>>> Does anyone have any suggestions?
>>> ___
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>>> and other Galaxy lists, please use the interface at:
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>>
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Re: [galaxy-dev] Installing Tool Dependencies

[Martin Čech]

All the links to the sources are at the bottom of the page and seem to
work, except of GPASS which is here:
http://stat.psu.edu/~yuzhang/software/GPASS.tar

I would double check with your users whether they actually need these
tools, since they are fairly old.

Martin

On Mon, Jul 16, 2018 at 12:56 PM Tom Misilo  wrote:

> Hi Martin,
>
>
>
> I will try and figure out where I came across the page (it may have been
> from Google).
>
>
>
> I am having trouble installing: BEAM, LPS, PASS, and GPASS. Conda cannot
> find any sources to install these packages.
>
>
>
> Thank you!
>
> Tom
>
>
>
> *From:* Martin Čech 
> *Sent:* Monday, July 16, 2018 12:42 PM
> *To:* Tom Misilo 
> *Cc:* galaxy-...@bx.psu.edu
> *Subject:* Re: [galaxy-dev] Installing Tool Dependencies
>
>
>
> Hello Tom,
>
>
>
> that page is very very outdated and I wouldn't trust it. Do you have any
> specific tools from that list that are giving you trouble? If not then I
> would ignore it completely.
>
>
>
> Majority of the tools are now installed through the Toolshed and
> dependencies are auto-managed by Galaxy's own Conda which should provide a
> much better experience.
>
>
>
> Martin
>
>
>
> p.s. from what page did you get to this list?
>
>
>
> On Mon, Jul 16, 2018 at 12:06 PM Tom Misilo  wrote:
>
> Hello,
>
>
>
> I am trying to help a research here at Florida Tech setup Galaxy locally
> to process their data. However, I am running into a problem installing some
> tool dependencies was on this page (
> https://moin.galaxyproject.org/Admin/Tools/ToolDependencies).
>
>
>
> For example, I am trying to install BEAM, LPS, PASS, and GPASS. However, I
> cannot find in the documentation for either the tools themselves or on
> Galaxy on how to set these tools up for use in Galaxy. Would you be able to
> assist in this matter?
>
>
>
> Thank you!
>
> <https://maps.google.com/?q=150+W.+University+Blvd+%0D%0A+Melbourne,+FL+32901=gmail=g>
>
> Tom
>
>
>
> Thomas Misilo
>
> Network Engineer
>
> Florida Institute of Technology
>
> Evans Library
>
> 150 W. University Blvd
> <https://maps.google.com/?q=150+W.+University+Blvd+%0D%0A+Melbourne,+FL+32901=gmail=g>
>
> Melbourne, FL 32901
> <https://maps.google.com/?q=150+W.+University+Blvd+%0D%0A+Melbourne,+FL+32901=gmail=g>
>
> Phone: 321-674-8831 <(321)%20674-8831>
>
> Fax: 321-724-2559 <(321)%20724-2559>
>
> misi...@fit.edu
>
>
>
> ___
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> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
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>
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>
>
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Re: [galaxy-dev] Installing Tool Dependencies

[Martin Čech]

Hello Tom,

that page is very very outdated and I wouldn't trust it. Do you have any
specific tools from that list that are giving you trouble? If not then I
would ignore it completely.

Majority of the tools are now installed through the Toolshed and
dependencies are auto-managed by Galaxy's own Conda which should provide a
much better experience.

Martin

p.s. from what page did you get to this list?

On Mon, Jul 16, 2018 at 12:06 PM Tom Misilo  wrote:

> Hello,
>
>
>
> I am trying to help a research here at Florida Tech setup Galaxy locally
> to process their data. However, I am running into a problem installing some
> tool dependencies was on this page (
> https://moin.galaxyproject.org/Admin/Tools/ToolDependencies).
>
>
>
> For example, I am trying to install BEAM, LPS, PASS, and GPASS. However, I
> cannot find in the documentation for either the tools themselves or on
> Galaxy on how to set these tools up for use in Galaxy. Would you be able to
> assist in this matter?
>
>
>
> Thank you!
>
> Tom
>
>
>
> Thomas Misilo
>
> Network Engineer
>
> Florida Institute of Technology
>
> Evans Library
>
> 150 W. University Blvd
>
> Melbourne, FL 32901
>
> Phone: 321-674-8831 <(321)%20674-8831>
>
> Fax: 321-724-2559 <(321)%20724-2559>
>
> misi...@fit.edu
>
>
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
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>
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Re: [galaxy-dev] From Paste to uWSGI

[Martin Čech]

Another recently updated resource for uwsgi is the training slides:
https://galaxyproject.github.io/dagobah-training/2018-gccbosc/10-uwsgi/uwsgi.html#1

M.

On Mon, Jul 9, 2018 at 11:31 AM Peter Briggs 
wrote:

> Hello Jochen
>
> I'm not aware of a tutorial but here are some observations from my (very)
> recent experiences upgrading a local paste-based 17.09 instance to a
> uwsgi-based 18.05 configuration. It's not comprehensive because the
> configuration will depend on decisions you need to make based on your local
> setup, but it might be helpful as a starting point.
>
> Before beginning:
>
> -- Commit to migrating from galaxy.ini to galaxy.yml (if not done
> previously)
>
> Even though its possible to stick with the old galaxy.ini file, it seems
> best to move to the new format - my feeling is, probably the migration will
> have to happen at some point anyway, and also the documentation is more
> focussed on the newer galaxy.yml version.
>
> -- Decide on how you're going to handle job submission (essentially, how
> you're going to replace the old job handler processes).
>
> There are a number of possibilities outlined in the documentation here:
>
>
> https://docs.galaxyproject.org/en/release_18.05/admin/scaling.html#deployment-options
>
> It seems important to figure this out at the beginning because it impacts
> a lot of the configuration specifics that follow. For our setup case "uwsgi
> + mules" looked like the most appropriate:
>
>
> https://docs.galaxyproject.org/en/release_18.05/admin/scaling.html#uwsgi-for-web-serving-with-mules-as-job-handlers
>
> Then once you're ready to start (nb backing up the database etc before
> starting are implicitly assumed!):
>
> -- Update the Galaxy source code
>
> The standard recipe for this seems to work okay i.e.
>
> git fetch origin && git checkout release_18.05 && git pull --ff-only
> origin release_18.05
>
> (You'll probably also need to run scripts/common_startup.sh to update the
> Python packages, and scripts/manage_db.py to update the database schema.)
>
> -- Create galaxy.yml and configure the "galaxy" section:
>
> You can make a galaxy.yml from the sample version and go through the
> "galaxy" section replicating the settings from galaxy.ini. (The settings in
> the "uwsgi" section can wait at this stage.)
> Don't forget to move galaxy.ini out of the way once you're done.
>
> -- Configure the "uwsgi" section of galaxy.yml:
>
> The options for various scenarios are given in the "Deployment/uwsgi"
> section:
>
> https://docs.galaxyproject.org/en/release_18.05/admin/scaling.html#uwsgi
>
> but the required settings seem to be spread out between different sections
> so (for me) it felt like it took some piecing together to get it to work
> when I first tried this.
>
> (Also I was thrown a little by the "socket" parameter not having a
> placeholder in sample galaxy.yml.)
>
> The core uwsgi options are here:
>
>
> https://docs.galaxyproject.org/en/release_18.05/admin/scaling.html#configuration-common-to-all-uwsgi-deployment-styles
>
> then you need to set other options dependent on:
>
> 1. how job submission is handled (e.g. options for the "uwsgi + mules"
> setup in my case)
> 2. how you're proxying Galaxy (for Apache or nginx it looks like it's just
> setting the uwsgi "socket" option, unless you're serving Galaxy from a URL
> prefix in which case there are a few more options needed - these are
> covered in the documentation.)
>
> -- Fix your job_conf.xml file
>
> If you have an existing job_conf.xml file in your config directory then
> you might need to update that too (specifically the "handlers" section)
> depending on the job submission handling you've decided to use.
>
> -- Use supervisor to manage your uwsgi processes
>
> The docs for this are here:
>
>
> https://docs.galaxyproject.org/en/release_18.05/admin/scaling.html#starting-and-stopping
>
> Essentially supervisor replaces "run.sh", so this becomes how you start
> and stop Galaxy (e.g. "supervisorctl start galaxy:" replaces
> "GALAXY_RUN_ALL=1 sh run.sh --daemon".)
>
> I think this is quite straightforward from the docs but again you need to
> tailor it for how you're handling job submission (e.g the "uwsgi + mules"
> doesn't need any handlers defining, but it looks like other strategies
> needs extra stuff defining here).
>
> -- Set up the proxying
>
> Assuming you're proxing via either Apache or nginx (we're using nginx),
> these are covered in the relevant sections:
>
> https://docs.galaxyproject.org/en/release_18.05/admin/apache.html
> https://docs.galaxyproject.org/en/release_18.05/admin/nginx.html
>
> The main difference I noticed for nginx is that you no longer need to use
> the "upstream"/"proxy_pass" directives, as nginx can talk directly to uwsgi
> using a "uwsgi_pass" directive that connects to the socket defined in the
> "uwsgi" section of galaxy.yml previously.
>
> (There's also a "gotcha" if you're nginx configuration also tries to serve
> "static/scripts/packed", which needs to be 

Re: [galaxy-dev] galaxy upgrade 18.05 problem

[Martin Čech]

Hi Matthias,

this used to be a (deprecated) symlink, which we removed in 18.05. You need
to change your proxy as can be seen here:
https://github.com/galaxyproject/ansible-galaxy-extras/pull/206/files

The release notes announcement:
https://docs.galaxyproject.org/en/master/releases/18.05_announce.html#breaking-changes

Thanks for using Galaxy,

Martin

On Mon, Jun 11, 2018 at 9:46 AM Matthias Bernt  wrote:

> Dear list,
>
> after upgrading to 18.05 I get an empty page when opening the galaxy
> website.
>
> The proxy logs say:
>
> [Mon Jun 11 15:20:10 2018] [error] [client 141.65.5.81] File does not
> exist: /data/galaxy_server/galaxy/static/scripts/packed, referer:
> https://galaxy.intranet.ufz.de/root/login?redirect=%2F
>
> Which is true, ie. the file/directory does not exist.
>
> Any ideas which step I forgot during the upgrade?
>
> Cheers,
> Matthias
>
>
>
> --
>
> ---
> Matthias Bernt
> Bioinformatics Service
> Molekulare Systembiologie (MOLSYB)
> Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
> Helmholtz Centre for Environmental Research GmbH - UFZ
> Permoserstraße 15, 04318 Leipzig, Germany
> 
> Phone +49 341 235 482296 <+49%20341%20235482296>,
> m.be...@ufz.de, www.ufz.de
>
> Sitz der Gesellschaft/Registered Office: Leipzig
> Registergericht/Registration Office: Amtsgericht Leipzig
> Handelsregister Nr./Trade Register Nr.: B 4703
> Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board:
> MinDirig Wilfried Kraus
> Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
> Prof. Dr. Dr. h.c. Georg Teutsch
> Administrative Geschäftsführerin/ Administrative Managing Director:
> Prof. Dr. Heike Graßmann
> ---
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Re: [galaxy-dev] problem with Visualization 'Scatterplot' in 18.05

[Martin Čech]

Hi Hans-Rudolf,

the problem is that the 18.05 release is missing the viz static files in
the proper folder. To be precise /config/plugins/visualizations/*/static
needs to be copied to /static/plugins/visualizations/*/static

To fix:

(make sure you have node 8.x.x and not newer)

$ cd client
$ ./node_modules/.bin/gulp plugins

I am sorry for the inconvenience, we will fix this in the release branch
early next week.

Martin







On Fri, Jun 8, 2018 at 10:00 AM Nicola Soranzo 
wrote:

> Dear Hans-Rudolf,
> I think this is being worked on at
> https://github.com/galaxyproject/galaxy/pull/6297 .
>
> Cheers,
> Nicola
>
> On 08/06/18 14:57, Hans-Rudolf Hotz wrote:
> >
> > just adding a little bit more information:
> >
> >  - this problem happens independent of using paste or uwsgi
> >
> >  - as far as I have tested all visualization plugins (with the
> > exception of trackster) are broken. For broken visualizations, other
> > than 'scatterplot', I get the error: "Load function 'load' not found"
> >
> >
> > Regards,
> > Hans-Rudolf
> >
> >
> > On 06/05/2018 05:14 PM, Hans-Rudolf Hotz wrote:
> >> Hi all
> >>
> >>
> >> I am in the process of upgrading our servers to 18.05. And I have
> >> encountered an issue with the Visualization tool "Scatterplot, Creates a
> >> 2D-scatterplot from tabular datapoints"
> >>
> >> I am starting with a simple bed file for chromosome 15 (downloaded with
> >> UCSC table browser tool). When I click on the Visualization icon,
> >> followed by "Scatterplot", I end up with an near empty page. I only get
> >> the title:
> >>
> >> Scatterplot of 'UCSC Main on Human: ncbiRefSeq
> >> (chr15:20010162-22868384)'
> >>
> >> UCSC Main on Human: ncbiRefSeq (chr15:20010162-22868384)
> >>
> >>
> >>
> >> This happens with our development server (after being upgraded from
> >> 17.09). It is the same using a new clone of 18.05 code.
> >>
> >> It also happens on usegalaxy.eu but it does work on usegalaxy.org
> >>
> >>
> >> As a side note: on usegalaxy.org, each visualization has its little
> icon
> >> (see: 'usegalaxy.org.png'), while on usegalaxy.eu, each visualization
> >> just has an eye (see: 'usegalaxy.eu.png')
> >>
> >>
> >> I hope there is an easy fix for this
> >>
> >>
> >> Regards, Hans-Rudolf
> >>
> >>
> >>
> >>
> >> ___
> >> Please keep all replies on the list by using "reply all"
> >> in your mail client.  To manage your subscriptions to this
> >> and other Galaxy lists, please use the interface at:
> >>https://lists.galaxyproject.org/
> >>
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> >>http://galaxyproject.org/search/
> >>
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[galaxy-dev] The Galaxy release 18.05 is out

[Martin Čech]

Dear Community,

We are happy to release Galaxy 18.05. Many thanks to committers and you,
the community. Enjoy the on time release and please let us know if you face
any issues.

The release notes are available at
https://docs.galaxyproject.org/en/release_18.05/releases/18.05_announce.html

Thanks for using Galaxy!

Martin,
on behalf of the Galaxy committers
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Re: [galaxy-dev] FTP service for galaxy with external authentication via SAML using shibboleth

[Martin Čech]

Hi all,

with the 'chunked and resumable uploads' PR in place (
https://github.com/galaxyproject/galaxy/pull/5516) the resiliency of the
built-in uploader should be pretty high, especially on browser like Chrome.
This feature will make it to 18.05 release.

M.

On Tue, Apr 17, 2018 at 2:20 PM Martin Demko <325...@mail.muni.cz> wrote:

> Dear Youssef,
> thank you a lot for your extensive answer. I need to digest this first but
> I
> believe it will help a lot. So far, I've just changed the quota for Galaxy
> upload tool and according to your answer, it looks like the best and
> easiest
> option anyway.
>
> Best wishes,
> Martin
>
>
> "Youssef  GHORBAL"  wrote on Tue, 17 Apr 2018
> 09:33:16 +:
> >
> > On 16 Apr 2018, at 11:53, Martin Demko <325...@mail.muni.cz 325...@mail.muni.cz>> wrote:
> >
> > Hi,
> > I'm currently solving a problem with authentication to FTP service for
> users
> > of
> > our galaxy server. We've successfully established an authentication via
> > shibboleth behind Nginx (not very easy, but doable :) but that also means
> > that
> > ProFTPD is not working anymore, as it doesn't support SAML
> > authentication.
> >
> > So my question is obvious, I'm looking for an easy and free FTP server
> with
> > SAML support, can anybody help me with an advice? I've already found
> > CompleteFTP and CrushFTP but both are paid and one is Windows-only
> > allegedly.
> > So how do you - people using external authentication via SAML - do
> > this?
> >
> > CrushFTP will support SAML auth only on HTTP transfers not FTP (the
> actual
> > protocol) tranfers.
> > SAML is HTTP centric spec, hooking it up to other non-HTTP portocols is
> > diffcult, more info here :
> > https://wiki.shibboleth.net/confluence/display/CONCEPT/ECP
> > http://www.cilogon.org/ws/saml-outside-the-browser
> >
> > You will not find any single FTP (the actual protocol) server with SAML
> > support. However, you can use HTTP uploader tools that you can hook up
> more
> > or less easly with SAML (bear in mind that Galaxy needs to have access to
> > files once uploaded which can add more complexity to the integration with
> > thirdparty upload tools) And since you're down the HTTP uploading path,
> you
> > may jus stick with Galaxy's own HTTP upload feature.
> >
> > If you need FTP, your best option, is to connect the ProfFTPD to the
> > LDAP/AD server used by the SAML IdP itself. This setup can only work in a
> > single oragnization (no SAML federation in action)
> >
> > If you have time, there are many JS libs that you can use to build a
> custom
> > file uploader (with SAML auth, HTML5 and resuming support) :
> > http://www.resumablejs.com
> > https://tus.io
> >
> > (and even in this situation, it will be difficult to handle CLI based
> > upload workflows)
> >
> > Youssef Ghorbal
> > Institut Pasteur
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Re: [galaxy-dev] question regarding GALXY software

[Martin Čech]

Hi David,

Galaxy does not add much on top of what the tools you need to run require
so if you have a laptop that you can run your analysis on you can run the
analysis using Galaxy also.

Martin

‪On Tue, Apr 10, 2018 at 11:41 AM ‫דויד קורנספן [David Kornspan]‬‎ <
davi...@moag.gov.il> wrote:‬

>
>
> *Hi,*
>
> I would appreciate your advice regarding the recommended portable computer
> specifications which will enable running the GALXY software for analysis of
> DNA and RNA seq of bacterial genomes.
>
>
>
> Thanks,
>
> David Kornspan
>
>
>
>
>
>
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Re: [galaxy-dev] GVL/Galaxy ver 18.01 instance error: R_COMM channel basic get exception: [Errno 32] Broken pipe

[Martin Čech]

Hi Leon, list,

this issue is now tracked here:
https://github.com/galaxyproject/cloudlaunch/issues/140

Martin

On Mon, Mar 26, 2018 at 5:14 AM Leon Parker 
wrote:

> We just stood up our first ever Genomics Virtual Lab appliance and used it
> to spool up a Galaxy Cluster for doing bioinformatics work.  We’ve worked a
> bit with the original “Cloudman” application and the ver 17.05 revision of
> Galaxy and it has worked fine, but we decided it might be a good time to
> migrate the GVL platform because it uses the latest, greatest version of
> Galaxy and provides additional tools, and the old “cloud man” approach has
> been deprecated, giving us further incentive to make the switch.
> Unfortunately, we’re encountering an error right out of the gate, when we
> spool up Galaxy through GVL, before we do anything with it.
>
> Within two minutes of Galaxy starting, we begin to see the following over
> and over again in the Cluster Info Log:
>
>
>- 20:55:20 - R_COMM channel basic get exception: [Errno 32] Broken pipe
>
>
> In addition, we can’t seem to access any Spot worker node instances we
> activate.  They launch but are never recognized and used.
>
> Not sure what this mean, as we are biologists, not informaticians nor
> python experts.  Any help would be most appreciated!
>
> --Leon
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[galaxy-dev] Release of Galaxy 18.01

[Martin Čech]

Dear Galaxy Fans,

The release of Galaxy 18.01 is out. Thanks to the Galaxy committers and
you, our community!

Full release notes:
https://docs.galaxyproject.org/en/release_18.01/releases/18.01_announce.html

*Highlights:*

*Performance and User Experience Improvements*
We made Galaxy more lively and responsive. Homepage, published workflows,
published/saved histories, and data libraries should all load much faster
now. Importing data from FTP will also take less of your time.

*Web Server and Configuration*
The default web server used by Galaxy has changed from Paste to uWSGI and
the default configuration file for Galaxy is now config/galaxy.yml instead
of config/galaxy.ini. To minimize the impact of this change on existing
Galaxy instances, if a Galaxy has a galaxy.ini file configured, it will
continue to use Paste by default unless additional steps are taken by the
administrator

*Dataset Collection Usability*
This release has significantly improved the usability of Galaxy dataset
collections. Dozens of improvements to collections have been made, some of
the key highlights include:
* Data library folders can now be sent to histories as a dataset collection.
* Failed dataset collection elements can now be fixed using job re-running
* Collections now appear with state and progress bars in the history panel
and contained datasets are hidden by default
* We added intuitive workflow post job actions for dataset collections
* The web interface now supports collections with arbitrary nesting and size
* More robust nametag discovery and propagation when using collections

*Client Architecture*
The architecture for the client code that powers the Galaxy user interface
has been significantly overhauled. The code base has been converted to ES6,
Yarn now powers the build and dependency management of the code, Prettier
is now used to ensure consistent code formatting, and the VueJS framework
has been integrated.

*New BAM datatypes*
Previously Galaxy only supported coordinate sorted BAM files by default
(the bam datatype). In addition, this release of Galaxy now supports three
new types of BAM:
* qname_sorted.bam, that ensures that the file is queryname sorted (e.g.
SO:queryname);
* qname_input_sorted.bam, that can be used to describe the output of
aligners which generally keep mate pairs adjacent
* unsorted.bam, that makes no assumptions about the sort order of the file.

*Experimental Job Caching*
Galaxy can now be configured to allow users the option of skipping
duplicated jobs if one with identical parameters has been previously
executed and simply reuse the previously generated outputs.

Thanks for using Galaxy!
http://galaxyproject.org
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Re: [galaxy-dev] Updating Bioblend on existing Galaxy installation

[Martin Čech]

The biostar thread corresponding to this question is at
https://biostar.usegalaxy.org/p/26849/.

M.

On Thu, Feb 22, 2018 at 5:26 PM Lachlan Musicman  wrote:

> Sorry all, moving this Q over to biostars.
>
> --
> "The antidote to apocalypticism is *apocalyptic civics*. Apocalyptic
> civics is the insistence that we cannot ignore the truth, nor should we
> panic about it. It is a shared consciousness that our institutions have
> failed and our ecosystem is collapsing, yet we are still here — and we are
> creative agents who can shape our destinies. Apocalyptic civics is the
> conviction that the only way out is through, and the only way through is
> together. "
>
> *Greg Bloom* @greggish
> https://twitter.com/greggish/status/873177525903609857
>
> On 22 February 2018 at 16:21, Lachlan Musicman  wrote:
>
>> Hola,
>>
>> I've just noticed that our Galaxy 17.09 installation has Bioblend 0.9
>> installed, and that one of the changes in Bioblend 0.10 was "support for
>> galaxy 17.09".
>>
>> Can someone hip me to the easiest way to update bioblend?
>>
>> Is it just to activate the venv and pip install -U bioblend?
>>
>> Cheers
>> L.
>>
>>
>>
>> --
>> "The antidote to apocalypticism is *apocalyptic civics*. Apocalyptic
>> civics is the insistence that we cannot ignore the truth, nor should we
>> panic about it. It is a shared consciousness that our institutions have
>> failed and our ecosystem is collapsing, yet we are still here — and we are
>> creative agents who can shape our destinies. Apocalyptic civics is the
>> conviction that the only way out is through, and the only way through is
>> together. "
>>
>> *Greg Bloom* @greggish
>> https://twitter.com/greggish/status/873177525903609857
>>
>
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Re: [galaxy-dev] User Registration Error

[Martin Čech]

Hi Dallas,

this really does look like a permissions issue, could you please double
check who owns that file? Alternatively you can just remove all the *.pyc
in Galaxy's folders, it will be recreated with proper permissions during
the first run.

Thanks for using Galaxy,

M.

On Tue, Jan 16, 2018 at 4:00 PM Thomas, Dallas 
wrote:

> Help Please,
>
>
>
> So I am feeling a bit dumb right now.  I have set-up another local Galaxy
> test server and have enabled all of the user authentication stuff in the
> galaxy.ini.  I am using nginx for proxy however am not using the external
> authentication or remote.  Every time a user clicks on the User->Register –
> there is the following error:
>
>
> Internal Server Error Galaxy was unable to successfully complete your
> request
>
> URL: http://10.115.0.65:8080/user/create
> Module galaxy.web.framework.middleware.error:*149* in __call__
> >>  app_iter *=* self*.*application
> *(*environ*,* sr_checker*)*
> Module paste.recursive:*84* in __call__
> >>  *return* self*.*application*(*
> environ*,* start_response*)*
> Module paste.httpexceptions:*633* in __call__
> >>  *return* self*.*application*(*
> environ*,* start_response*)*
> Module galaxy.web.framework.base:*133* in __call__
> >>  *return* self*.*handle_request*(*
> environ*,* start_response *)*
> Module galaxy.web.framework.base:*191* in handle_request
> >>  body *=* method*(* trans*,* 
> kwargs *)*
> Module galaxy.webapps.galaxy.controllers.user:*746* in create
> >>  status*=*status *)*
> Module galaxy.web.framework.webapp:*810* in fill_template
> >>  *return* self*.*
> fill_template_mako*(* filename*,* kwargs *)*
> Module galaxy.web.framework.webapp:*818* in fill_template_mako
> >>  template *=* template_lookup*.*
> get_template*(* filename *)*
> Module mako.lookup:*218* in get_template
> >>  *return* self*.*_load*(*srcfile
> *,* uri*)*
> Module mako.lookup:*283* in _load
> >>  self*.*template_args*)*
> Module mako.template:*218* in __init__
> >>  module *=* self*.*
> _compile_from_file*(*path*,* filename*)*
> Module mako.template:*245* in _compile_from_file
> >>  module *=* imp*.*load_source*(*
> self*.*module_id*,* path*,* open*(*path*,* 'rb'*))*
> *IOError: [Errno 13] Permission denied:
> '/home/galaxy/galaxy_dist/database/compiled_templates/user/register.mako.py
> '*
> extra data 
>
>
> full traceback 
>
> text version 
>
> This may be an intermittent problem due to load or other unpredictable
> factors, reloading the page may address the problem.
>
>
>
> Any help would be very much appreciated.
>
>
>
> Sincerely
>
> Dallas Thomas
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Re: [galaxy-dev] Enable viewing of large HTML files

[Martin Čech]

Hi Peter,

I believe the 1MB is hard coded in
https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/managers/hdas.py#L222
and
cannot be configured.

That said you can change it on your instance, I have also opened an issue
to allow configuring this value.
https://github.com/galaxyproject/galaxy/issues/4924

Martin

On Fri, Nov 3, 2017 at 8:00 AM Peter Briggs 
wrote:

> Dear Devs
>
> We have a locally developed tool which takes in a collection of Fastq
> pairs and produces a number of outputs which includes a number of HTML
> files.
>
> For relatively small numbers of input files all the HTML outputs can be
> viewed without issue in Galaxy. However we've observed that for large
> collections of Fastqs, the size of one of the HTML files can be very large
> (several megabytes) and by default attempting to view these in Galaxy
> results in the "This dataset is large and only the first megabyte is shown
> below" message, followed by the initial HTML markup rendered as text.
>
> As clicking on the "show all" link renders the entire HTML file correctly,
> is there a way to force Galaxy to shortcut the truncation for HTML (or at
> least apply a larger limit for determining when files are too large to be
> shown all at once)?
>
> We're currently using 17.05 in our production instance.
>
> Thanks for advance for any help or suggestions,
>
> Best wishes
>
> Peter
>
>
> --
> Peter Briggs peter.bri...@manchester.ac.uk
> Bioinformatics Core Facility University of Manchester
> B.1083 Michael Smith Bldg Tel: (0161) 2751482
>
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[galaxy-dev] Release of Galaxy 17.09

[Martin Čech]

Dear Galaxy Fans,

The release* of Galaxy **17.09* is out. Thanks to the #usegalaxy committers
and you, our community!

*Full *release
* notes: *
https://docs.galaxyproject.org/en/master/releases/17.09_announce.html

Highlights:
*Singularity - *Tool execution using the HPC-friendly container technology
Singularity is now supported. Custom containers can be specified by the
Galaxy admin on a per job destination basis or standardized containers
corresponding to Conda requirements can be built or downloaded
automatically using the mulled toolkit built into Galaxy (just like is
possible for Docker). For more information checkout presentation at
http://jmchilton.github.io/writing/gcc2017slides/biocontainers.html from
the 2017 Galaxy Community Conference.
*Download entire collection - *Downloading whole colections is now possible
from the history interface. Thanks to @mvdbeek.
*Switch tool versions in workflows - *You can now select exactly what
version of tool you want to use when building workflows.Thanks to @mvdbeek.


*Thanks for using Galaxy!*
*http://galaxyproject.org *
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Re: [galaxy-dev] Problems with the test tool shed?

[Martin Čech]

Done, seems up now.

Thanks for the report.

M.

On Tue, Oct 17, 2017 at 2:22 PM Von Kuster, Greg  wrote:

> Hi all,
>
> I’m wondering if the TTS can be restarted.  I’ve been seeing this
> of-and-on all afternoon.
>
> Thanks!
>
> Galaxy 
> The Test Tool Shed could not be reached
>
> You are seeing this message because a request to The Test Tool Shed timed
> out or was refused. This may be a temporary issue which could be resolved
> by retrying the operation you were performing. If you receive this message
> repeatedly or for an extended amount of time, please contact an
> administrator.
>
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Re: [galaxy-dev] Additional Information about users in the API

[Martin Čech]

Stephan, Milen,

lately Galaxy undergoes DB migrations very rarely and if so it usually just
adds tables/columns in a very clear manner.

API should shield you from any changes breaking your DB script but to be
honest I would not expect any unless you are gathering data on some complex
object relations (which API won't give you anyways).

Best,

Martin


On Tue, Apr 25, 2017 at 8:30 AM Stephan Oepen  wrote:

> hi martin, thanks for the immediate follow-up!
>
> > Our aim at using the API is the simplicity it provides.
>
> part of my rationale in looking at the API for reporting purposes was
> stability: my impression is that the galaxy-internal database schema
> undergoes relatively frequent revisions, but i would assume the API to
> hide some of those changes from us?
>
> best wishes, oe
>
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Re: [galaxy-dev] Galaxy User IDs and Group IDs

[Martin Čech]

Hi Rob,

especially on a new Galaxy they tend to because every Galaxy table has its
own id series which is in turn encoded with the same secret. So when you
create your first user and your first group, they will have the same id
(1). Same with first history, first dataset etc.

iow: Galaxy objects do not have unique IDs in the whole Galaxy, just within
the object group.

Hope this helps.

Martin

On Mon, Apr 24, 2017 at 3:44 PM Lemley, Rob 
wrote:

> Hi everyone,
>
> This may seem like a silly question, but are user id's and group id's
> expected to be the "same"?
>
> For example:
> >>> gi.users.get_users()
> [{u'username': u'user1', u'model_class': u'User', u'id':
> u'f2db41e1fa331b3e', u'email': u'X'},
>  {u'username': u'user2', u'model_class': u'User', u'id':
> u'f597429621d6eb2b', u'email': u'X'}]
>
> >>> gi.groups.get_groups()
> [{u'url': u'/api/groups/f2db41e1fa331b3e', u'model_class': u'Group',
> u'id': u'f2db41e1fa331b3e', u'name': u'group1'},
>  {u'url': u'/api/groups/f597429621d6eb2b', u'model_class': u'Group',
> u'id': u'f597429621d6eb2b', u'name': u'group2'}]
>
>
> This is just a dev instance I set up really quick, so these are the first
> two users/groups I've created. If this is expected behavior I'll carry on,
> just seems odd to me.
>
> Thanks!
>
> -Rob
> --
> Rob Lemley
> Systems Administrator - CIRC
> University of Rochester
>
>
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Re: [galaxy-dev] Additional Information about users in the API

[Martin Čech]

Hi Milen,

I don't think Galaxy exposes what you ask for through an API and a PR to
make it do so is  certainly welcomed. Please note that this information
(about other users) should be only exposed to an admin.

Additionally is there a reason why you are gathering these stats through an
API and not from the database via a script? Example of such server-based
script (for job stats gathering) is in Galaxy's codebase:
https://github.com/galaxyproject/galaxy/blob/dev/scripts/grt.py Let me know
if you want to know more about this.

Thanks

Martin

On Mon, Apr 24, 2017 at 8:32 AM Milen Kouylekov 
wrote:

> Dear Team,
>
> Hi, my name is Milen Kouylekov and I am working on the galaxy portal
> customized for natural language technology applications.
> http://lap.clarino.uio.no.
>
> I wrote an reporting script that uses Galaxy API to summarize the user
> activity. The idea of the script is to send regular reports with the
> information available to the reporting server as well as additional
> information like queries that failed to execute etc. I have managed to
> retrieve using the API most of the relevant information except the
> following:
>
> 1) User creation date.
> 2) User last access date.
>
> I have investigated that user object and see that information is part of
> it. My question is:
>
> Is there a way to access this information through the API? If not can I
> make a feature request? It is an information useful for administration
> of a galaxy instance.
>
> Cheers Milen
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Re: [galaxy-dev] Login message

[Martin Čech]

Timo: Yes please, github issues are the right place for these ideas.

thanks

Martin

On Wed, Apr 5, 2017 at 10:32 AM Timo Janßen <timo.jans...@gwdg.de> wrote:

> On 03/29/2017 05:36 PM, Martin Čech wrote:
> > the message is defined in lib/galaxy/webapps/galaxy/controllers/user.py
> as
> > variable REQUIRE_LOGIN_TEMPLATE . It does not seem configurable but you
> > could modify it directly.
>
> Hi Martin,
>
> thank you very much! Modifying the file directly worked perfectly,
> although it is a bit hackish. I think it would be nice if this was
> configurable because if the Galaxy instance is configured to be usable
> for logged in users only, this is the first page the user sees. There
> could be a html page like /static/welcome.html for the main site.
>
> Also I think there should be an option to hide the password reset link
> because if external authentication is used, the password shouldn't be
> changeable in Galaxy. For me I managed to do this by editing
> templates/user/login.mako but it would be nicer if there was an option
> in galaxy.ini
>
> Should I open a Github issue for my proposals?
>
> Best regards,
> Timo
>
> --
> 
> Timo Janßen
> Wissenschaftliche Hilfskraft
> Arbeitsgruppe "Anwendungs- und Informationssysteme"
> Tel.: +49(0)551/201-1791 <+49%20551%202011791>
> E-Mail: timo.jans...@gwdg.de
> 
> Gesellschaft für wissenschaftliche Datenverarbeitung mbH Göttingen
> (GWDG)
> Am Faßberg 11, 37077 Göttingen, URL: http://www.gwdg.de
> Tel.: +49 551 201-1510 <+49%20551%202011510>, Fax: +49 551 201-2150
> <+49%20551%202012150>, E-Mail: g...@gwdg.de
> Service-Hotline: Tel.: +49 551 201-1523 <+49%20551%202011523>, E-Mail:
> supp...@gwdg.de
>
> Geschäftsführer: Prof. Dr. Ramin Yahyapour
> Aufsichtsratsvorsitzender: Prof. Dr. Norbert Lassau
> Sitz der Gesellschaft: Göttingen
> Registergericht: Göttingen, Handelsregister-Nr. B 598
> 
> Zertifiziert nach ISO 9001
> 
>
>
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Re: [galaxy-dev] Login message

[Martin Čech]

Hi Timo,

the message is defined in lib/galaxy/webapps/galaxy/controllers/user.py as
variable REQUIRE_LOGIN_TEMPLATE . It does not seem configurable but you
could modify it directly.

Thanks for using Galaxy

Martin

On Wed, Mar 29, 2017 at 11:32 AM Timo Janßen  wrote:

> Hi,
>
> is it possible to change the message that is shown on the login page? At
> the moment it says "This Galaxy instance has been configured such that
> only users who are logged in may use it. If you don't already have an
> account, you may create one."
>
> I looked for the file where the text is defined but couldn't find it.
>
> Best regards,
> Timo
> --
> 
> Timo Janßen
> Wissenschaftliche Hilfskraft
> Arbeitsgruppe "Anwendungs- und Informationssysteme"
> Tel.: +49(0)551/201-1791 <+49%20551%202011791>
> E-Mail: timo.jans...@gwdg.de
> 
> Gesellschaft für wissenschaftliche Datenverarbeitung mbH Göttingen
> (GWDG)
> Am Faßberg 11, 37077 Göttingen, URL: http://www.gwdg.de
> Tel.: +49 551 201-1510 <+49%20551%202011510>, Fax: +49 551 201-2150
> <+49%20551%202012150>, E-Mail: g...@gwdg.de
> Service-Hotline: Tel.: +49 551 201-1523 <+49%20551%202011523>, E-Mail:
> supp...@gwdg.de
>
> Geschäftsführer: Prof. Dr. Ramin Yahyapour
> Aufsichtsratsvorsitzender: Prof. Dr. Norbert Lassau
> Sitz der Gesellschaft: Göttingen
> Registergericht: Göttingen, Handelsregister-Nr. B 598
> 
> Zertifiziert nach ISO 9001
> 
>
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/
___
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Re: [galaxy-dev] Search Tool Shed

[Martin Čech]

The Tool Shed itself is loaded into the iframe (served from a different
domain) - that is why some more strict security settings have problems with
it.

M.

On Thu, Mar 9, 2017 at 2:52 PM Matthias Bernt <m.be...@ufz.de> wrote:

> Hi Martin,
>
> thanks for your reply. The reason was the Privacy Badger browser plugin.
> Might it be that data is exchanged with the toolshed page?
>
> Anyway, I disabled the plugin and the page works.
>
> Best,
> Matthias
>
> On 08.03.2017 16:20, Martin Čech wrote:
> > Hi Matthias,
> >
> > it is supposed to open an iframe in the right panel with view of MTS
> > categories for browsing. Do you see a warning icon in the right of your
> > browser's URL bar? I think I saw this before when there was https/https
> > mismatch. How does your config/tool_sheds_conf.xml look like? Do you see
> > any errors/warnings in the browser's JS console?
> >
> > Martin
> >
> >
> >
> > On Wed, Mar 8, 2017 at 9:56 AM Matthias Bernt <m.be...@ufz.de
> > <mailto:m.be...@ufz.de>> wrote:
> >
> > Dear mailing list,
> >
> > What is the expected behavior if I click in the Admin area under
> "Search
> > Tool Shed" on the "Galaxy Main Tool Shed" button (or any of the
> Browse
> > .. or Search .. actions that are available via the black triangle
> > submenu)?
> >
> > I remember that a new tab with the corresponding Tool Shed page
> opened
> > in the browser.
> >
> > This is currently not happening in my installation. What could be the
> > problem? As a work around I can trigger the Browse action via right
> > click and "open link in new tab".
> >
> > As far as I can see this is not a JavaScript problem.
> >
> > Best,
> > Matthias
> >
> >
> >
> > --
> >
> > ---
> > Matthias Bernt
> > Bioinformatics Service
> > Molekulare Systembiologie (MOLSYB)
> > Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
> > Helmholtz Centre for Environmental Research GmbH - UFZ
> > Permoserstraße 15, 04318 Leipzig, Germany
> > Phone +49 341 235 482296 <+49%20341%20235482296>
> <tel:+49%20341%20235482296>,
> > m.be...@ufz.de <mailto:m.be...@ufz.de>, www.ufz.de <
> http://www.ufz.de>
> >
> > Sitz der Gesellschaft/Registered Office: Leipzig
> > Registergericht/Registration Office: Amtsgericht Leipzig
> > Handelsregister Nr./Trade Register Nr.: B 4703
> > Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board:
> > MinDirig Wilfried Kraus
> > Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
> > Prof. Dr. Dr. h.c. Georg Teutsch
> > Administrative Geschäftsführerin/ Administrative Managing Director:
> > Prof. Dr. Heike Graßmann
> > ---
> >
> > ___
> > Please keep all replies on the list by using "reply all"
> > in your mail client.  To manage your subscriptions to this
> > and other Galaxy lists, please use the interface at:
> >   https://lists.galaxyproject.org/
> >
> > To search Galaxy mailing lists use the unified search at:
> >   http://galaxyproject.org/search/mailinglists/
> >
>
> --
>
> ---
> Matthias Bernt
> Bioinformatics Service
> Molekulare Systembiologie (MOLSYB)
> Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
> Helmholtz Centre for Environmental Research GmbH - UFZ
> Permoserstraße 15, 04318 Leipzig, Germany
> Phone +49 341 235 482296 <+49%20341%20235482296>,
> m.be...@ufz.de, www.ufz.de
>
> Sitz der Gesellschaft/Registered Office: Leipzig
> Registergericht/Registration Office: Amtsgericht Leipzig
> Handelsregister Nr./Trade Register Nr.: B 4703
> Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board:
> MinDirig Wilfried Kraus
> Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
> Prof. Dr. Dr. h.c. Georg Teutsch
> Administrative Geschäftsführerin/ Administrative Managing Director:
> Prof. Dr. Heike Graßmann
> ---
>
>
___
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Re: [galaxy-dev] Shared Data Library, large number of files

[Martin Čech]

The code at L120 does not exist in 16.07. It was broken in 16.10 and fixed
for 17.01. I made a PR to backport the fix to 16.10:
https://github.com/galaxyproject/galaxy/pull/3728

You shouldn't be seeing the 'Cannot read property 'masthead' of
undefined' error in 16.07 and it should be fixed in 16.10 after that PR is
merged. 17.01 or dev shouldn't have this problem already.

Please let me know how this works for you.

Thanks,

Martin



On Wed, Mar 8, 2017 at 3:09 PM D K <danielforti...@gmail.com> wrote:

> Hi Martin,
>
> I've pasted the file you requested here:
>
> http://collabedit.com/xcx5b
>
> Thanks!
>
> On Wed, Mar 8, 2017 at 11:04 AM, Martin Čech <mar...@bx.psu.edu> wrote:
>
> Can you please share your '/client/galaxy/scripts/layout/menu.js' file
> with me? (e.g. using https://gist.github.com or similar).
>
> thanks
>
> M.
>
>
> On Wed, Mar 8, 2017 at 1:34 PM D K <danielforti...@gmail.com> wrote:
>
> Hi Martin,
>
> I've tried this on both v16.07 and v16.10
>
> D
>
>
>
> On Wed, Mar 8, 2017 at 10:29 AM, Martin Čech <mar...@bx.psu.edu> wrote:
>
> Daniel:
>
> what version is your Galaxy?
>
> Martin
>
> On Wed, Mar 8, 2017 at 12:40 PM D K <danielforti...@gmail.com> wrote:
>
> I've copied and pasted the javascript error below. Any help would be
> greatly appreciated. Thanks!
>
> Uncaught TypeError: Cannot read property 'masthead' of undefined
> at n. (menu.js:120)
> at Function.each (jquery.js:370)
> at HTMLDocument. (menu.js:117)
> at l (jquery.js:3232)
> at Object.add [as done] (jquery.js:3291)
> at t.fn.init.vt.fn.ready (jquery.js:3542)
> at callback (menu.js:116)
> at Object.t.success (backbone.js:1051)
> at l (jquery.js:3232)
> at Object.fireWith [as resolveWith] (jquery.js:3362)
>
>
> On Thu, Mar 2, 2017 at 10:43 AM, D K <danielforti...@gmail.com> wrote:
>
> Hi Martin,
>
> I do get a javascript error, I've attached a screenshot of the relevant
> window. I also tried logging in as a non-admin user and had the same issue.
> In this Galaxy instance are 5 data libraries, each with about 150
> individual folders, and each folder has a variable number of fastq.gz files.
>
> Thanks!
>
> On Thu, Mar 2, 2017 at 10:13 AM, Martin Čech <mar...@bx.psu.edu> wrote:
>
> Daniel:
>
> Could you please open browser console and look for javascript errors on
> the page that fails to load for you? Additionally I assume you are an admin
> when trying this (admins load all of the instance's libraries) could you
> try loading the library list as a normal user? How many libraries do you
> have on the instance?
>
> Thanks
>
> Martin
>
> On Thu, Mar 2, 2017 at 12:38 PM D K <danielforti...@gmail.com> wrote:
>
> Hi Martin / Hans / Devon,
>
> I can confirm that I am using the new UI from the top menu. Right now when
> I click on the link I often do not even get the list of libraries whereas
> when I click on the admin Data Library link I at least see the list of
> libraries (although I can't open any of them since they are so large). I've
> tried refreshing the page, deleting the cookies for the session and using
> Incognito mode, using chrome and firefox both from a linux and windows
> machine and can confirm this behavior on all systems. However, occasionally
> when clicking the Shared Data Library link from the top I do get a list of
> libraries and can navigate them, but this has only happened once during my
> tests and I cannot replicate this behavior.
>
> Thanks for the assistance!
>
> On Thu, Mar 2, 2017 at 5:47 AM, Martin Čech <mar...@bx.psu.edu> wrote:
>
> Hi all,
>
> *Devon* is correct -the old data library UI under Admin menu is still in
> place (because it has some features perceived as important to some admins).
> However majority of users and most of the admins are using the interface
> under 'Shared Data' I hope and the old UI is deprecated since 15.10 (
> https://docs.galaxyproject.org/en/master/releases/15.10_announce.html). I
> created a PR to adjust the label in the admin interface to make this clear:
> https://github.com/galaxyproject/galaxy/pull/3694
>
> The old UI is very slow for large libraries but the new UI under Shared
> Data/Data Libraries in the top menu shouldn't have this kind of issues for
> hundreds of folders/datasets that are mentioned here.
>
> *Daniel* are you using the new UI form the top menu? If so are you
> experiencing this only with a specific folder full of linked datasets or
> does it occur for any folder with many datasets in it?
>
> Martin
>
>
>
> On Thu, Mar 2, 2017 at 3:49 AM Devon Ryan <dpr...@dpryan.com> wrote:
>
> I ob

Re: [galaxy-dev] Shared Data Library, large number of files

[Martin Čech]

Can you please share your '/client/galaxy/scripts/layout/menu.js' file with
me? (e.g. using https://gist.github.com or similar).

thanks

M.

On Wed, Mar 8, 2017 at 1:34 PM D K <danielforti...@gmail.com> wrote:

> Hi Martin,
>
> I've tried this on both v16.07 and v16.10
>
> D
>
>
>
> On Wed, Mar 8, 2017 at 10:29 AM, Martin Čech <mar...@bx.psu.edu> wrote:
>
> Daniel:
>
> what version is your Galaxy?
>
> Martin
>
> On Wed, Mar 8, 2017 at 12:40 PM D K <danielforti...@gmail.com> wrote:
>
> I've copied and pasted the javascript error below. Any help would be
> greatly appreciated. Thanks!
>
> Uncaught TypeError: Cannot read property 'masthead' of undefined
> at n. (menu.js:120)
> at Function.each (jquery.js:370)
> at HTMLDocument. (menu.js:117)
> at l (jquery.js:3232)
> at Object.add [as done] (jquery.js:3291)
> at t.fn.init.vt.fn.ready (jquery.js:3542)
> at callback (menu.js:116)
> at Object.t.success (backbone.js:1051)
> at l (jquery.js:3232)
> at Object.fireWith [as resolveWith] (jquery.js:3362)
>
>
> On Thu, Mar 2, 2017 at 10:43 AM, D K <danielforti...@gmail.com> wrote:
>
> Hi Martin,
>
> I do get a javascript error, I've attached a screenshot of the relevant
> window. I also tried logging in as a non-admin user and had the same issue.
> In this Galaxy instance are 5 data libraries, each with about 150
> individual folders, and each folder has a variable number of fastq.gz files.
>
> Thanks!
>
> On Thu, Mar 2, 2017 at 10:13 AM, Martin Čech <mar...@bx.psu.edu> wrote:
>
> Daniel:
>
> Could you please open browser console and look for javascript errors on
> the page that fails to load for you? Additionally I assume you are an admin
> when trying this (admins load all of the instance's libraries) could you
> try loading the library list as a normal user? How many libraries do you
> have on the instance?
>
> Thanks
>
> Martin
>
> On Thu, Mar 2, 2017 at 12:38 PM D K <danielforti...@gmail.com> wrote:
>
> Hi Martin / Hans / Devon,
>
> I can confirm that I am using the new UI from the top menu. Right now when
> I click on the link I often do not even get the list of libraries whereas
> when I click on the admin Data Library link I at least see the list of
> libraries (although I can't open any of them since they are so large). I've
> tried refreshing the page, deleting the cookies for the session and using
> Incognito mode, using chrome and firefox both from a linux and windows
> machine and can confirm this behavior on all systems. However, occasionally
> when clicking the Shared Data Library link from the top I do get a list of
> libraries and can navigate them, but this has only happened once during my
> tests and I cannot replicate this behavior.
>
> Thanks for the assistance!
>
> On Thu, Mar 2, 2017 at 5:47 AM, Martin Čech <mar...@bx.psu.edu> wrote:
>
> Hi all,
>
> *Devon* is correct -the old data library UI under Admin menu is still in
> place (because it has some features perceived as important to some admins).
> However majority of users and most of the admins are using the interface
> under 'Shared Data' I hope and the old UI is deprecated since 15.10 (
> https://docs.galaxyproject.org/en/master/releases/15.10_announce.html). I
> created a PR to adjust the label in the admin interface to make this clear:
> https://github.com/galaxyproject/galaxy/pull/3694
>
> The old UI is very slow for large libraries but the new UI under Shared
> Data/Data Libraries in the top menu shouldn't have this kind of issues for
> hundreds of folders/datasets that are mentioned here.
>
> *Daniel* are you using the new UI form the top menu? If so are you
> experiencing this only with a specific folder full of linked datasets or
> does it occur for any folder with many datasets in it?
>
> Martin
>
>
>
> On Thu, Mar 2, 2017 at 3:49 AM Devon Ryan <dpr...@dpryan.com> wrote:
>
> I observe the same thing on 16.07. As an example, I'm just opened a
> data library under Admin->Data->Data Libraries and this took about a
> minute and a half. It looks like this is related to the quantity of
> data in this folder. The associated entry in the uwsgi log is as
> follows:
>
> [pid: 357|app: 0|req: 2059/5647] 10.1.6.77 () {44 vars in 1220 bytes}
> [Thu Mar  2 08:40:19 2017] GET
>
> /library_common/browse_library?sort=name=All=All=False=library_admin=browse=355326571f7132ff
> => generated 21761790 bytes in 108644 msecs (HTTP/1.1 200) 2 headers
> in 73 bytes (14 switches on core 2)
>
> So this library is causing ~21 megs of data to be returned to the
> browser, which I presume is the source of the issue.
>

Re: [galaxy-dev] Shared Data Library, large number of files

[Martin Čech]

Daniel:

what version is your Galaxy?

Martin

On Wed, Mar 8, 2017 at 12:40 PM D K <danielforti...@gmail.com> wrote:

> I've copied and pasted the javascript error below. Any help would be
> greatly appreciated. Thanks!
>
> Uncaught TypeError: Cannot read property 'masthead' of undefined
> at n. (menu.js:120)
> at Function.each (jquery.js:370)
> at HTMLDocument. (menu.js:117)
> at l (jquery.js:3232)
> at Object.add [as done] (jquery.js:3291)
> at t.fn.init.vt.fn.ready (jquery.js:3542)
> at callback (menu.js:116)
> at Object.t.success (backbone.js:1051)
> at l (jquery.js:3232)
> at Object.fireWith [as resolveWith] (jquery.js:3362)
>
>
> On Thu, Mar 2, 2017 at 10:43 AM, D K <danielforti...@gmail.com> wrote:
>
> Hi Martin,
>
> I do get a javascript error, I've attached a screenshot of the relevant
> window. I also tried logging in as a non-admin user and had the same issue.
> In this Galaxy instance are 5 data libraries, each with about 150
> individual folders, and each folder has a variable number of fastq.gz files.
>
> Thanks!
>
> On Thu, Mar 2, 2017 at 10:13 AM, Martin Čech <mar...@bx.psu.edu> wrote:
>
> Daniel:
>
> Could you please open browser console and look for javascript errors on
> the page that fails to load for you? Additionally I assume you are an admin
> when trying this (admins load all of the instance's libraries) could you
> try loading the library list as a normal user? How many libraries do you
> have on the instance?
>
> Thanks
>
> Martin
>
> On Thu, Mar 2, 2017 at 12:38 PM D K <danielforti...@gmail.com> wrote:
>
> Hi Martin / Hans / Devon,
>
> I can confirm that I am using the new UI from the top menu. Right now when
> I click on the link I often do not even get the list of libraries whereas
> when I click on the admin Data Library link I at least see the list of
> libraries (although I can't open any of them since they are so large). I've
> tried refreshing the page, deleting the cookies for the session and using
> Incognito mode, using chrome and firefox both from a linux and windows
> machine and can confirm this behavior on all systems. However, occasionally
> when clicking the Shared Data Library link from the top I do get a list of
> libraries and can navigate them, but this has only happened once during my
> tests and I cannot replicate this behavior.
>
> Thanks for the assistance!
>
> On Thu, Mar 2, 2017 at 5:47 AM, Martin Čech <mar...@bx.psu.edu> wrote:
>
> Hi all,
>
> *Devon* is correct -the old data library UI under Admin menu is still in
> place (because it has some features perceived as important to some admins).
> However majority of users and most of the admins are using the interface
> under 'Shared Data' I hope and the old UI is deprecated since 15.10 (
> https://docs.galaxyproject.org/en/master/releases/15.10_announce.html). I
> created a PR to adjust the label in the admin interface to make this clear:
> https://github.com/galaxyproject/galaxy/pull/3694
>
> The old UI is very slow for large libraries but the new UI under Shared
> Data/Data Libraries in the top menu shouldn't have this kind of issues for
> hundreds of folders/datasets that are mentioned here.
>
> *Daniel* are you using the new UI form the top menu? If so are you
> experiencing this only with a specific folder full of linked datasets or
> does it occur for any folder with many datasets in it?
>
> Martin
>
>
>
> On Thu, Mar 2, 2017 at 3:49 AM Devon Ryan <dpr...@dpryan.com> wrote:
>
> I observe the same thing on 16.07. As an example, I'm just opened a
> data library under Admin->Data->Data Libraries and this took about a
> minute and a half. It looks like this is related to the quantity of
> data in this folder. The associated entry in the uwsgi log is as
> follows:
>
> [pid: 357|app: 0|req: 2059/5647] 10.1.6.77 () {44 vars in 1220 bytes}
> [Thu Mar  2 08:40:19 2017] GET
>
> /library_common/browse_library?sort=name=All=All=False=library_admin=browse=355326571f7132ff
> => generated 21761790 bytes in 108644 msecs (HTTP/1.1 200) 2 headers
> in 73 bytes (14 switches on core 2)
>
> So this library is causing ~21 megs of data to be returned to the
> browser, which I presume is the source of the issue.
>
> As an aside, the old data library API is still in use in the admin
> section until at least 16.07. Perhaps this has been changed since
> then, I hadn't planed to update our system until the end of the month.
> For what it's worth, opening the same library via "shared data" takes
> ~100 msec.
>
> Devon
> --
> Devon Ryan, Ph.D.
> Email: dpr...@dpryan.com
> Data Manager/Bioinformatician
>

Re: [galaxy-dev] Search Tool Shed

[Martin Čech]

Hi Matthias,

it is supposed to open an iframe in the right panel with view of MTS
categories for browsing. Do you see a warning icon in the right of your
browser's URL bar? I think I saw this before when there was https/https
mismatch. How does your config/tool_sheds_conf.xml look like? Do you see
any errors/warnings in the browser's JS console?

Martin



On Wed, Mar 8, 2017 at 9:56 AM Matthias Bernt  wrote:

> Dear mailing list,
>
> What is the expected behavior if I click in the Admin area under "Search
> Tool Shed" on the "Galaxy Main Tool Shed" button (or any of the Browse
> .. or Search .. actions that are available via the black triangle submenu)?
>
> I remember that a new tab with the corresponding Tool Shed page opened
> in the browser.
>
> This is currently not happening in my installation. What could be the
> problem? As a work around I can trigger the Browse action via right
> click and "open link in new tab".
>
> As far as I can see this is not a JavaScript problem.
>
> Best,
> Matthias
>
>
>
> --
>
> ---
> Matthias Bernt
> Bioinformatics Service
> Molekulare Systembiologie (MOLSYB)
> Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
> Helmholtz Centre for Environmental Research GmbH - UFZ
> Permoserstraße 15, 04318 Leipzig, Germany
> Phone +49 341 235 482296 <+49%20341%20235482296>,
> m.be...@ufz.de, www.ufz.de
>
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> Registergericht/Registration Office: Amtsgericht Leipzig
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> Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board:
> MinDirig Wilfried Kraus
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> Prof. Dr. Dr. h.c. Georg Teutsch
> Administrative Geschäftsführerin/ Administrative Managing Director:
> Prof. Dr. Heike Graßmann
> ---
>
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Re: [galaxy-dev] Shared Data Library, large number of files

[Martin Čech]

Hi all,

*Devon* is correct -the old data library UI under Admin menu is still in
place (because it has some features perceived as important to some admins).
However majority of users and most of the admins are using the interface
under 'Shared Data' I hope and the old UI is deprecated since 15.10 (
https://docs.galaxyproject.org/en/master/releases/15.10_announce.html). I
created a PR to adjust the label in the admin interface to make this clear:
https://github.com/galaxyproject/galaxy/pull/3694

The old UI is very slow for large libraries but the new UI under Shared
Data/Data Libraries in the top menu shouldn't have this kind of issues for
hundreds of folders/datasets that are mentioned here.

*Daniel* are you using the new UI form the top menu? If so are you
experiencing this only with a specific folder full of linked datasets or
does it occur for any folder with many datasets in it?

Martin



On Thu, Mar 2, 2017 at 3:49 AM Devon Ryan  wrote:

> I observe the same thing on 16.07. As an example, I'm just opened a
> data library under Admin->Data->Data Libraries and this took about a
> minute and a half. It looks like this is related to the quantity of
> data in this folder. The associated entry in the uwsgi log is as
> follows:
>
> [pid: 357|app: 0|req: 2059/5647] 10.1.6.77 () {44 vars in 1220 bytes}
> [Thu Mar  2 08:40:19 2017] GET
>
> /library_common/browse_library?sort=name=All=All=False=library_admin=browse=355326571f7132ff
> => generated 21761790 bytes in 108644 msecs (HTTP/1.1 200) 2 headers
> in 73 bytes (14 switches on core 2)
>
> So this library is causing ~21 megs of data to be returned to the
> browser, which I presume is the source of the issue.
>
> As an aside, the old data library API is still in use in the admin
> section until at least 16.07. Perhaps this has been changed since
> then, I hadn't planed to update our system until the end of the month.
> For what it's worth, opening the same library via "shared data" takes
> ~100 msec.
>
> Devon
> --
> Devon Ryan, Ph.D.
> Email: dpr...@dpryan.com
> Data Manager/Bioinformatician
> Max Planck Institute of Immunobiology and Epigenetics
> Stübeweg 51
> 79108 Freiburg
> Germany
>
>
> On Thu, Mar 2, 2017 at 8:30 AM, Hans-Rudolf Hotz  wrote:
> >
> > this sounds more like a browser issue to me
> > which browser do you use? what happens when you use a different browser?
> and
> > what happens when you just reload the page
> >
> >
> > Hans-Rudolf
> >
> > On 03/01/2017 06:17 PM, D K wrote:
> >>
> >> Actually, when I click on the Shared Data-> Data Libraries link I get
> >> only the Galaxy banner and a blank page, so I'm not even seeing the data
> >> libraries themselves.
> >>
> >> If I use the Admin link and then click Data libraries, I can see the
> >> actual libraries. But when I try to enter one of the libraries with lots
> >> of files it hangs.
> >>
> >>
> >> On Wed, Mar 1, 2017 at 9:03 AM, D K  >> > wrote:
> >>
> >> Hi Hans,
> >>
> >> I'm running 16.10. If I'm not mistaken, the old Data Library
> >> interface is still accessible in the Admin menu isn't it? I have the
> >> same issue when navigating to a Data Library either from the Admin
> >> or Shared Data links. I also tried this in 16.07 with the same
> >> result.  If it makes a difference, I'm using PostgreSQL and Apache.
> >>
> >> Dwight
> >>
> >>
> >>
> >> On Tue, Feb 28, 2017 at 11:47 PM, Hans-Rudolf Hotz  >> > wrote:
> >>
> >> Hi Daniel
> >>
> >> Just double checking which version of galaxy are you running? In
> >> other words: are you still using the old Data Library interface?
> >> (if I remember correctly, the old UI was deprecated in 15.10)
> >> We had similar issues with the old UI.
> >>
> >> The new one works fine and is very fast. E.g. we have a 'MISEQ'
> >> folder with more than 100 sub folders and a HISEQ folder with
> >> more than 600 sub folders. Each containing up to 100plus fastq
> >> and text files.
> >>
> >> Regards, Hans-Rudolf
> >>
> >>
> >>
> >> On 03/01/2017 12:13 AM, D K wrote:
> >>
> >> Hi,
> >>
> >> I've noticed that the more files / folders (think hundreds
> >> of folders
> >> each with 20+ fastq files) I add to a Shared Data Library,
> >> the longer
> >> and longer it takes to initially navigate the folder
> >> structure (after
> >> clicking on the specific Shared Data Library). Just opening
> >> up the
> >> Shared Data Library can take several minutes and often the
> >> browser times
> >> out. Is there a way to speed this up?
> >>
> >> If it's relevant, when I add shared data, it's linked rather
> >> than copied
> >> into Galaxy. Any 

Re: [galaxy-dev] regarding tool dependencies

[Martin Čech]

Hi Nir,

there is very well maintained Docker image with fully configured Galaxy
available here: http://bgruening.github.io/docker-galaxy-stable/

The documentation for Galaxy administration is linked from here:
https://new.galaxyproject.org/docs/#administration - most notably the
recent slide decks for administration training are available here:
https://gvlproject.github.io/dagobah-training/

If you encounter any problems come to chat with us here:
https://gitter.im/galaxyproject/Lobby

Please let us know if you are interested in more.

Martin



On Fri, Feb 17, 2017 at 12:14 PM Nir Shachaf <nir.shac...@weizmann.ac.il>
wrote:

> Dear Martin,
>
> I appreciate your detailed reply. On zero order, my tool, along with other
> existing Galaxy "metabolomics" tools should work in-house, and therefore I
> can rely on system dependencies, which might mater be resolved through some
> help from the community.
>
> However, I would like to raise a slightly bigger issue, as at least for
> me, setting up the Galaxy framework is a very intricate job, evolving
> editing several configuration files which goes much beyond the setting of
> package dependencies. In my opinion it would be very useful to have some
> "quick start recipes", or a predefined VM which can work out of the box,
> including, e.g. a per-configured demo users' DB and a linked FTP server for
> uploading files, etc. At least, a tutorial on how to setup such a system on
> several popular Linux configurations would be greatly appreciated! At the
> moment, I have abandoned the idea of setting up Galaxy in my lab, due to
> time-consuming configuration problems... hopefully, we can re-try in the
> future.
>
> Many thanks once more,
> Nir.
>
> --
> *From:* Martin Čech [mar...@bx.psu.edu]
> *Sent:* Thursday, February 09, 2017 6:46 PM
> *To:* Nir Shachaf; galaxy-...@bx.psu.edu
> *Subject:* Re: [galaxy-dev] regarding tool dependencies
>
> Hello Nir,
>
> the tool publishing  process looks like this: tools for Galaxy are
> contributed by developers like you to the Tool Shed
> https://toolshed.g2.bx.psu.edu/ which serves as an 'appstore' for
> Galaxies worldwide. Any Galaxy administrator can then instal the tool. Some
> tools have dependencies, yours seem to depend on R. The recommended way to
> have Galaxy installed these dependencies for you is to use Conda (list of
> some available R packages here: https://anaconda.org/r/repo?type=conda).
> To learn more about Conda please visit
> https://docs.galaxyproject.org/en/master/admin/conda_faq.html
>
> Alternatively, when you do not care about sharing your tool, and you do
> not need to track reproducibility you can add any tool to Galaxy locally
> (add the .xml wrapper and point tool_conf.xml at it and restart Galaxy).
> When the tool is executed and no dependencies are found Galaxy will look
> for its executable and if it is on the $PATH it will just use it.
>
> Please let us know if you have more questions.
>
> Thanks for using Galaxy,
>
> Martin
>
>
> On Thu, Feb 9, 2017 at 11:01 AM Nir Shachaf <nir.shac...@weizmann.ac.il>
> wrote:
>
> Dear Galaxy-dev team,
>
> As a research scientist in the dept. of Plant Sciences I would like to
> contribute a tool to the 'Metabolomics' tool-box under Galaxy. The tool is
> principally written in R, with some dependencies (namely: R>=3.x, and
> several R packages). Following the documentation in:
>
> https://wiki.galaxyproject.org/Admin/Tools/ToolDependencies
>
> https://wiki.galaxyproject.org/Admin/Config/ToolDependencies
>
> I admit I get confused by the numerous possibilities offered by the
> framework. My main concern is to be able to link the Galaxy server to tools
> already installed on my development environment, and NOT to depend on the
> tools available in the tool-shed repository (as many are not there, and
> there are specific versions requirements).
>
> Could you kindly direct me to the relevant solution, or a user's-list
> post, if applicable?
>
> Many thanks in advance,
> Nir Shachaf,
> Plant Sciences Dept.,
> Weizmann Inst. of Science,
> Rehovot, Israel.
> ___
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> in your mail client.  To manage your subscriptions to this
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>
>
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Re: [galaxy-dev] Last stable galaxy Release 16.10 or 17.01 ?

[Martin Čech]

Hello,

16.10 is the latest release however release of 17.01 is imminent and will
probably happen early next week. The release_17.01 branch is what
usegalaxy.org runs for the past few weeks without any big issues.
The choice is yours but updating to release_17.01 now is alright I think as
along as you keep it updated with what will be added in the future.

Thanks for using Galaxy,

Martin

On Fri, Feb 17, 2017 at 10:49 AM NGS & Bioinformatics Platform <
bi...@wiv-isp.be> wrote:

> Dear galaxy-dev list members,
>
>
>
> Can somebody tell us, which version of galaxy is the last official stable
> release ?  16.10 branch has been merge with master but not the 17.01.
> Additionally this 17.01 branch seems to have a lot of recent commit,  is it
> normal  ?
>
> Is it safe to update our local galaxy repository with these 17.01  changes
> or is it better to wait a little  and stay with  galaxy 16.10  for the
> moment ?
>
>
>
> Thanks for your help.
>
>
>
>
> *  -- *
>
> *Checked as being free of known viruses.*
>
>
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Re: [galaxy-dev] Upgrade migration scripts

[Martin Čech]

Hi Matthias,

DB migrations need only to be run when there is a change in DB schema in
between the releases. That is not the case between 16.10 and 17.01 so there
is no migration to be run.

When there is a migration to run, the startup process of Galaxy will abort
and you will be presented with a message that includes the command to run
($ sh manage_db.sh upgrade).

The tool migrations are even rarer than DB migrations, and there was not a
one in past ~2 years I think. It would work similarly to the process above.

In standard cases, the only thing admin is recommended to do is to backup
DB before running the upgrade script.

Thank you for using Galaxy and let us know if you have more questions!

Martin

On Wed, Feb 15, 2017 at 10:52 AM Matthias Bernt  wrote:

> Der galaxy-dev list,
>
> I just updated my 16.10 installation to 17.01 in order to see how
> upgrading works.
>
> I followed https://wiki.galaxyproject.org/Admin/Maintenance where point
> 8 is to run migration scripts.
>
> Also the Admin Course
> (
> https://martenson.github.io/dagobah-training/10-upgrading-release/upgrading.html#9
> )
> refers to tool and DB migration steps that need(?) to be invoked.
>
> I checked the output of run.sh and it seems to me that all migration
> scripts are run automatically: eg. there is output like:
>
> migrate.versioning.script.base DEBUG 2017-02-15 13:56:53,451 Loading
> script lib/galaxy/model/migrate/versions/0001_initial_tables.py...
> migrate.versioning.script.base DEBUG 2017-02-15 13:56:53,451 Script
> lib/galaxy/model/migrate/versions/0001_initial_tables.py loaded
> successfully
> ...
>
> So I was wondering what the admin should do here? Just check for errors
> or problems?
>
> Cheers,
> Matthias
>
>
> ___
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Re: [galaxy-dev] ImportError and Project life cycle

[Martin Čech]

Hi Matthias,

what version of Galaxy are you running?

The tool you have installed seems to support only new Galaxies that have
Conda dependency resolution enabled. We are currently in the middle of the
transition of the Galaxy's ecosystem to this new dependency manager so
there are rough edges here and there - sorry about that. You can read
details about Conda and dependency resolution here:
https://docs.galaxyproject.org/en/master/admin/conda_faq.html

Since Galaxy 16.07 you can switch the `conda_auto_init` in Galaxy's config
to True and after restart Galaxy will install Conda itself.

Therefore I recommend you (with Galaxy newer than 16.07) to uninstall the
tool, install Conda (with conda_auto_init) and install the tool again. That
will install the needed dependency for the tool. If you have older Galaxy
please update it.

Please let us know about any questions you have and thanks for using Galaxy.

Martin

On Fri, Feb 10, 2017 at 10:38 AM Peter Cock 
wrote:

> On Fri, Feb 10, 2017 at 3:26 PM, Matthias Bernt  wrote:
> > Dear galaxy-dev list,
> >
> > I'm currently trying to introduce myself to the galaxy server, i.e.,
> > learning how to use and administer a galaxy server.
> >
> > I have installed galaxy following this excellent tutorial:
> >
> > https://github.com/martenson/dagobah-training
> >
> > Then I tried the tool "FASTQ Quality Trimmer by sliding window" which is
> > mentioned in NGS101-6 tutorial. I installed the tool from tool shed, but
> I
> > get a python error (the Admin panel shows that all dependencies are
> > installed):
> >
> > Traceback (most recent call last):
> >   File
> > "/home/berntm/shed_tools/
> toolshed.g2.bx.psu.edu/repos/devteam/fastq_trimmer_by_quality/25c24379693a/fastq_trimmer_by_quality/fastq_trimmer_by_quality.py
> ",
> > line 3, in 
> > from galaxy_utils.sequence.fastq import fastqReader, fastqWriter
> >   File "/home/berntm/galaxy/lib/galaxy_utils/sequence/fastq.py", line 7,
> in
> > 
> > from six import Iterator, string_types
> > ImportError: No module named six
> >
> > Do you have an idea what could be wrong? I guess that this is to little
> > information, but I did not know which kind of additional information
> would
> > be helpful.
>
> This appears to be a missing dependency on the Python module "six"
> which is used to help write code which will work under both Python 2
> and Python 3.
>
> This is likely a recent regression - hopefully one of the Galaxy team
> can comment on this, likely the Tool Shed definition for this tool needs
> a minor tweak (and then you can apply the update via the Galaxy
> Admin controls within your browser).
>
> > Another question: At my institution quite a lot of NGS projects are
> carried
> > out. After a project is finished all methods and data are stored to a
> long
> > term read only tape archive. For the future the idea is to use galaxy.
> Which
> > options are there to implement such a project life cycle with galaxy?
>
> Not that I personally am aware of, no. There are optional disk quotas to
> encourage users to remove (delete) old data.
>
> > A last general question: would it be better to send a separate mail to
> the
> > list when I have multiple questions?
>
> Yes please, with useful email subjects would be best.
>
> Peter
> ___
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Re: [galaxy-dev] regarding tool dependencies

[Martin Čech]

Hello Nir,

the tool publishing  process looks like this: tools for Galaxy are
contributed by developers like you to the Tool Shed
https://toolshed.g2.bx.psu.edu/ which serves as an 'appstore' for Galaxies
worldwide. Any Galaxy administrator can then instal the tool. Some tools
have dependencies, yours seem to depend on R. The recommended way to have
Galaxy installed these dependencies for you is to use Conda (list of some
available R packages here: https://anaconda.org/r/repo?type=conda). To
learn more about Conda please visit
https://docs.galaxyproject.org/en/master/admin/conda_faq.html

Alternatively, when you do not care about sharing your tool, and you do not
need to track reproducibility you can add any tool to Galaxy locally (add
the .xml wrapper and point tool_conf.xml at it and restart Galaxy). When
the tool is executed and no dependencies are found Galaxy will look for its
executable and if it is on the $PATH it will just use it.

Please let us know if you have more questions.

Thanks for using Galaxy,

Martin


On Thu, Feb 9, 2017 at 11:01 AM Nir Shachaf 
wrote:

> Dear Galaxy-dev team,
>
> As a research scientist in the dept. of Plant Sciences I would like to
> contribute a tool to the 'Metabolomics' tool-box under Galaxy. The tool is
> principally written in R, with some dependencies (namely: R>=3.x, and
> several R packages). Following the documentation in:
>
> https://wiki.galaxyproject.org/Admin/Tools/ToolDependencies
>
> https://wiki.galaxyproject.org/Admin/Config/ToolDependencies
>
> I admit I get confused by the numerous possibilities offered by the
> framework. My main concern is to be able to link the Galaxy server to tools
> already installed on my development environment, and NOT to depend on the
> tools available in the tool-shed repository (as many are not there, and
> there are specific versions requirements).
>
> Could you kindly direct me to the relevant solution, or a user's-list
> post, if applicable?
>
> Many thanks in advance,
> Nir Shachaf,
> Plant Sciences Dept.,
> Weizmann Inst. of Science,
> Rehovot, Israel.
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   https://lists.galaxyproject.org/
>
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>   http://galaxyproject.org/search/mailinglists/
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Re: [galaxy-dev] Tools using Galaxy's Python library?

[Martin Čech]

Hi folks,

the two of the Galaxy-born libraries have sources at our GitHub:

https://github.com/galaxyproject/gops
https://github.com/galaxyproject/sequence_utils

Any improvements or PyPI-readiness work are welcome.

Best,
Martin

On Tue, Jan 31, 2017 at 7:08 AM Peter Cock 
wrote:

> Thanks Nicola,
>
> I didn't spot the missing slash, but planemo lint did - for anyone
> else copy-and-pasting:
>
>  version="1.0.1">galaxy_sequence_utils
>
> For anyone not yet using BioConda with Galaxy, there is also a Tool
> Shed entry here:
>
>
> https://toolshed.g2.bx.psu.edu/view/iuc/package_galaxy_sequence_utils_1_0_1/
>
> I am therefore adding this to my tool_dependencies.xml files:
>
> 
>  />
> 
>
> I still need to work out how best to make this available under TravisCI,
> given I am not currently using BioConda for the dependencies.
>
> @IUC: Should this also be released on PyPI for easy install via pip?
>
> Peter
>
>
> On Tue, Jan 31, 2017 at 11:15 AM, Nicola Soranzo 
> wrote:
> > Hi Peter,
> > adding
> >
> >  > version="1.0.1">galaxy_sequence_utils
> >
> > to each of these tools should solve the problem, there is a Bioconda
> package
> > which provides the Python library:
> >
> > https://anaconda.org/bioconda/galaxy_sequence_utils
> >
> > Cheers,
> > Nicola
> >
> >
> > On 31/01/17 10:39, Peter Cock wrote:
> >>
> >> Hi all,
> >>
> >> A few of my tools have for a long time used Galaxy's own parsing
> >> functionality in order to avoid an external dependency. Lately
> >> this has stopped working on my TravisCI testing with planemo
> >> using the Galaxy dev branch (the stable master branch is fine):
> >> e.g.
> >>
> >> https://travis-ci.org/peterjc/pico_galaxy/builds/196655736
> >>
> >> The tools fail with things like:
> >>
> >> |  from galaxy_utils.sequence.fasta import fastaReader, fastaWriter
> >> |  ImportError: No module named galaxy_utils.sequence.fasta
> >>
> >>
> >> or:
> >>
> >> |  from galaxy_utils.sequence.fastq import fastqReader
> >> |  ImportError: No module named galaxy_utils.sequence.fastq
> >>
> >> Is this a temporary regression in Galaxy, or a deliberate change?
> >> Do the tools need to do something to explicit have access to the
> >> Galaxy Python library, or are they now considered private?
> >> If so, I can update these tools to use an explicit dependency
> >> for parsing FASTA and FASTQ (e.g. Biopython).
> >>
> >> Thanks,
> >>
> >> Peter
> >> ___
> >> Please keep all replies on the list by using "reply all"
> >> in your mail client.  To manage your subscriptions to this
> >> and other Galaxy lists, please use the interface at:
> >>https://lists.galaxyproject.org/
> >>
> >> To search Galaxy mailing lists use the unified search at:
> >>http://galaxyproject.org/search/mailinglists/
> >
> >
> ___
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Re: [galaxy-dev] Can't downgrade database.

[Martin Čech]

Makis,

you need to run the downgrade command (sh manage_db.sh downgrade
--version=129) from the folder with the newer Galaxy. The old one does not
have the downgrading scripts.

Thanks for using Galaxy.

Martin

On Tue, Jan 17, 2017 at 7:33 AM Makis Ladoukakis 
wrote:

> Hello everyone,
>
>
> I tried to download a newer version of Galaxy (I had 15.10 and pulled
> 16.01 in a different directory) and now for some reason in my old working
> directory I get the error:
>
>
> Your database has version '133' but this code expects version '129'.
>
> Please backup your database and then migrate the schema by running 'sh
> manage_db.sh upgrade'.
>
>
> when I tried:
>
>
> sh manage_db.sh downgrade --version=129
>
>
> I got the error:
>
> Traceback (most recent call last):
>   File "./scripts/manage_db.py", line 33, in 
> invoke_migrate_main()
>   File "./scripts/manage_db.py", line 30, in invoke_migrate_main
> main( repository=repo, url=db_url )
>   File
> "/home/anastasia_dev/galaxy/eggs/sqlalchemy_migrate-0.9.6-py2.7.egg/migrate/versioning/shell.py",
> line 209, in main
> ret = command_func(**kwargs)
>   File
> "/home/anastasia_dev/galaxy/eggs/sqlalchemy_migrate-0.9.6-py2.7.egg/migrate/versioning/api.py",
> line 202, in downgrade
> return _migrate(url, repository, version, upgrade=False, err=err,
> **opts)
>   File "", line 2, in _migrate
>   File
> "/home/anastasia_dev/galaxy/eggs/sqlalchemy_migrate-0.9.6-py2.7.egg/migrate/versioning/util/__init__.py",
> line 160, in with_engine
> return f(*a, **kw)
>   File
> "/home/anastasia_dev/galaxy/eggs/sqlalchemy_migrate-0.9.6-py2.7.egg/migrate/versioning/api.py",
> line 345, in _migrate
> changeset = schema.changeset(version)
>   File
> "/home/anastasia_dev/galaxy/eggs/sqlalchemy_migrate-0.9.6-py2.7.egg/migrate/versioning/schema.py",
> line 82, in changeset
> changeset = self.repository.changeset(database, start_ver, version)
>   File
> "/home/anastasia_dev/galaxy/eggs/sqlalchemy_migrate-0.9.6-py2.7.egg/migrate/versioning/repository.py",
> line 225, in changeset
> changes = [self.version(v).script(database, op) for v in versions]
>   File
> "/home/anastasia_dev/galaxy/eggs/sqlalchemy_migrate-0.9.6-py2.7.egg/migrate/versioning/repository.py",
> line 189, in version
> return self.versions.version(*p, **k)
>   File
> "/home/anastasia_dev/galaxy/eggs/sqlalchemy_migrate-0.9.6-py2.7.egg/migrate/versioning/version.py",
> line 160, in version
> return self.versions[VerNum(vernum)]
> KeyError: 
>
>
>
>
> I checked earlier posts stating  that i need to remove all .pyc files
> before downgrading. I did just that but nothing worked.
>
>
> Any ideas?
>
>
> Thank you in advance,
>
> Efthymios Ladoukakis
>
>
>
>
> ___
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Re: [galaxy-dev] Is there demand for rate limiting in Galaxy?

[Martin Čech]

Max:

you are correct, the dev branch is what would be the best to develop
against. Also feel free to open PR with work in progress at any point. I am
sure you will get useful feedback.

Thank you for using Galaxy,

Martin

On Wed, Nov 23, 2016 at 5:40 AM Maximilian Friedersdorff 
wrote:

>
>
> 
> Un o’r 4 prifysgol uchaf yn y DU a’r orau yng Nghymru am fodlonrwydd
> myfyrwyr.
> (Arolwg Cenedlaethol y Myfyrwyr 2016)
> www.aber.ac.uk
>
> Top 4 UK university and best in Wales for student satisfaction
> (National Student Survey 2016)
> www.aber.ac.uk
>
>
>
> -- Forwarded message --
> From: Maximilian Friedersdorff 
> To:
> Cc: Maximilian Friedersdorff , "
> galaxy-dev@lists.galaxyproject.org" 
> Date: Wed, 23 Nov 2016 10:40:11 +
> Subject: Re: [galaxy-dev] Is there demand for rate limiting in Galaxy?
> > I think there is a demand and partially Galaxy has support for these
> > kind of limits for a user. Please have a look at:
> >
> >
> https://github.com/galaxyproject/galaxy/blob/dev/config/job_conf.xml.sample_advanced#L725
>
> Yes I'm aware of the existing limits.  An ideal (from my point of view)
> implementation would simply add another possible type to these.
>
> > An extension to these would be super cool!
>
> Ok that's all I needed to hear :-).  I guess I should base any changes
> on the [dev] branch?
>
> Thanks
>
> Max
>
> PS. My apologies for the email signature below, over which I have no
> control.
> ___
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Re: [galaxy-dev] Restart Galaxy without interruption

[Martin Čech]

Hi Gildas,

the approach which Main Galaxy takes is as described by Nate in the
exercise document linked by Laure. Exerpt here:

"In addition, you can gracefully restart the uWSGI Galaxy process with sudo
supervisorctl signal HUP gx:galaxy. uWSGI is configured to start Galaxy in
a "master" process and then fork the configured number of worker processes.
Because of this, if sent a SIGHUP signal, it will kill the workers but the
master process will hold its socket open, blocking client (browser)
connections until new workers are forked. This prevents users from seeing a
proxy error page during restarts."

Using this, you can restart both the uWSGI server and Galaxy handlers with:

$ sudo supervisorctl signal HUP gx:galaxy && sudo supervisorctl restart
gx:handler0 gx:handler1

without supervisor it would be something like $ pkill -HUP -o -u 
uwsgi

Thanks for using Galaxy,

Martin

On Wed, Nov 16, 2016 at 5:19 AM Laure QUINTRIC 
wrote:

> Hi Gildas,
>
> Have a look here :
> https://github.com/martenson/dagobah-training/tree/master/advanced/002a-systemd-supervisor
>
> See ya.
>
>
> Laure
>
> Le 14/11/2016 à 21:35, Gildas Le Corguillé a écrit :
>
> Hi,
>
> Since Galaxy need to be restarted sometime (load datatype, add ressources
> in .loc, apply changes in the galaxy.ini), is anybody of you have solutions
> to restart it without interrupt the service?
>
> We are now using nginx, uwsgi and supervisord.
>
> My hope is to split the Galaxy process in two group (1 uwsgi and 2 job
> handlers per group). That way, we will be able to restart the group1 and
> then the group2.
>
>
> I was planning to set the 2 uwsgi servers and delegate the load balancing
> to ngnix (https://www.nginx.com/resources/admin-guide/load-balancer/)
> But maybe, some of you already implemented that and can provide me some
> advices or warnings.
>
> The job handler part seems easier to deal with
> --server-name=handler1_%(process_num)s
> --server-name=handler2_%(process_num)s
>
> Thanks by advance
>
> Gildas
>
> -
> Gildas Le Corguillé - Bioinformatician/Bioanalyste
>
> Plateform ABiMS (Analyses and Bioinformatics for Marine Science)
> http://abims.sb-roscoff.fr
>
> Member of the Workflow4Metabolomics project
> http://workflow4metabolomics.org
>
> Station Biologique de Roscoff - UPMC/CNRS - FR2424
> Place Georges Teissier 29680 Roscoff FRANCE
> tel: +33 2 98 29 23 81 <+33%202%2098%2029%2023%2081>
> --
>
>
>
>
>
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>
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Re: [galaxy-dev] Elastic Bean Stalk

[Martin Čech]

Hi Ryan,

if you are planning to use Galaxy on AWS I recommend you to have a look at
the CloudMan (https://wiki.galaxyproject.org/CloudMan). It will help you
orchestrate the instances and scale to meet the needs of your users.

It has been a while since I used the EB, but generally when scaling Galaxy
you do not want to scale the whole webserver/app stack because you only
need the worker nodes for jobs. Cloudman brings this setup to you with no
strings attached.

How many users and what type of jobs/load are we talking about?

Thanks.

Martin

On Tue, Nov 15, 2016 at 11:26 AM Ryan G  wrote:

> Hi all - I was wondering, if we deploy Galaxy in AWS, can we take
> advantage of Elastic BeanStalk to scale our instances based on demand
> instead of trying to configure Galaxy to perform well for our users?
>
> Ryan
>
> ___
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Re: [galaxy-dev] Changing Tool Shed URL

[Martin Čech]

Thank you very much for sharing Youssef. Very helpful.

Martin

On Fri, Oct 21, 2016 at 10:20 AM Youssef GHORBAL 
wrote:

> Hello,
>
> Two other tables need to be adapated (they reference tool_id)
> Table “job" and table “workflow_step”
>
> Youssef Ghorbal
> Institut Pasteur
> -
> > On 21 Oct 2016, at 00:36, Youssef Ghorbal 
> wrote:
> >
> > Hello,
> >
> >   What worked for us was this action sequence :
> >   - stop Galaxy
> >   - update config/tool_sheds_file.xml (change the URL from the old
> one to the new one)
> >   - “sed” shed_tool_conf.xml to change the “guid", the tool_shed and
> the “file” to replace the old prefix with the new prefix.
> >   - update the tool_version table (the tool_id column) to change the
> old prefix to the new prefix.
> >   - update the tool_shed_repositoriy table to change the tool_shed
> column to use the new tooshed prefix
> >   - update the directory shed_tools to rename the directory from the
> old prefix to the new prefix (care to adapt the subdirectories too :
> ./mytoolshed.url/xxx => ./mytoolshed2.url/)
> >   - start Galaxy (and cross your fingers)
> >
> >   Hope this help !
> >
> > Youssef Ghorbal
> > Institut Pasteur
> > -
> >> On 20 Oct 2016, at 00:16, Youssef GHORBAL 
> wrote:
> >>
> >> Hello,
> >>
> >>  I’m wondering if there is any way to change an established Tool
> Shed URL.
> >>  I have a Galaxy instance and a Tool Shed instance (
> http://mytoolshed.url/xxx) A lot of tools have beed installed from that
> Tool Shed inside Galaxy (tools referenced inside workflows etc)
> >>  I want to change the Tool Shed URL from http://mytoolshed.url/xxx
> to http://mytoolshed2.url/.
> >>
> >>  Galaxy and Tool Shed seems to use parts of the URL as a guid for
> tools.
> >>
> >>  Tool Shed does not seem to bother to be called by either URLs (it
> generates guids with the new URLs scheam for new tools though)
> >>
> >>  Galaxy does not seem to handle it, I changed the
> tool_sheds_conf.xml to point to new URL, but when I update a tool on the
> Tool Shed, Galaxy gets the new version but it generates buggy tool panel
> (the tool is cited twice)
> >>  I also tried to mess around with the shed_tool_conf.xml apdapting
> the guids and the  items with no luck.
> >>
> >>  Can someone point me to the right direction ? How the matching is
> done between shed_tool_conf.xml entries, the tool_version and
> tool_shed_repository tables.
> >>
> >>  Thank you for your help.
> >>
> >> Youssef Ghorbal
> >> Institut Pasteur
> >> ___
> >> Please keep all replies on the list by using "reply all"
> >> in your mail client.  To manage your subscriptions to this
> >> and other Galaxy lists, please use the interface at:
> >> https://lists.galaxyproject.org/
> >>
> >> To search Galaxy mailing lists use the unified search at:
> >> http://galaxyproject.org/search/mailinglists/
> >
>
> ___
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Re: [galaxy-dev] KeyError: 'tool_panel_section' when installing a new tool

[Martin Čech]

At the top of the 'manage installed tools' page there is a filter that
hides uninstalled and deactivated tools. Click 'advanced search' and then
'Deactivated or uninstalled'. Do you see your tool deactivated there?

M.

On Wed, Oct 19, 2016 at 9:49 AM Pierre Lindenbaum <
pierre.lindenb...@univ-nantes.fr> wrote:

> On 10/19/2016 03:36 PM, Martin Čech wrote:
> > Hi Pierre,
> >
> > It seems that instead of uninstalling you de-activated the repository.
> > I would uninstall the repository again.
>
>   admin > manage installed tools > there is no tool installed.
>
>
> Search toolshed > select > >> preview and install > "Install to Galaxy"
>  > all unchecked / empty ; submit > ERROR
>
>
> Pierre
>
>
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Re: [galaxy-dev] KeyError: 'tool_panel_section' when installing a new tool

[Martin Čech]

Hi Pierre,

It seems that instead of uninstalling you de-activated the repository. I
would uninstall the repository again. Please mind that there is this UX
hurdle when you want to uninstall - you have to _check_ the checkbox
labeled "Check to uninstall or leave blank to deactivate" that is in the
bottom of the uninstall page.

Hope this helps and please let us know when it does not.

Thanks,

Martin



On Wed, Oct 19, 2016 at 9:29 AM Pierre Lindenbaum <
pierre.lindenb...@univ-nantes.fr> wrote:

> On 10/19/2016 03:23 PM, Martin Čech wrote:
> > Hi Pierre,
> >
> > how old is your Tool Shed? When was the last time a tool installation
> > from it succeeded?
> >
>
> Hi martin,
>
> here is the log from the toolshed :
>
> commit 73f46f4e08141f78927056fa3e4709d0ab323972
> Merge: 05e6682 27dc31a
> Author: Nicola Soranzo
> Date:   Wed Nov 18 10:06:53 2015 +
>
>
> I was able to install my tool from this toolshed a few minutes ago.
> The second attempt failed.
>
> Thanks for the helps,
>
> Pierre
>
>
> > thanks
> >
> > M.
> >
> > On Wed, Oct 19, 2016 at 9:20 AM Pierre Lindenbaum
> > <pierre.lindenb...@univ-nantes.fr
> > <mailto:pierre.lindenb...@univ-nantes.fr>> wrote:
> >
> > Hi all, I got a "Internal Server Error" ==> "KeyError:
> > 'tool_panel_section' " when I'm trying to install a new tool from our
> > toolshed (see stacktrace below).
> >
> > My galaxy instance was cloned from
> >
> >
> > commit 217854827ac7dfc88c5388cd2ecb24fffd86c060
> > Merge: 056a7e0 ad0d0bc
> > Author: Björn Grüning <bjo...@gruenings.eu
> > <mailto:bjo...@gruenings.eu>>
> > Date:   Mon Oct 10 10:23:37 2016 +0200
> >
> > with only a few minor(?) (admin...) modifications under config/*
> > This error was raised when I've removed + re-installed a tool from
> the
> > toolshed.
> >
> > How can I fix this ?
> >
> > Thanks
> >
> > Pierre
> >
> >
> > 127.0.0.1 - - [19/Oct/2016:15:15:44 +0200] "POST
> > /admin_toolshed/prepare_for_install HTTP/1.1" 500 -
> > "
> http://127.0.0.1:8080/admin_toolshed/prepare_for_install?changeset_revisions=a38c6719c9c3_ids=9b8af19fb3feae8b_shed_url=http%3A%2F%2Fmasked.host.fr%2Ftoolshed%2F
> "
> > "Mozilla/5.0 (X11; Ubuntu; Linux i686; rv:49.0) Gecko/20100101
> > Firefox/49.0"
> > Error - : 'tool_panel_section'
> > URL: http://127.0.0.1:8080/admin_toolshed/prepare_for_install
> > File
> >
>  
> '/home/lindenb/tmp/GALAXY/galaxy.gitlab/lib/galaxy/web/framework/middleware/error.py',
> > line 151 in __call__
> >app_iter = self.application(environ, sr_checker)
> > File
> >
>  
> '/home/lindenb/tmp/GALAXY/galaxy.gitlab/.venv/local/lib/python2.7/site-packages/paste/recursive.py',
> > line 85 in __call__
> >return self.application(environ, start_response)
> > File
> >
>  
> '/home/lindenb/tmp/GALAXY/galaxy.gitlab/.venv/local/lib/python2.7/site-packages/paste/httpexceptions.py',
> > line 640 in __call__
> >return self.application(environ, start_response)
> > File
> >
>  '/home/lindenb/tmp/GALAXY/galaxy.gitlab/lib/galaxy/web/framework/base.py',
> > line 135 in __call__
> >return self.handle_request( environ, start_response )
> > File
> >
>  '/home/lindenb/tmp/GALAXY/galaxy.gitlab/lib/galaxy/web/framework/base.py',
> > line 194 in handle_request
> >body = method( trans, **kwargs )
> > File
> >
>  
> '/home/lindenb/tmp/GALAXY/galaxy.gitlab/lib/galaxy/web/framework/decorators.py',
> > line 98 in decorator
> >return func( self, trans, *args, **kwargs )
> > File
> >
>  
> '/home/lindenb/tmp/GALAXY/galaxy.gitlab/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py',
> > line 1080 in prepare_for_install
> >install_repository_manager.handle_tool_shed_repositories(
> > installation_dict )
> > File
> >
>  
> '/home/lindenb/tmp/GALAXY/galaxy.gitlab/lib/tool_shed/galaxy_install/install_manager.py',
> > line 633 in handle_tool_shed_repositories
> >new_tool_panel_section_label=new_tool_panel_section_label )
> > File
> >
>  
> '/home/lindenb/tmp/GALAXY/galaxy.gitlab/lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py',
> > line 198 in create_repository_de

Re: [galaxy-dev] KeyError: 'tool_panel_section' when installing a new tool

[Martin Čech]

Hi Pierre,

how old is your Tool Shed? When was the last time a tool installation from
it succeeded?

thanks

M.

On Wed, Oct 19, 2016 at 9:20 AM Pierre Lindenbaum <
pierre.lindenb...@univ-nantes.fr> wrote:

Hi all, I got a "Internal Server Error" ==> "KeyError:
'tool_panel_section' " when I'm trying to install a new tool from our
toolshed (see stacktrace below).

My galaxy instance was cloned from


commit 217854827ac7dfc88c5388cd2ecb24fffd86c060
Merge: 056a7e0 ad0d0bc
Author: Björn Grüning 
Date:   Mon Oct 10 10:23:37 2016 +0200

with only a few minor(?) (admin...) modifications under config/*
This error was raised when I've removed + re-installed a tool from the
toolshed.

How can I fix this ?

Thanks

Pierre


127.0.0.1 - - [19/Oct/2016:15:15:44 +0200] "POST
/admin_toolshed/prepare_for_install HTTP/1.1" 500 -
"
http://127.0.0.1:8080/admin_toolshed/prepare_for_install?changeset_revisions=a38c6719c9c3_ids=9b8af19fb3feae8b_shed_url=http%3A%2F%2Fmasked.host.fr%2Ftoolshed%2F
"
"Mozilla/5.0 (X11; Ubuntu; Linux i686; rv:49.0) Gecko/20100101 Firefox/49.0"
Error - : 'tool_panel_section'
URL: http://127.0.0.1:8080/admin_toolshed/prepare_for_install
File
'/home/lindenb/tmp/GALAXY/galaxy.gitlab/lib/galaxy/web/framework/middleware/error.py',
line 151 in __call__
   app_iter = self.application(environ, sr_checker)
File
'/home/lindenb/tmp/GALAXY/galaxy.gitlab/.venv/local/lib/python2.7/site-packages/paste/recursive.py',
line 85 in __call__
   return self.application(environ, start_response)
File
'/home/lindenb/tmp/GALAXY/galaxy.gitlab/.venv/local/lib/python2.7/site-packages/paste/httpexceptions.py',
line 640 in __call__
   return self.application(environ, start_response)
File
'/home/lindenb/tmp/GALAXY/galaxy.gitlab/lib/galaxy/web/framework/base.py',
line 135 in __call__
   return self.handle_request( environ, start_response )
File
'/home/lindenb/tmp/GALAXY/galaxy.gitlab/lib/galaxy/web/framework/base.py',
line 194 in handle_request
   body = method( trans, **kwargs )
File
'/home/lindenb/tmp/GALAXY/galaxy.gitlab/lib/galaxy/web/framework/decorators.py',
line 98 in decorator
   return func( self, trans, *args, **kwargs )
File
'/home/lindenb/tmp/GALAXY/galaxy.gitlab/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py',
line 1080 in prepare_for_install
   install_repository_manager.handle_tool_shed_repositories(
installation_dict )
File
'/home/lindenb/tmp/GALAXY/galaxy.gitlab/lib/tool_shed/galaxy_install/install_manager.py',
line 633 in handle_tool_shed_repositories
   new_tool_panel_section_label=new_tool_panel_section_label )
File
'/home/lindenb/tmp/GALAXY/galaxy.gitlab/lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py',
line 198 in create_repository_dependency_objects
   self.app.installed_repository_manager.activate_repository(
repository_db_record )
File
'/home/lindenb/tmp/GALAXY/galaxy.gitlab/lib/tool_shed/galaxy_install/installed_repository_manager.py',
line 94 in activate_repository
   tool_panel_dict = repository.metadata[ 'tool_panel_section' ]
KeyError: 'tool_panel_section'

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Re: [galaxy-dev] Paste/Fetch data, indicate filename before download data (default = Pasted Entry)

[Martin Čech]

Hi Floreline,

I am afraid you cannot choose the name of the dataset in advance. You can
however change it once it is in your history by accessing the edit menu
under the pencil icon.

Would that help?

thank you for using Galaxy

p.s. The pencil icon you mention in the upload dialog seems to not actually
be a button, but merely an illustration.

Martin

I am afraid this is not possible. You can rename it once
On Fri, Oct 7, 2016 at 12:31 PM Floreline TOUCHARD <
floreline.touch...@gmail.com> wrote:

> Hello Community,
>
> When I use the paste/fetch functionality to download data, the filename is
> display as "Pasted Entry" into my history panel.
>
> Is it possible to indicate the filename I would like to be display into
> the history before the download ? I can see an edit button into the upload
> window but there is no action on click.
>
>
>
> Thanks in advance,
>
> Floreline
> ___
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Re: [galaxy-dev] Help wanted: setting up a production server

[Martin Čech]

Hi Steve,

make sure to check out https://wiki.galaxyproject.org/Events

There are 2 extensive admin trainings going to happen in near future.
November in Salt Lake City and February in Melbourne.

Martin

On Fri, Oct 7, 2016 at 4:23 PM Steve Cassidy 
wrote:

> Hi all,
>   I’m working on setting up a Galaxy server for use with speech and
> language data.  While I can probably get there myself eventually, I’m
> thinking it would be good to get some (paid) help if it were available.
>
> If you have some experience setting up a public facing Galaxy instance,
> and you have some time available in the next couple of weeks, please get in
> touch.
>
> Any location is probably ok as long as we can work out how to reimburse
> you.  We (and the servers) are based in Australia but I’m currently in New
> York.
>
> Thanks,
>
> Steve
>
> —
> Department of Computing, Macquarie University
> http://web.science.mq.edu.au/~cassidy
>
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Re: [galaxy-dev] how to make an exact clone of the usegalaxy.org

[Martin Čech]

The link in the first answer is not up to date because things moved,
however it should be probably linking to here
https://github.com/galaxyproject/ephemeris/blob/master/ephemeris/shed_install.py

Martin

On Mon, Sep 26, 2016 at 11:02 AM Beginner TI <ruiwang...@gmail.com> wrote:

> Hi Martin,
>
> Thanks!
>
> The first link doesn't really work...upon going to github it gave me 404.
> After I explored a bit more
> it says itself that it may not work now. :-(
>
> However the second one looks quite promising!
>
> Cheers,
> Rui
>
> On Mon, Sep 26, 2016 at 7:55 AM, Martin Čech <mar...@bx.psu.edu> wrote:
>
>> Hi Rui,
>>
>> there is no 'mirror' button to obtain Main's toolset yet, but many pieces
>> are in place to help you with this.
>>
>> Please see the following answers for guides and links:
>>
>> https://biostar.usegalaxy.org/p/11338/
>> https://biostar.usegalaxy.org/p/19660/
>>
>> Thanks,
>>
>> Martin
>>
>>
>>
>>
>>
>> On Mon, Sep 26, 2016 at 10:50 AM Beginner TI <ruiwang...@gmail.com>
>> wrote:
>>
>>> Hey Guys,
>>>
>>> I have seen this question being asked quite some times, but there wasn't
>>> any definitive answers. Today I'm doing a new local install. Upon getting
>>> the latest github repo, I still only got a small portion of galaxy main. Is
>>> there any way to include all the tools there automatically?
>>>
>>> Thanks,
>>> Rui
>>> ___
>>> Please keep all replies on the list by using "reply all"
>>> in your mail client.  To manage your subscriptions to this
>>> and other Galaxy lists, please use the interface at:
>>>   https://lists.galaxyproject.org/
>>>
>>> To search Galaxy mailing lists use the unified search at:
>>>   http://galaxyproject.org/search/mailinglists/
>>
>>
>
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Re: [galaxy-dev] samtools

[Martin Čech]

Hi Rui,

you can install the following suite which includes about a dozen of wrapped
samtools.

https://toolshed.g2.bx.psu.edu/view/devteam/suite_samtools_1_2/5b673ccc8747

Martin

On Mon, Sep 26, 2016 at 11:05 AM Beginner TI  wrote:

> I did see that if I click each individual tool, and then in the options, I
> could find the tool xml file, but this would require manually clicking each
> of it. Is there any way we could get these in batch? I shouldn't be the
> first or last person that want to make an identical clone of main galaxy
> instance, so I assume that there are some good/easy ways I'm missing?
>
> thanks,
> Rui
>
> On Sun, Sep 25, 2016 at 1:05 AM, Beginner TI  wrote:
>
>> Hi All,
>>
>> I compiled samtools from source, and just realized that I don't have
>> those tool xml files. Tried to google but failed to find any samtools
>> wrapper. This is quite surprising since the main instance has it. Does
>> anyone happen to know where we could obtain those files that are used by
>> galaxy main instance? I don't want to use tool_shed and prefer to install
>> all tools manually. In that case, how could I access the tool xml files
>> that are used by tool_shed installation process?
>>
>> Thanks,
>> Rui
>>
>
> ___
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Re: [galaxy-dev] how to make an exact clone of the usegalaxy.org

[Martin Čech]

Hi Rui,

there is no 'mirror' button to obtain Main's toolset yet, but many pieces
are in place to help you with this.

Please see the following answers for guides and links:

https://biostar.usegalaxy.org/p/11338/
https://biostar.usegalaxy.org/p/19660/

Thanks,

Martin





On Mon, Sep 26, 2016 at 10:50 AM Beginner TI  wrote:

> Hey Guys,
>
> I have seen this question being asked quite some times, but there wasn't
> any definitive answers. Today I'm doing a new local install. Upon getting
> the latest github repo, I still only got a small portion of galaxy main. Is
> there any way to include all the tools there automatically?
>
> Thanks,
> Rui
> ___
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> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
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>
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Re: [galaxy-dev] Trimmomatic tool is not visible in the workflow editor

[Martin Čech]

I think you might need to update since I believe the trimmomatic tool uses
features that are not available in the 15.03 Galaxy workflow editor/engine.

M.

On Tue, Sep 13, 2016, 21:45 Amarathunga A. Dineli Karunath <
dineli_karunathil...@nuhs.edu.sg> wrote:

> Hi Martin,
>
>
>
> It’s 15.03.
>
>
>
> Regards,
>
> Dineli
>
>
>
> *From:* Martin Čech [mailto:mar...@bx.psu.edu]
> *Sent:* Tuesday, September 13, 2016 10:31 PM
> *To:* Amarathunga A. Dineli Karunath; galaxy-...@bx.psu.edu
> *Subject:* Re: [galaxy-dev] Trimmomatic tool is not visible in the
> workflow editor
>
>
>
> Hi Dineli,
>
>
>
> what version of Galaxy do you have installed?
>
>
>
> thanks
>
>
>
> Martin
>
>
>
> On Tue, Sep 13, 2016 at 10:27 AM Amarathunga A. Dineli Karunath <
> dineli_karunathil...@nuhs.edu.sg> wrote:
>
> Hi,
>
> I have a local galaxy instance and have installed many tools from the
> galaxy tool shed. Recently I have installed Trimmomatic tool and
> installation was successful but when I go to build a workflow, trimmomatic
> tool is not visible in the tool panel. It works fine in all other places.
> Could you please help me on this? Please refer the attachments I have
> provided.
>
> Thanks & Regards,
>
> Dineli
>
>
>
>
> --
>
>
> Important: This email is confidential and may be privileged. If you are
> not the intended recipient, please delete it and notify us immediately; you
> should not copy or use it for any purpose, nor disclose its contents to any
> other person. Thank you.
>
> ___
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>
>
> --
>
> Important: This email is confidential and may be privileged. If you are
> not the intended recipient, please delete it and notify us immediately; you
> should not copy or use it for any purpose, nor disclose its contents to any
> other person. Thank you.
>
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Re: [galaxy-dev] Can't log in to Galaxy instance using Safari web browser

[Martin Čech]

Stephanie:

can you log in to usegalaxy.org or test.galaxyproject.org using Safari?
Also please try to login to your instance using Safari private window.

Martin

On Tue, Sep 13, 2016 at 11:33 AM Stephanie LE GRAS <sleg...@igbmc.fr> wrote:

> Hi Martin,
>
>
>
> Thank you for your feedback. We don’t have any javascript errors…
>
>
>
> Stephanie
>
>
>
> *De : *Martin Čech <mar...@bx.psu.edu>
> *Date : *mardi 13 septembre 2016 16:36
> *À : *Stephanie Le Gras <sleg...@igbmc.fr>, "
> galaxy-dev@lists.galaxyproject.org" <galaxy-dev@lists.galaxyproject.org>
> *Objet : *Re: [galaxy-dev] Can't log in to Galaxy instance using Safari
> web browser
>
>
>
> Hello Stephanie,
>
> I have just tested this on 16.07 and on `dev` branch of Galaxy and it
> works for both in my case. Can you please check the browser's console for
> javascript errors?
>
>
>
> Thanks,
>
>
>
> Martin
>
> On Tue, Sep 13, 2016 at 10:22 AM Stephanie LE GRAS <sleg...@igbmc.fr>
> wrote:
>
> Hi there (again),
>
>
>
> Another problem we are currently facing is that we cannot log in anymore
> on our galaxy instance using Safari. It’s working with Firefox and Chrome
> but when we are using Safari (with the right password and login) we just
> see a green box saying that we successfully logged in and we go back to the
> log in page.
>
>
>
> This is a problem we are encountering on our test instance that we’ve just
> updated to the latest release release_16.07.
>
>
>
> Any idea about what the problem can be ?
>
>
>
> Many thanks in advance for any help,
>
>
>
> Best regards,
>
>
>
> Stephanie
>
> --
>
> Stephanie Le Gras
>
> INSERM
> Computational scientist - Bioinformatician
> GenomEast platform (former Microarray and Sequencing platform)
> IGBMC
> 1, rue Laurent Fries
> 67404 ILLKIRCH Cedex
> France
> Tel. : +33 (0)3 88 65 32 73
>
>
>
> ___
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>
>
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Re: [galaxy-dev] Can't log in to Galaxy instance using Safari web browser

[Martin Čech]

Hello Stephanie,

I have just tested this on 16.07 and on `dev` branch of Galaxy and it works
for both in my case. Can you please check the browser's console for
javascript errors?

Thanks,

Martin

On Tue, Sep 13, 2016 at 10:22 AM Stephanie LE GRAS  wrote:

> Hi there (again),
>
>
>
> Another problem we are currently facing is that we cannot log in anymore
> on our galaxy instance using Safari. It’s working with Firefox and Chrome
> but when we are using Safari (with the right password and login) we just
> see a green box saying that we successfully logged in and we go back to the
> log in page.
>
>
>
> This is a problem we are encountering on our test instance that we’ve just
> updated to the latest release release_16.07.
>
>
>
> Any idea about what the problem can be ?
>
>
>
> Many thanks in advance for any help,
>
>
>
> Best regards,
>
>
>
> Stephanie
>
> --
>
> Stephanie Le Gras
>
> INSERM
> Computational scientist - Bioinformatician
> GenomEast platform (former Microarray and Sequencing platform)
> IGBMC
> 1, rue Laurent Fries
> 67404 ILLKIRCH Cedex
> France
> Tel. : +33 (0)3 88 65 32 73
>
>
> ___
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> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
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>
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Re: [galaxy-dev] Trimmomatic tool is not visible in the workflow editor

[Martin Čech]

Hi Dineli,

what version of Galaxy do you have installed?

thanks

Martin

On Tue, Sep 13, 2016 at 10:27 AM Amarathunga A. Dineli Karunath <
dineli_karunathil...@nuhs.edu.sg> wrote:

> Hi,
>
> I have a local galaxy instance and have installed many tools from the
> galaxy tool shed. Recently I have installed Trimmomatic tool and
> installation was successful but when I go to build a workflow, trimmomatic
> tool is not visible in the tool panel. It works fine in all other places.
> Could you please help me on this? Please refer the attachments I have
> provided.
>
> Thanks & Regards,
>
> Dineli
>
>
>
> --
>
> Important: This email is confidential and may be privileged. If you are
> not the intended recipient, please delete it and notify us immediately; you
> should not copy or use it for any purpose, nor disclose its contents to any
> other person. Thank you.
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   https://lists.galaxyproject.org/
>
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Re: [galaxy-dev] delete user and all trace of user

[Martin Čech]

Hi Edgar,

the 'active' column won't help you, that relates to the account activation
feature vie email.

Your other approach seems more viable. I would try deleting the smallest
subset of constrained entries - but unless you learn/understand the logic
behind the rows being deleted you are risking to end in an inconsistent
state. I would also limit this on the 'deleted' users only as a purged user
does not have to be deleted I think.

Martin

On Fri, Sep 9, 2016 at 7:41 AM Fernandez Edgar <edgar.fernan...@umontreal.ca>
wrote:

> Hello Martin,
>
>
>
> Thanks for the answer.
>
> I was hoping to find a way to remove the user or at the very least hide
> them from the ADMIN user page.
>
>
>
> After a small research in the database, I found a column called "ACTIVE"
> in the galaxy_user table.
>
> Can that column help me at all?
>
>
>
> OR
>
>
>
> I could write a script that search all the deleted/purged users, picks up
> their ID in the galaxy_user table and destroys all the lines in all the
> tables that has that FOREIGN KEY???
>
>
>
> Let me know what you think…
>
>
>
> *Edgar Fernandez*
>
> System Administrator (Linux)
>
> Direction Générale des Technologies de l'Information et de la Communication
>
> *Université de Montréal*
>
>
>
> PAVILLON ROGER-GAUDRY, bureau X-210
>
> (  Bur. : *1-514-343-6111 poste 16568*
>
>
>
>
>
> *From:* Martin Čech [mailto:mar...@bx.psu.edu]
> *Sent:* September-08-16 12:30 PM
> *To:* Fernandez Edgar <edgar.fernan...@umontreal.ca>;
> galaxy-...@bx.psu.edu
> *Subject:* Re: [galaxy-dev] delete user and all trace of user
>
>
>
> Hi Edgar,
>
>
>
> there is no built-in way in Galaxy to remove a user completely. 'Deleting'
> just flips the flag in the DB and 'purging' is related to their
> data/histories. You need to access the DB directly if you want to
> completely remove a user. Beware that there might be constraints/relations
> attached to the user row.
>
>
>
> Thanks for using Galaxy,
>
>
>
> Martin
>
>
>
> On Thu, Sep 8, 2016 at 12:22 PM Fernandez Edgar <
> edgar.fernan...@umontreal.ca> wrote:
>
> Hello gents!
>
>
>
> I’ve successfully got my version 16.04 up and running and everything is
> still there (user, groups roles, data and tools).
>
> Unfortunately , I’m still having a problem with deleting a user. I’ve
> purge him and then I deleted him.
>
> but, he still shows up in my list of users as "purged".
>
>
>
> Is there a way to completely remove him from galaxy?
>
> Do I need to run a script in a cron job to clean my galaxy periodically?
>
>
>
> Thanks in advance!
>
>
>
> *Edgar Fernandez*
>
> System Administrator (Linux)
>
> Direction Générale des Technologies de l'Information et de la Communication
>
> *Université de Montréal*
>
>
>
> PAVILLON ROGER-GAUDRY, bureau X-210
>
> (  Bur. : *1-514-343-6111 poste 16568*
>
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
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>
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>
>
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Re: [galaxy-dev] delete user and all trace of user

[Martin Čech]

Hi Edgar,

there is no built-in way in Galaxy to remove a user completely. 'Deleting'
just flips the flag in the DB and 'purging' is related to their
data/histories. You need to access the DB directly if you want to
completely remove a user. Beware that there might be constraints/relations
attached to the user row.

Thanks for using Galaxy,

Martin

On Thu, Sep 8, 2016 at 12:22 PM Fernandez Edgar <
edgar.fernan...@umontreal.ca> wrote:

> Hello gents!
>
>
>
> I’ve successfully got my version 16.04 up and running and everything is
> still there (user, groups roles, data and tools).
>
> Unfortunately , I’m still having a problem with deleting a user. I’ve
> purge him and then I deleted him.
>
> but, he still shows up in my list of users as "purged".
>
>
>
> Is there a way to completely remove him from galaxy?
>
> Do I need to run a script in a cron job to clean my galaxy periodically?
>
>
>
> Thanks in advance!
>
>
>
> *Edgar Fernandez*
>
> System Administrator (Linux)
>
> Direction Générale des Technologies de l'Information et de la Communication
>
> *Université de Montréal*
>
>
>
> PAVILLON ROGER-GAUDRY, bureau X-210
>
> (  Bur. : *1-514-343-6111 poste 16568*
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
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Re: [galaxy-dev] Testtoolshed status

[Martin Čech]

This has been fixed now, thanks Steve for the report and sorry for the
trouble.

Martin

On Fri, Sep 2, 2016 at 10:20 AM Dave Bouvier  wrote:

> Steve,
>
> Thank you for reporting this issue, we've determined a potential cause
> and are working to correct it.
>
> -
> Dave Bouvier
> http://galaxyproject.org
> http://usegalaxy.org
>
> On 09/02/2016 03:29 AM, Steve Cassidy wrote:
> > I’m getting a 500 response from the testtoolshed when I try to upload a
> > tool via planemo:
> >
> > ➜  alveo-galaxy-tools git:(master) ✗ planemo shed_update --shed_target
> > testtoolshed apitools
> > cd '/Users/steve/projects/alveo-galaxy-tools/apitools' && git rev-parse
> HEAD
> > cd '/Users/steve/projects/alveo-galaxy-tools/apitools' && git diff
> --quiet
> > Could not update alveoimport
> > Unexpected HTTP status code: 500: 
> >   Internal Server Error
> >   
> > Internal Server Error
> > The server has either erred or is incapable of performing
> > the requested operation.
> >
> > 
> > 
> > 
> > WSGI Server
> >   
> > 
> >
> > Repository metadata updated successfully for repository alveoimport.
> > Failed to update a repository.
> >
> > In addition, I just got a “Tool Shed could not be reached” message via
> > the web interface, so i’m wondering if something is up.
> >
> > Thanks,
> >
> > Steve
> > —
> > Department of Computing, Macquarie University
> > http://web.science.mq.edu.au/~cassidy
> >
> >
> >
> > ___
> > Please keep all replies on the list by using "reply all"
> > in your mail client.  To manage your subscriptions to this
> > and other Galaxy lists, please use the interface at:
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> >
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Re: [galaxy-dev] error on startup

[Martin Čech]

Cris: maybe check what ports are configured for your Galaxy and/or Tool
Shed to make sure they are not in conflict. I don't know enough about AWS
to help you more, maybe someone else will jump in.

M.

On Thu, Sep 1, 2016 at 1:48 PM Cristel Thomas <cristel.tho...@gmail.com>
wrote:

> No previous instance of reports running, and I'm not sure what to check as
> far as ports.
> our AWS guy said it might be an issue with AWS but I don't know enough
> about all this to confirm (or to know how to confirm).
>
> thanks for your help.
>
> On Thu, Sep 1, 2016 at 1:39 PM, Martin Čech <mar...@bx.psu.edu> wrote:
>
>> Cris: please check whether some previous instance of Reports isn't still
>> running and/or check your ports using e.g. `netstat`
>> M.
>>
>> On Thu, Sep 1, 2016 at 1:19 PM Cristel Thomas <cristel.tho...@gmail.com>
>> wrote:
>>
>>> Hi Martin,
>>> the config is:
>>> port = 8081
>>> host = 0.0.0.0
>>>
>>> this is the first time we have that issue though, and the instance has
>>> been running just fine until now. I don't think we've changed anything.
>>>
>>> On Thu, Sep 1, 2016 at 12:40 PM, Martin Čech <mar...@bx.psu.edu> wrote:
>>>
>>>> Hi Cris,
>>>>
>>>> what `host` and `port` is in your reports.ini config file? This
>>>> stacktrace would point at something already running at the same port.
>>>>
>>>> Martin
>>>>
>>>> On Thu, Sep 1, 2016 at 12:36 PM Cristel Thomas <
>>>> cristel.tho...@gmail.com> wrote:
>>>>
>>>>> Galaxy admins,
>>>>> One of you has probably seen the below error before, can someone
>>>>> explain? for background, we're running our instance on a AWS server (if
>>>>> that makes a difference)
>>>>>
>>>>>
>>>>> galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,545 Enabling
>>>>> 'sample_tracking' controller, class: SampleTracking
>>>>> galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,545 Enabling
>>>>> 'system' controller, class: System
>>>>> galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,546 Enabling
>>>>> 'workflows' controller, class: Workflows
>>>>> galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,546 Enabling
>>>>> 'users' controller, class: Users
>>>>> galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,547 Enabling
>>>>> 'jobs' controller, class: Jobs
>>>>> galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,547 Enabling
>>>>> 'root' controller, class: Report
>>>>> galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,547 Enabling
>>>>> 'home' controller, class: HomePage
>>>>> galaxy.webapps.reports.buildapp DEBUG 2016-05-19 12:43:40,548 Enabling
>>>>> 'httpexceptions' middleware
>>>>> galaxy.webapps.reports.buildapp DEBUG 2016-05-19 12:43:40,549 Enabling
>>>>> 'recursive' middleware
>>>>> galaxy.webapps.reports.buildapp DEBUG 2016-05-19 12:43:40,551 Enabling
>>>>> 'error' middleware
>>>>> galaxy.webapps.reports.buildapp DEBUG 2016-05-19 12:43:40,551 Enabling
>>>>> 'trans logger' middleware
>>>>> galaxy.webapps.reports.buildapp DEBUG 2016-05-19 12:43:40,552 Enabling
>>>>> 'x-forwarded-host' middleware
>>>>> Starting server in PID 14676.
>>>>> Traceback (most recent call last):
>>>>>   File "./scripts/paster.py", line 26, in 
>>>>> serve.run()
>>>>>   File
>>>>> "/home/galaxy/immport-galaxy/lib/galaxy/util/pastescript/serve.py", line
>>>>> 1061, in run
>>>>> invoke(command, command_name, options, args[1:])
>>>>>   File
>>>>> "/home/galaxy/immport-galaxy/lib/galaxy/util/pastescript/serve.py", line
>>>>> 1067, in invoke
>>>>> exit_code = runner.run(args)
>>>>>   File
>>>>> "/home/galaxy/immport-galaxy/lib/galaxy/util/pastescript/serve.py", line
>>>>> 223, in run
>>>>> result = self.command()
>>>>>   File
>>>>> "/home/galaxy/immport-galaxy/lib/galaxy/util/pastescript/serve.py", line
>>>>> 673, in command
>>>>> serve()
>>>>>   File
>>>>> "/home/galaxy/immport-galaxy/lib/galaxy/util/pastescript/serve.py", line
>>>>> 6

Re: [galaxy-dev] error on startup

[Martin Čech]

Cris: please check whether some previous instance of Reports isn't still
running and/or check your ports using e.g. `netstat`
M.

On Thu, Sep 1, 2016 at 1:19 PM Cristel Thomas <cristel.tho...@gmail.com>
wrote:

> Hi Martin,
> the config is:
> port = 8081
> host = 0.0.0.0
>
> this is the first time we have that issue though, and the instance has
> been running just fine until now. I don't think we've changed anything.
>
> On Thu, Sep 1, 2016 at 12:40 PM, Martin Čech <mar...@bx.psu.edu> wrote:
>
>> Hi Cris,
>>
>> what `host` and `port` is in your reports.ini config file? This
>> stacktrace would point at something already running at the same port.
>>
>> Martin
>>
>> On Thu, Sep 1, 2016 at 12:36 PM Cristel Thomas <cristel.tho...@gmail.com>
>> wrote:
>>
>>> Galaxy admins,
>>> One of you has probably seen the below error before, can someone
>>> explain? for background, we're running our instance on a AWS server (if
>>> that makes a difference)
>>>
>>>
>>> galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,545 Enabling
>>> 'sample_tracking' controller, class: SampleTracking
>>> galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,545 Enabling
>>> 'system' controller, class: System
>>> galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,546 Enabling
>>> 'workflows' controller, class: Workflows
>>> galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,546 Enabling 'users'
>>> controller, class: Users
>>> galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,547 Enabling 'jobs'
>>> controller, class: Jobs
>>> galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,547 Enabling 'root'
>>> controller, class: Report
>>> galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,547 Enabling 'home'
>>> controller, class: HomePage
>>> galaxy.webapps.reports.buildapp DEBUG 2016-05-19 12:43:40,548 Enabling
>>> 'httpexceptions' middleware
>>> galaxy.webapps.reports.buildapp DEBUG 2016-05-19 12:43:40,549 Enabling
>>> 'recursive' middleware
>>> galaxy.webapps.reports.buildapp DEBUG 2016-05-19 12:43:40,551 Enabling
>>> 'error' middleware
>>> galaxy.webapps.reports.buildapp DEBUG 2016-05-19 12:43:40,551 Enabling
>>> 'trans logger' middleware
>>> galaxy.webapps.reports.buildapp DEBUG 2016-05-19 12:43:40,552 Enabling
>>> 'x-forwarded-host' middleware
>>> Starting server in PID 14676.
>>> Traceback (most recent call last):
>>>   File "./scripts/paster.py", line 26, in 
>>> serve.run()
>>>   File
>>> "/home/galaxy/immport-galaxy/lib/galaxy/util/pastescript/serve.py", line
>>> 1061, in run
>>> invoke(command, command_name, options, args[1:])
>>>   File
>>> "/home/galaxy/immport-galaxy/lib/galaxy/util/pastescript/serve.py", line
>>> 1067, in invoke
>>> exit_code = runner.run(args)
>>>   File
>>> "/home/galaxy/immport-galaxy/lib/galaxy/util/pastescript/serve.py", line
>>> 223, in run
>>> result = self.command()
>>>   File
>>> "/home/galaxy/immport-galaxy/lib/galaxy/util/pastescript/serve.py", line
>>> 673, in command
>>> serve()
>>>   File
>>> "/home/galaxy/immport-galaxy/lib/galaxy/util/pastescript/serve.py", line
>>> 650, in serve
>>> server(app)
>>>   File
>>> "/home/galaxy/immport-galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line
>>> 234, in server_wrapper
>>> **context.local_conf)
>>>   File
>>> "/home/galaxy/immport-galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line
>>> 94, in fix_call
>>> val = callable(*args, **kw)
>>>   File
>>> "/home/galaxy/immport-galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py",
>>> line 1361, in server_runner
>>> serve(wsgi_app, **kwargs)
>>>   File
>>> "/home/galaxy/immport-galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py",
>>> line 1310, in serve
>>> request_queue_size=request_queue_size)
>>>   File
>>> "/home/galaxy/immport-galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py",
>>> line 1153, in __init__
>>> request_queue_size=request_queue_size)
>>>   File
>>> "/home/galaxy/immport-galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py",
>>> line 1132, in __init__
>>> request_queue_siz

Re: [galaxy-dev] error on startup

[Martin Čech]

Hi Cris,

what `host` and `port` is in your reports.ini config file? This stacktrace
would point at something already running at the same port.

Martin

On Thu, Sep 1, 2016 at 12:36 PM Cristel Thomas 
wrote:

> Galaxy admins,
> One of you has probably seen the below error before, can someone explain?
> for background, we're running our instance on a AWS server (if that makes a
> difference)
>
>
> galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,545 Enabling
> 'sample_tracking' controller, class: SampleTracking
> galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,545 Enabling 'system'
> controller, class: System
> galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,546 Enabling
> 'workflows' controller, class: Workflows
> galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,546 Enabling 'users'
> controller, class: Users
> galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,547 Enabling 'jobs'
> controller, class: Jobs
> galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,547 Enabling 'root'
> controller, class: Report
> galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,547 Enabling 'home'
> controller, class: HomePage
> galaxy.webapps.reports.buildapp DEBUG 2016-05-19 12:43:40,548 Enabling
> 'httpexceptions' middleware
> galaxy.webapps.reports.buildapp DEBUG 2016-05-19 12:43:40,549 Enabling
> 'recursive' middleware
> galaxy.webapps.reports.buildapp DEBUG 2016-05-19 12:43:40,551 Enabling
> 'error' middleware
> galaxy.webapps.reports.buildapp DEBUG 2016-05-19 12:43:40,551 Enabling
> 'trans logger' middleware
> galaxy.webapps.reports.buildapp DEBUG 2016-05-19 12:43:40,552 Enabling
> 'x-forwarded-host' middleware
> Starting server in PID 14676.
> Traceback (most recent call last):
>   File "./scripts/paster.py", line 26, in 
> serve.run()
>   File "/home/galaxy/immport-galaxy/lib/galaxy/util/pastescript/serve.py",
> line 1061, in run
> invoke(command, command_name, options, args[1:])
>   File "/home/galaxy/immport-galaxy/lib/galaxy/util/pastescript/serve.py",
> line 1067, in invoke
> exit_code = runner.run(args)
>   File "/home/galaxy/immport-galaxy/lib/galaxy/util/pastescript/serve.py",
> line 223, in run
> result = self.command()
>   File "/home/galaxy/immport-galaxy/lib/galaxy/util/pastescript/serve.py",
> line 673, in command
> serve()
>   File "/home/galaxy/immport-galaxy/lib/galaxy/util/pastescript/serve.py",
> line 650, in serve
> server(app)
>   File
> "/home/galaxy/immport-galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line
> 234, in server_wrapper
> **context.local_conf)
>   File
> "/home/galaxy/immport-galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line
> 94, in fix_call
> val = callable(*args, **kw)
>   File
> "/home/galaxy/immport-galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py",
> line 1361, in server_runner
> serve(wsgi_app, **kwargs)
>   File
> "/home/galaxy/immport-galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py",
> line 1310, in serve
> request_queue_size=request_queue_size)
>   File
> "/home/galaxy/immport-galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py",
> line 1153, in __init__
> request_queue_size=request_queue_size)
>   File
> "/home/galaxy/immport-galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py",
> line 1132, in __init__
> request_queue_size=request_queue_size)
>   File
> "/home/galaxy/immport-galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py",
> line 345, in __init__
> HTTPServer.__init__(self, server_address, RequestHandlerClass)
>   File "/usr/lib/python2.7/SocketServer.py", line 419, in __init__
> self.server_bind()
>   File "/usr/lib/python2.7/BaseHTTPServer.py", line 108, in server_bind
> SocketServer.TCPServer.server_bind(self)
>   File "/usr/lib/python2.7/SocketServer.py", line 430, in server_bind
> self.socket.bind(self.server_address)
>   File "/usr/lib/python2.7/socket.py", line 224, in meth
> return getattr(self._sock,name)(*args)
> socket.error: [Errno 99] Cannot assign requested address
> Removing PID file reports_webapp.pid
>
>
> Thanks,
> Cris
> ___
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Re: [galaxy-dev] problem with local toolshed

[Martin Čech]

Hello Vincent,

This looks like an encoding problem we we can fix. Could you please try the
following patch?

https://gist.github.com/martenson/22f6efc7cd577ea6af85a11694091d5f

Thanks,

Martin

On Wed, Aug 24, 2016 at 5:17 AM Vincent Cahais  wrote:

> Hello,
>
> I cannot use my toolshed anymore because of a bug.
>
> The service is running, but the web page display this error :
>
> Module galaxy.web.framework.middleware.error:*151* in __call__
> >>  app_iter = self.application(environ,
> sr_checker)
> Module paste.recursive:*85* in __call__
> >>  return self.application(environ,
> start_response)
> Module galaxy.webapps.tool_shed.framework.middleware.hg:*218* in __call__
> >>  return self.app( environ,
> start_response )
> Module paste.httpexceptions:*640* in __call__
> >>  return self.application(environ,
> start_response)
> Module galaxy.web.framework.base:*131* in __call__
> >>  return self.handle_request( environ,
> start_response )
> Module galaxy.web.framework.base:*190* in handle_request
> >>  body = method( trans, **kwargs )
> Module galaxy.webapps.tool_shed.controllers.repository:*1963* in index
> >>  status=status )
> Module galaxy.web.framework.webapp:*858* in fill_template
> >>  return self.fill_template_mako(
> filename, **kwargs )
> Module galaxy.web.framework.webapp:*872* in fill_template_mako
> >>  return template.render( **data )
> Module mako.template:*445* in render
> >>  return runtime._render(self,
> self.callable_, args, data)
> Module mako.runtime:*829* in _render
> >>  **_kwargs_for_callable(callable_, data))
> Module mako.runtime:*864* in _render_context
> >>  _exec_template(inherit, lclcontext,
> args=args, kwargs=kwargs)
> Module mako.runtime:*890* in _exec_template
> >>  callable_(context, *args, **kwargs)
> Module _base_base_panels_mako:*123* in render_body
> >>  __M_writer(unicode(self.left_panel()))
> Module _webapps_tool_shed_index_mako:*166* in render_left_panel
> >>  
> >> __M_writer(filters.html_escape(unicode(trans.app.shed_counter.generation_time
> )))
> *UnicodeDecodeError: 'ascii' codec can't decode byte 0xc3 in position 2:
> ordinal not in range(128)*
>
> Thanks,
>
> Vincent
> ___
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Re: [galaxy-dev] Adding packages to depot.galaxyproject.org

[Martin Čech]

Peter:

depot is something we plan on maintaining and providing as a service as
long as Galaxy. The cargo-port we will also expand in future (eg to provide
dynamic fallback at installation time. It is the right place to put your
mira backups (and any other packages you care about in recipes).

Cheers,
M.

On Mon, Aug 8, 2016 at 9:54 AM Peter Cock  wrote:

> On Mon, Aug 8, 2016 at 2:41 PM, Eric Rasche  wrote:
> > Hi Peter,
> >
> > The cargo port is the ideal place for this, however it does not support
> > manual uploads of files.
> >
>
> Thanks Eric,
>
> You mean https://github.com/galaxyproject/cargo-port
>
> Is that something which might be addressed in future? The use case
> is when a previously public file stops working (either temporarily or
> permanently), so you can't use the official URL to make the cached
> copy?
>
> Would it be OK to use a short lived URL like a personal dropbox URL,
> and then once cached, update urls.tsv with the original official
> (but broken) URL?
>
> Peter
> ___
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[galaxy-dev] Fwd: New galaxy parameter type

[Martin Čech]

forwarding to the list


-- Forwarded message -
From: Katherine Beaulieu <katherine.beaulieu...@gmail.com>
Date: Fri, Jul 15, 2016 at 3:45 PM
Subject: Re: [galaxy-dev] New galaxy parameter type
To: Martin Čech <mar...@bx.psu.edu>


Thanks Peter, I will look into that. The reason I am asking is because of
what Mohammed asked earlier as well. I developed two tools which allow you
to import and export information from a program called irods but you need
to be able to authenticate with irods to be able to do so. Thanks again for
always being helpful!

On Fri, Jul 15, 2016 at 3:10 PM, Martin Čech <mar...@bx.psu.edu> wrote:

> Katherine please disregard my answer, I probably misread your question. :)
> M.
>
> On Fri, Jul 15, 2016 at 3:05 PM Peter Cock <p.j.a.c...@googlemail.com>
> wrote:
>
>> Did you mean parameter as in input field shown
>> to the user? Like a combobox or text field?
>>
>> Since this happened to come up earlier today, here's
>> a rejected pull request which added a password
>> parameter - that ought to give you a rough idea:
>>
>> https://github.com/galaxyproject/galaxy/pull/393
>>
>> Peter
>>
>> On Fri, Jul 15, 2016 at 7:46 PM, Katherine Beaulieu
>> <katherine.beaulieu...@gmail.com> wrote:
>> > Hi everyone,
>> > I am looking to implement a new parameter type for galaxy tool
>> development.
>> > Does anyone know what would be involved in doing something like this or
>> > perhaps what files would need to be edited?
>> >
>> >
>> > ___
>> > Please keep all replies on the list by using "reply all"
>> > in your mail client.  To manage your subscriptions to this
>> > and other Galaxy lists, please use the interface at:
>> >   https://lists.galaxyproject.org/
>> >
>> > To search Galaxy mailing lists use the unified search at:
>> >   http://galaxyproject.org/search/mailinglists/
>> ___
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>
>
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Re: [galaxy-dev] New galaxy parameter type

[Martin Čech]

Katherine please disregard my answer, I probably misread your question. :)
M.

On Fri, Jul 15, 2016 at 3:05 PM Peter Cock 
wrote:

> Did you mean parameter as in input field shown
> to the user? Like a combobox or text field?
>
> Since this happened to come up earlier today, here's
> a rejected pull request which added a password
> parameter - that ought to give you a rough idea:
>
> https://github.com/galaxyproject/galaxy/pull/393
>
> Peter
>
> On Fri, Jul 15, 2016 at 7:46 PM, Katherine Beaulieu
>  wrote:
> > Hi everyone,
> > I am looking to implement a new parameter type for galaxy tool
> development.
> > Does anyone know what would be involved in doing something like this or
> > perhaps what files would need to be edited?
> >
> >
> > ___
> > Please keep all replies on the list by using "reply all"
> > in your mail client.  To manage your subscriptions to this
> > and other Galaxy lists, please use the interface at:
> >   https://lists.galaxyproject.org/
> >
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> >   http://galaxyproject.org/search/mailinglists/
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Re: [galaxy-dev] New galaxy parameter type

[Martin Čech]

Hi Katherine,

an example of a datatype addition can be seen in this PR:
https://github.com/galaxyproject/galaxy/pull/2452

You need to define a class and teach it to sniff files of your defined type
(with a doctest) and how to generate peek for the datatype's datasets in
history.

Let us know if you have more questions and thanks for using Galaxy.

Martin

On Fri, Jul 15, 2016 at 2:46 PM Katherine Beaulieu <
katherine.beaulieu...@gmail.com> wrote:

> Hi everyone,
> I am looking to implement a new parameter type for galaxy tool
> development. Does anyone know what would be involved in doing something
> like this or perhaps what files would need to be edited?
>
> ___
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Re: [galaxy-dev] Writing test for dataset collection

[Martin Čech]

Hi Cristel,

for a start I please have a look at
http://planemo.readthedocs.io/en/latest/writing_advanced.html#test-driven-development
and
let us know if you have further questions. The documentation regarding this
is a still bit scarce, I am sorry.

Martin

On Mon, Jul 11, 2016 at 3:24 PM Cristel Thomas 
wrote:

> Dear galaxy developers,
>
> Can someone point me to a resource explaining how to write the test
> section of the xml for tools dealing with dataset collections? as input as
> well as output.
>
> Thanks much,
> Cris
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Re: [galaxy-dev] showing progress on running tasks

[Martin Čech]

Hi Ryan,

multiple tool stages do not necessarily equally split runtime so you
wouldn't have 'time progress bar' but 'unscaled progress bar'. The
usefulness of such I would put somewhere in between a loading animation and
stats estimate. This would also require every tool to be enhanced as well
as the framework as opposed to the proposed stats solution that could work
with every used tool building on past data without putting more
requirements on the tool developer. Whole another book of problems would be
how (and if) is this handled in job schedulers such as Slurm - where most
of the big jobs live.

To summarize: having tool reporting progress stages is possible to
implement but has many drawbacks.

Thanks,
Martin

On Fri, Jul 8, 2016 at 12:41 PM Ryan G <ngsbioinformat...@gmail.com> wrote:

> Hi Martin - I was actually thinking to let the tool itself tell Galaxy
> about the progress instead of Galaxy estimating that.
>
> If instance, if the tool know it has 5 stages, it can report back to
> Galaxy 20,40,60,80,and 100 % complete.
>
> I know this is complex but could be a nice feature.
>
> Please excuse any typos -- Sent from my iPhone
>
> On Jul 8, 2016, at 10:47 AM, Martin Čech <mar...@bx.psu.edu> wrote:
>
> Hi Ryan,
>
> This is a fairly complex problem because the length of the run depends
> most often on input size, job algorithms, and computational capacity all of
> which are quite difficult to estimate.
> We have discussed it before and one of the ways to approach this is to
> gather statistics from as many jobs as possible and then provide the user
> with some estimates based on this data on similar jobs to theirs.
>
> For the way to gather the data please see
> https://github.com/galaxyproject/galaxy/pull/2455 from Eric Rasche. With
> the data (or at least data format) we can start working on an algorithm
> that would make a guess on a new job length.
>
> However, there are many other approaches to this problem.
>
> Thanks,
>
> Martin
>
> On Fri, Jul 8, 2016 at 10:34 AM Ryan G <ngsbioinformat...@gmail.com>
> wrote:
>
>> Hi all - I know this isn't currently a feature, but wanted to find out
>> about what it would take to implement
>>
>> We developed some custom tools that are long runningmultiple hours.
>> The tools run through various steps of an analysis.
>>
>> Is there a way to display progress of a task in the history?   Possibly
>> as a small progress bar?   Or provide some feedback via an html page in the
>> main frame?
>>
>> Ryan
>>
>> ___
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>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>   https://lists.galaxyproject.org/
>>
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>>   http://galaxyproject.org/search/mailinglists/
>
>
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Re: [galaxy-dev] showing progress on running tasks

[Martin Čech]

Hi Ryan,

This is a fairly complex problem because the length of the run depends most
often on input size, job algorithms, and computational capacity all of
which are quite difficult to estimate.
We have discussed it before and one of the ways to approach this is to
gather statistics from as many jobs as possible and then provide the user
with some estimates based on this data on similar jobs to theirs.

For the way to gather the data please see
https://github.com/galaxyproject/galaxy/pull/2455 from Eric Rasche. With
the data (or at least data format) we can start working on an algorithm
that would make a guess on a new job length.

However, there are many other approaches to this problem.

Thanks,

Martin

On Fri, Jul 8, 2016 at 10:34 AM Ryan G  wrote:

> Hi all - I know this isn't currently a feature, but wanted to find out
> about what it would take to implement
>
> We developed some custom tools that are long runningmultiple hours.
> The tools run through various steps of an analysis.
>
> Is there a way to display progress of a task in the history?   Possibly as
> a small progress bar?   Or provide some feedback via an html page in the
> main frame?
>
> Ryan
>
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
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Re: [galaxy-dev] How to replace 'BioMart Central server' in the "Get Data" tools ?

[Martin Čech]

The correct link is this: http://galaxy-dev.fmi.ch/tool_
runner/biomart?type=text=Homo%20sapiens%20genes%20%
28GRCh38.p5%29=http://www.ensembl.org/biomart/martview/
7ee294b9ae51a27f1e7ed96e712c5792?

On Wed, Jun 8, 2016 at 11:33 AM Martin Čech <mar...@bx.psu.edu> wrote:

> This looks like an Ensembl problem, because they are prefixing the
> redirect url with "http://www.ensembl.org/
> <http://www.ensembl.org/galaxy-dev.fmi.ch/tool_runner/biomart?type=text=Homo%20sapiens%20genes%20%28GRCh38.p5%29=http://www.ensembl.org/biomart/martview/7ee294b9ae51a27f1e7ed96e712c5792?do_export=1=1>".
> If you just go to http://
> galaxy-dev.fmi.ch/tool_runner/biomart?type=text=Homo%20sapiens%20genes%20%28GRCh38.p5%29=http://www.ensembl.org/biomart/martview/7ee294b9ae51a27f1e7ed96e712c5792?do_export=1=1
> <http://www.ensembl.org/galaxy-dev.fmi.ch/tool_runner/biomart?type=text=Homo%20sapiens%20genes%20%28GRCh38.p5%29=http://www.ensembl.org/biomart/martview/7ee294b9ae51a27f1e7ed96e712c5792?do_export=1=1>
>  it
> will most probably work.
>
> They might be whitelisting usegalaxy.org to not add prefix, or some other
> bug, I will try contacting them, thank you for the report.
>
> Martin
>
> On Wed, Jun 8, 2016 at 11:19 AM Hans-Rudolf Hotz <h...@fmi.ch> wrote:
>
>> Hi Martin
>>
>> we are still on "15.10" (minor version "2")
>>
>> However, I see the same issues on other public galaxy server which are
>> already on 16.04
>>
>>
>>
>> http://www.ensembl.org/galaxy-dev.fmi.ch/tool_runner/biomart?type=text=Homo%20sapiens%20genes%20%28GRCh38.p5%29=http://www.ensembl.org/biomart/martview/7ee294b9ae51a27f1e7ed96e712c5792?do_export=1=1
>>
>>
>>
>> Hans-Rudolf
>>
>>
>> On 06/08/2016 04:36 PM, Martin Čech wrote:
>> > Hello Hans-Rudolf,
>> >
>> > What version of Galaxy are you using? Can you please share a specific
>> > URL you were sent to that returns a 404?
>> >
>> > thanks
>> >
>> > M.
>> >
>> >
>> > On Wed, Jun 8, 2016 at 4:53 AM Hans-Rudolf Hotz <h...@fmi.ch
>> > <mailto:h...@fmi.ch>> wrote:
>> >
>> > Hi all
>> >
>> > Please allow me to come back to this old problem:
>> >
>> > On usegalaxy.org <http://usegalaxy.org>, the tool is now pointing
>> to
>> > http://www.ensembl.org/biomart/martview (see also:
>> >
>> https://github.com/galaxyproject/galaxy/commit/c49e7803fa1814abd04afb26b54965fb7af612ac
>> > ) and it seems to work, i.e stuff is sent to usegalaxy.org
>> > <http://usegalaxy.org>.
>> >
>> > If I try to do the same on our local galaxy server, I still run
>> into the
>> > same problem as last November: the requests are not send to Galaxy,
>> but
>> > end up on the ensembl web page, where they cause a "Error 404 -
>> Page not
>> > found".
>> >
>> > Is there anything else, I need to change?
>> >
>> >
>> > Thank you very much for your help
>> > Hans-Rudolf
>> >
>> >
>> >
>> > On 11/17/2015 08:40 AM, Hans-Rudolf Hotz wrote:
>> >  > Hi
>> >  >
>> >  > As you probably know, the central BioMart server is currently
>> >  > unavailable (see: http://www.biomart.org/notice.html). Hence,
>> the
>> > "Get
>> >  > Data -> BioMart Central server" tool in our local Galaxy
>> installation
>> >  > does not work anymore - well, this is also the case on
>> > usegalaxy.org <http://usegalaxy.org>.
>> >  >
>> >  >
>> >  > We can easily switch the tool to point to a different Mart
>> > server, i.e.:
>> >  >
>> >  > Change: http://www.biomart.org/biomart/martview;
>> 
>> >  >
>> >  > to: > > action="http://www.ebi.ac.uk/uniprot/biomart/martview; 
>> >  >
>> >  >
>> >  > However, we would like to switch to the ensembl Mart server:
>> >  >
>> >  > http://www.ensembl.org/biomart/martview
>> >  >
>> >  >
>> >  > It looks like the ensembl Mart server is nowadays embedded in the
>> >  > ensembl web site, and the requests are not send to Galaxy, but
>> > end up on
>> >  > the ensembl web page, where they cause a "Error 404 - Page not
&

Re: [galaxy-dev] How to replace 'BioMart Central server' in the "Get Data" tools ?

[Martin Čech]

This looks like an Ensembl problem, because they are prefixing the redirect
url with "http://www.ensembl.org/
<http://www.ensembl.org/galaxy-dev.fmi.ch/tool_runner/biomart?type=text=Homo%20sapiens%20genes%20%28GRCh38.p5%29=http://www.ensembl.org/biomart/martview/7ee294b9ae51a27f1e7ed96e712c5792?do_export=1=1>".
If you just go to http://
galaxy-dev.fmi.ch/tool_runner/biomart?type=text=Homo%20sapiens%20genes%20%28GRCh38.p5%29=http://www.ensembl.org/biomart/martview/7ee294b9ae51a27f1e7ed96e712c5792?do_export=1=1
<http://www.ensembl.org/galaxy-dev.fmi.ch/tool_runner/biomart?type=text=Homo%20sapiens%20genes%20%28GRCh38.p5%29=http://www.ensembl.org/biomart/martview/7ee294b9ae51a27f1e7ed96e712c5792?do_export=1=1>
it
will most probably work.

They might be whitelisting usegalaxy.org to not add prefix, or some other
bug, I will try contacting them, thank you for the report.

Martin

On Wed, Jun 8, 2016 at 11:19 AM Hans-Rudolf Hotz <h...@fmi.ch> wrote:

> Hi Martin
>
> we are still on "15.10" (minor version "2")
>
> However, I see the same issues on other public galaxy server which are
> already on 16.04
>
>
>
> http://www.ensembl.org/galaxy-dev.fmi.ch/tool_runner/biomart?type=text=Homo%20sapiens%20genes%20%28GRCh38.p5%29=http://www.ensembl.org/biomart/martview/7ee294b9ae51a27f1e7ed96e712c5792?do_export=1=1
>
>
>
> Hans-Rudolf
>
>
> On 06/08/2016 04:36 PM, Martin Čech wrote:
> > Hello Hans-Rudolf,
> >
> > What version of Galaxy are you using? Can you please share a specific
> > URL you were sent to that returns a 404?
> >
> > thanks
> >
> > M.
> >
> >
> > On Wed, Jun 8, 2016 at 4:53 AM Hans-Rudolf Hotz <h...@fmi.ch
> > <mailto:h...@fmi.ch>> wrote:
> >
> > Hi all
> >
> > Please allow me to come back to this old problem:
> >
> > On usegalaxy.org <http://usegalaxy.org>, the tool is now pointing to
> > http://www.ensembl.org/biomart/martview (see also:
> >
> https://github.com/galaxyproject/galaxy/commit/c49e7803fa1814abd04afb26b54965fb7af612ac
> > ) and it seems to work, i.e stuff is sent to usegalaxy.org
> > <http://usegalaxy.org>.
> >
> > If I try to do the same on our local galaxy server, I still run into
> the
> > same problem as last November: the requests are not send to Galaxy,
> but
> > end up on the ensembl web page, where they cause a "Error 404 - Page
> not
> > found".
> >
> > Is there anything else, I need to change?
> >
> >
> > Thank you very much for your help
> > Hans-Rudolf
> >
> >
> >
> > On 11/17/2015 08:40 AM, Hans-Rudolf Hotz wrote:
> >  > Hi
> >  >
> >  > As you probably know, the central BioMart server is currently
> >  > unavailable (see: http://www.biomart.org/notice.html). Hence, the
> > "Get
> >  > Data -> BioMart Central server" tool in our local Galaxy
> installation
> >  > does not work anymore - well, this is also the case on
> > usegalaxy.org <http://usegalaxy.org>.
> >  >
> >  >
> >  > We can easily switch the tool to point to a different Mart
> > server, i.e.:
> >  >
> >  > Change: http://www.biomart.org/biomart/martview;
> 
> >  >
> >  > to:  > action="http://www.ebi.ac.uk/uniprot/biomart/martview; 
> >  >
> >  >
> >  > However, we would like to switch to the ensembl Mart server:
> >  >
> >  > http://www.ensembl.org/biomart/martview
> >  >
> >  >
> >  > It looks like the ensembl Mart server is nowadays embedded in the
> >  > ensembl web site, and the requests are not send to Galaxy, but
> > end up on
> >  > the ensembl web page, where they cause a "Error 404 - Page not
> > found".
> >  > Unfortunately, I am not that savvy about the inner works of the
> > ensembl
> >  > web site anymore ;)
> >  >
> >  >
> >  > Has anyone else looked into this problem and found already a
> > solution?
> >  >
> >  > Thank you very much for any help
> >  >
> >  >
> >  > Hans-Rudolf
> >  >
> >  >
> > ___
> > Please keep all replies on the list by using "reply all"
> > in your mail client.  To manage your subscriptions to this
> > and other Galaxy lists, please use the interface at:
> > https://lists.galaxyproject.org/
> >
> > To search Galaxy mailing lists use the unified search at:
> > http://galaxyproject.org/search/mailinglists/
> >
>
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Re: [galaxy-dev] How to get the encoded ID from the HistoryDatasetAssociation?

[Martin Čech]

Hello Malcolm,

encoded_id is a database row id that has been ran through this method (
https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/web/security/__init__.py#L46)
using the 'secret' from galaxy.ini config.

You should be able to do something like this in the mako:

${trans.security.encode_id( hda.id )}

thank you for using Galaxy

Martin


On Wed, Jun 8, 2016 at 11:16 AM Malcolm Tobias  wrote:

>
> I'm really close to having a way to visualize radiological images in
> Galaxy,
> but need help in getting past the final hurdle.
>
> In the mako file, I can see how to pass parameters to the javascript that
> does
> the visualization.  It's expecting a URL to the dataset, like:
>
> params["images"] = ["/datasets/78176dfc865c8302/display/"];
>
> From what I can gather 78176dfc865c8302 is the encoded ID for the dataset.
> From variables like hda.name and hda.id I can see various properties of
> the
> dataset, but not the encoded ID.
>
> Any suggestions on how to do this?
>
> Thanks in advance.
>
> Malcolm
>
> --
> Malcolm Tobias
> 314.362.1594
>
>
> ___
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> in your mail client.  To manage your subscriptions to this
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>
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Re: [galaxy-dev] How to replace 'BioMart Central server' in the "Get Data" tools ?

[Martin Čech]

Hello Hans-Rudolf,

What version of Galaxy are you using? Can you please share a specific URL
you were sent to that returns a 404?

thanks

M.


On Wed, Jun 8, 2016 at 4:53 AM Hans-Rudolf Hotz  wrote:

> Hi all
>
> Please allow me to come back to this old problem:
>
> On usegalaxy.org, the tool is now pointing to
> http://www.ensembl.org/biomart/martview (see also:
>
> https://github.com/galaxyproject/galaxy/commit/c49e7803fa1814abd04afb26b54965fb7af612ac
> ) and it seems to work, i.e stuff is sent to usegalaxy.org.
>
> If I try to do the same on our local galaxy server, I still run into the
> same problem as last November: the requests are not send to Galaxy, but
> end up on the ensembl web page, where they cause a "Error 404 - Page not
> found".
>
> Is there anything else, I need to change?
>
>
> Thank you very much for your help
> Hans-Rudolf
>
>
>
> On 11/17/2015 08:40 AM, Hans-Rudolf Hotz wrote:
> > Hi
> >
> > As you probably know, the central BioMart server is currently
> > unavailable (see: http://www.biomart.org/notice.html). Hence, the "Get
> > Data -> BioMart Central server" tool in our local Galaxy installation
> > does not work anymore - well, this is also the case on usegalaxy.org.
> >
> >
> > We can easily switch the tool to point to a different Mart server, i.e.:
> >
> > Change: http://www.biomart.org/biomart/martview; 
> >
> > to: http://www.ebi.ac.uk/uniprot/biomart/martview; 
> >
> >
> > However, we would like to switch to the ensembl Mart server:
> >
> > http://www.ensembl.org/biomart/martview
> >
> >
> > It looks like the ensembl Mart server is nowadays embedded in the
> > ensembl web site, and the requests are not send to Galaxy, but end up on
> > the ensembl web page, where they cause a "Error 404 - Page not found".
> > Unfortunately, I am not that savvy about the inner works of the ensembl
> > web site anymore ;)
> >
> >
> > Has anyone else looked into this problem and found already a solution?
> >
> > Thank you very much for any help
> >
> >
> > Hans-Rudolf
> >
> >
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
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Re: [galaxy-dev] Tool shed tools, manual dep installation

[Martin Čech]

David,

You can have multiple versions of tool 'installed' manually (i.e. without
shed).

That said, there is an option of working with the IUC to make the wanted
packages to be up-to-date and secure. i am pretty sure any PRs this
direction will get merged.

M.

On Wed, Apr 13, 2016 at 11:39 AM David Trudgian <
david.trudg...@utsouthwestern.edu> wrote:

> Hi Martin,
>
> Thanks for the input - yes there is going to be maintenance headache
> either way, private tool-shed or not. If we don't go with our own tool-shed
> though, am I right in thinking we lose versioning for tools? I.E.
> installing manually into 'tools' and tool_conf.xml I can't use 
> tags like the tool shed stuff does in shed_tool.conf. The infosec concern
> is mainly with libraries which are provided by tool-shed dependency package
> installs, not the main software package the tool wrapper is calling. With a
> tool shed it's feasible then we could keep older versions of tools/wrappers
> for reproducibility, rebuilding them against updated (but compatible)
> libraries when there's a security issue, perhaps?
>
> Glad to know that my idea of the workflow isn't totally wrong though.
>
> Thanks,
>
> DT
>
> --
> David Trudgian Ph.D.
> Computational Scientist, BioHPC
> Lyda Hill Department of Bioinformatics
> UT Southwestern Medical Center
> Dallas, TX 75390-9039
> Tel: (214) 648-4833
>
> From: Martin Čech [mailto:mar...@bx.psu.edu]
> Sent: Wednesday, April 13, 2016 8:47 AM
> To: David Trudgian <david.trudg...@utsouthwestern.edu>;
> galaxy-dev@lists.galaxyproject.org
> Subject: Re: [galaxy-dev] Tool shed tools, manual dep installation
>
> Hi David,
>
> one thing that you might be missing is that the wrapper for the
> infosec-approved version might not exist yet (you would have to adapt the
> older shed-wrapped version if there were any relevant changes). But this
> largely depends on what software you want to use.
>
> Besides that your flow seems quite accurate. I would probably argue
> against own tool shed, as the maintenance overhead will probably not be
> worth it for you.
>
> Let us know if we can help in any way,
>
> thank you for using Galaxy.
>
> Martin
>
> On Tue, Apr 12, 2016 at 5:42 PM David Trudgian <
> david.trudg...@utsouthwestern.edu> wrote:
> Hi All,
>
> I’m currently caught between the requests of our Galaxy users to install
> things from main tool-shed, and our information security dept’s concerns
> r.e. the automated installation of tool-deps on our systems. Due to
> restrictive web access policies for servers here our galaxy server can’t
> access SourceForge, where many tool-dep downloads are. A request to unblock
> this for a particular tool-dep package led to our infosec justifiably
> raising concerns r.e. a tool-dep package that is quite out of date (details
> sent off list previously). We’re now currently unable to install tool-shed
> tools that users have requested.
>
> The current proposal from our infosec dept is to get all our deps from
> system repos etc. However the way I’m aware of implementing this for
> tool-shed tools, which need to run across our cluster, would be something
> pretty arduous like:
>
> * Clone the tool from the upstream toolshed repo
> * Edit the tool code to remove the package requirements
> * Identify and install all the requirements on the cluster as system pkgs
> / environment modules – with attention to versions so things work as
> expected
> * Edit the tool code so it knows to load the right environment modules /
> set right PATH when it runs
> * Install the tool into our galaxy ‘tools’ dir , not the ‘shed_tools’
> * Manually add the tool to galaxy’s tool_conf.xml.main
> * Schedule downtime to restart galaxy
> * Test things out
>
> …. or we have to host our own tool shed, import tools we want from
> upstream, edit out the package requirements, provide the deps ourselves.
> These have all the headaches of merging things in when upstream shed-tools
> change.
>
> Just wondering if I’m missing anything? I know you can turn off ‘handle
> repository dependencies’ when installing a tool, but the tool still defines
> ‘requirements’ in its XML file and shows ‘Missing repository/tool
> dependencies’ in the Admin.  Has anyone had any experience of dealing with
> this kind of situation?
>
> Many thanks!
>
> --
> David Trudgian Ph.D.
> Computational Scientist, BioHPC
> Lyda Hill Department of Bioinformatics
> UT Southwestern Medical Center
> Dallas, TX 75390-9039
> Tel: (214) 648-4833
>
>
> 
> UT Southwestern
> Medical Center
>
> The future of medicine, today.
> _

Re: [galaxy-dev] Tool shed tools, manual dep installation

[Martin Čech]

Hi David,

one thing that you might be missing is that the wrapper for the
infosec-approved version might not exist yet (you would have to adapt the
older shed-wrapped version if there were any relevant changes). But this
largely depends on what software you want to use.

Besides that your flow seems quite accurate. I would probably argue against
own tool shed, as the maintenance overhead will probably not be worth it
for you.

Let us know if we can help in any way,

thank you for using Galaxy.

Martin

On Tue, Apr 12, 2016 at 5:42 PM David Trudgian <
david.trudg...@utsouthwestern.edu> wrote:

> Hi All,
>
>
>
> I’m currently caught between the requests of our Galaxy users to install
> things from main tool-shed, and our information security dept’s concerns
> r.e. the automated installation of tool-deps on our systems. Due to
> restrictive web access policies for servers here our galaxy server can’t
> access SourceForge, where many tool-dep downloads are. A request to unblock
> this for a particular tool-dep package led to our infosec justifiably
> raising concerns r.e. a tool-dep package that is quite out of date (details
> sent off list previously). We’re now currently unable to install tool-shed
> tools that users have requested.
>
>
>
> The current proposal from our infosec dept is to get all our deps from
> system repos etc. However the way I’m aware of implementing this for
> tool-shed tools, which need to run across our cluster, would be something
> pretty arduous like:
>
>
>
> * Clone the tool from the upstream toolshed repo
>
> * Edit the tool code to remove the package requirements
>
> * Identify and install all the requirements on the cluster as system pkgs
> / environment modules – with attention to versions so things work as
> expected
>
> * Edit the tool code so it knows to load the right environment modules /
> set right PATH when it runs
>
> * Install the tool into our galaxy ‘tools’ dir , not the ‘shed_tools’
>
> * Manually add the tool to galaxy’s tool_conf.xml.main
>
> * Schedule downtime to restart galaxy
>
> * Test things out
>
>
>
> …. or we have to host our own tool shed, import tools we want from
> upstream, edit out the package requirements, provide the deps ourselves.
> These have all the headaches of merging things in when upstream shed-tools
> change.
>
>
>
> Just wondering if I’m missing anything? I know you can turn off ‘handle
> repository dependencies’ when installing a tool, but the tool still defines
> ‘requirements’ in its XML file and shows ‘Missing repository/tool
> dependencies’ in the Admin.  Has anyone had any experience of dealing with
> this kind of situation?
>
>
>
> Many thanks!
>
>
>
> --
> David Trudgian Ph.D.
> Computational Scientist, BioHPC
>
> Lyda Hill Department of Bioinformatics
> UT Southwestern Medical Center
> Dallas, TX 75390-9039
> Tel: (214) 648-4833
>
>
>
> --
>
> UT Southwestern
>
> Medical Center
>
> The future of medicine, today.
> ___
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Re: [galaxy-dev] Request help to configure local galaxy in Git

[Martin Čech]

Hi Manonanthini,

Windows is not a supported platform for Galaxy and we do not have any
official tutorials, tests or even proofs that it can be done.

I recommend you run a virtual machine with a Linux image and install Galaxy
there. Depending on what you want to do you can grab our pre-populated
Ubuntu image with Galaxy and Planemo set up that is designed to serve as a
Galaxy tool development environment:
http://planemo.readthedocs.org/en/latest/appliance.html#launching-the-appliance-virtualbox-ova
or
just grab a generic Ubuntu image and install Galaxy yourself following the
tutorial at getgalaxy.org

Thanks for using Galaxy.

Regards,

Martin

On Mon, Mar 28, 2016 at 2:57 PM Manonanthini Shanmuganathan <
manonanth...@gmail.com> wrote:

> Hi Galaxy Developer,
> I have been trying to install Galaxy in my windows system using git.I
> have tried using cygwin also.I have been trying for this since March
> 2nd , I am getting this error,
>
> "ManoNathan@Mano MINGW64 ~/galaxy ((v16.01))
> $ sh run.sh
> Fetching
> https://pypi.python.org/packages/source/v/virtualenv/virtualenv-13.1.2.
>
> tar.gz
>   % Total% Received % Xferd  Average Speed   TimeTime Time
> Current
>  Dload  Upload   Total   SpentLeft
> Speed
> 100 1679k  100 1679k0 0   357k  0  0:00:04  0:00:04 --:--:--
> 447k
> Verifying /tmp/galaxy-virtualenv-GUksti/virtualenv-13.1.2.tar.gz
> checksum is
> aabc8ef18cddbd8a2a9c7f92bc43e2fea54b1147330d65db920ef3ce9812e3dc
> Traceback (most recent call last):
>   File "", line 1, in 
> IOError: [Errno 2] No such file or directory:
> '/tmp/galaxy-virtualenv-GUksti/virtualenv-13.1.2.tar.gz'
>
> "
> So I am unable to run galaxy in my system.Please help me in this regard.
> I have installed XAMPP(for mysql and apache server) in my system(Windows
> 10).
>
> Thanks and Regards,
> Manonanthini Thangam
> PhD Scholar,
> Bioinformatics Lab,
> AU-KBC Research Centre,
> MIT Campus,Anna University,
> Chromepet,Chennai.
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Re: [galaxy-dev] automatic adding of a tab in a fastq header

[Martin Čech]

Thank you for all the help Peter!

Also this is already backported and fixed in 16.01

Sorry for causing this bug in the first place.
M.

On Tue, Mar 22, 2016, 18:29 Peter Cock <p.j.a.c...@googlemail.com> wrote:

> Well done for solving this Fabien, with only a small hint from me.
> I'm glad to see your suggested fix has already been applied to
> the Galaxy repository so should be in the next stable release.
>
> Thank you!
>
> Peter
>
> (Also thank you Martin, Nicola, Dan, etc)
>
>
> On Tue, Mar 22, 2016 at 8:43 PM, Martin Čech <mar...@bx.psu.edu> wrote:
> > Thank you very much for solving this Fabien, The PR with your fix has
> been
> > created here: https://github.com/galaxyproject/galaxy/pull/1985
> >
> > Martin
> >
> >
> > On Mon, Mar 21, 2016 at 5:43 PM fmareuil <fmare...@pasteur.fr> wrote:
> >>
> >> Hi Peter,
> >>
> >> I worked on it today and I found  the reason of this bug. In the
> upload.py
> >> tool, the existence of dataset.space_to_tab is tested. In the old
> version of
> >> the data library, when the option was unchecked, the value space_to_tab
> was
> >> None and the test worked. But in the new version the value of
> space_to_tab
> >> is "False", it's a string and the test "if dataset.space_to_tab" returns
> >> True.
> >> It is possible to fix it with a little correction of the
> >> "/lib/galaxy/webapps/galaxy/api/lda_datasets.py".
> >> I join a patch with this email.
> >> I can propose a pull request if you want.
> >>
> >> Best,
> >>
> >> Fabien
> >>
>
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Re: [galaxy-dev] automatic adding of a tab in a fastq header

[Martin Čech]

Thank you very much for solving this Fabien, The PR with your fix has been
created here: https://github.com/galaxyproject/galaxy/pull/1985

Martin

On Mon, Mar 21, 2016 at 5:43 PM fmareuil  wrote:

> Hi Peter,
>
> I worked on it today and I found  the reason of this bug. In the upload.py
> tool, the existence of dataset.space_to_tab is tested. In the old version
> of the data library, when the option was unchecked, the value space_to_tab
> was None and the test worked. But in the new version the value of
> space_to_tab is "False", it's a string and the test "if
> dataset.space_to_tab" returns True.
> It is possible to fix it with a little correction of the
> "/lib/galaxy/webapps/galaxy/api/lda_datasets.py".
> I join a patch with this email.
> I can propose a pull request if you want.
>
> Best,
>
> Fabien
>
>
> --
> Fabien Mareuil | Centre d'Informatique pour la Biologie
> fabien.mare...@pasteur.fr | Institut Pasteur
> 25,28 rue du Docteur Roux 75015 Paris, France
>
>
> On 21/03/2016 09:45, fmareuil wrote:
>
> Hi Peter,
>
> I tested it on the last version of the dev and master branches.
>
> step-by-step :
> I click on the "shared data/Data Libraries", I select my library and I
> click on the button to upload a file and I select the option "from User
> Directory". I select my fastqsanger file (sequences headers are like this :
> @HWI-D00395:188:HYGNFADXX:2:1108:1315:1965 1:N:0:ATGAGC
> with a space between @HWI-D00395:188:HYGNFADXX:2:1108:1315:1965 and
> 1:N:0:ATGAGC and I import it (with or without the auto-detect option).
> When I look the file in a history, the space between
> @HWI-D00395:188:HYGNFADXX:2:1108:1315:1965 and 1:N:0:ATGAGC has been
> replaced by a tab.
>
> I didn't have this problem with "shared data/ Data Libraries deprecated".
>
> Thank a lot for your help,
> Best,
>
> Fabien
>
> On 18/03/2016 18:59, Peter Cock wrote:
>
> Can you provide more details - in particular the version of Galaxy you
> are running? A step-by-step description of how you did the data import
> might be useful too for the Galaxy team to try to reproduce this.
>
> Peter
>
> On Fri, Mar 18, 2016 at 5:34 PM, Fabien Mareuil 
>  wrote:
>
> Hi Peter,
>
> Thank a lot for this information, I didn't found this option for the new
> version of the Data Libraries.
> This could explain why there is this conversion.
> I tested it with an automatic format detection and when I set explicitly
> the
> format but in the two cases a tab was added.
>
> Fabien
>
>
> Le 18/03/2016 17:04, Peter Cock a écrit :
>
> Hi Fabien,
>
> There is a Galaxy upload option to turn spaces into tabs, useful for
> tables of data. Is that being ticked by mistake? That would explain
> this problem.
>
> Also I would check if the FASTQ file format is being detected
> automatically, or set explicitly (e.g. fastqsanger)? Doing that ought
> to prevent any changes.
>
> Peter
>
> On Fri, Mar 18, 2016 at 3:26 PM, Fabien Mareuil 
> 
> wrote:
>
> Hi,
>
> We got a problem with the new version of Data libraries. When we upload a
> fastq file from a User Directory, a tabulation character is added in the
> header in replacement of a space character.
>
> from @HWI-D00395:188:HYGNFADXX:2:1108:1315:1965 1:N:0:ATGAGC to
> @HWI-D00395:188:HYGNFADXX:2:1108:1315:1965  1:N:0:ATGAGC
>
>
> This behavior causes an error with cutadapt 1.6 (maybe with other tools)
> because it doesn't work with tab character. With the direct upload tool
> or
> the deprecated version of Data Libraries no tab character is added. Do
> you
> have some idea to correct this problem? Thanks a lot Best regards --
> Fabien Mareuil | Centre d'Informatique pour la Biologie
> fabien.mare...@pasteur.fr | Institut Pasteur 25,28 rue du Docteur Roux
> 75015
> Paris, France
>
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>
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Re: [galaxy-dev] Please help fix toolshed repository: trtr

[Martin Čech]

Hi Lance,

Dave Bouvier removed the unwanted folder on the TS side. (It wasn't ever
tracked by mercurial). You should be ok now.

Sorry for the inconvenience.

Thank you for using Galaxy.

Martin

On Tue, Mar 15, 2016 at 5:41 PM Lance Parsons <lpars...@princeton.edu>
wrote:

> When I clone the repo, I don't see that folder:
>
>hg clone https://toolshed.g2.bx.psu.edu/repos/mrvollger/trtr
>
> Lance
>
> Martin Čech wrote:
>
>
> Hi Lance,
>
> it seems the whole .git/ folder got accidentally uploaded there and it
> causes trouble. I recommend using the direct mercurial access
> (https://toolshed.g2.bx.psu.edu/repos/mrvollger/trtr), delete the
> folder, commit the change and push it to the TS repository.
>
> Please let me know how it goes.
>
> Martin
>
> On Tue, Mar 15, 2016 at 4:54 PM Lance Parsons <lpars...@princeton.edu
>
> <mailto:lpars...@princeton.edu>> wrote:
>
> I was helping someone with their toolshed repository and we ran
> into an issue, there is an old folder "myTools" in the repository
> that we cannot delete. It has a second copy of the tool
> (inadvertently). However, when we upload a new version with
> Planemo, the directory remains. Attempts to delete it via the
> toolshed web interface result in internal server errors. Can an
> admin take a look?
>
> https://toolshed.g2.bx.psu.edu/view/mrvollger/trtr/13cad5d36301
>
>
> --
> Lance Parsons - Scientific Programmer
> Carl C. Icahn Laboratory - Room 136
> Lewis-Sigler Institute for Integrative Genomics
> Princeton University
>
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>
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Re: [galaxy-dev] Using forms to collect user info at registration

[Martin Čech]

Hello Peter,

you are right, this seems broken, sorry about that.
I have created an issue to track the resolution of this bug:
https://github.com/galaxyproject/galaxy/issues/1937

Thank you for reporting it.

Martin

On Wed, Mar 16, 2016 at 10:16 AM Peter Briggs 
wrote:

> Hello
>
> I'm trying to set up a form within Galaxy to collect some user info at
> registration time. The only documentation I've found on this
> functionality is:
>
> https://wiki.galaxyproject.org/Admin/Config/User%20Information
>
> which seems to be precisely what I need.
>
> However I can't make this work as described. When I set up a form and
> then go to the registration page, instead of the additional form options
> I get a single field called "User type" with a drop-down menu widget
> with a single option ("User registration form" i.e. the name of the form
> that I created).
>
> I've looked to see if there is a config option to turn something on, or
> if I need to create a role, but so far nothing I've tried seems to make
> a difference.
>
> Does anyone have any suggestions on how I might get this feature to
> operate as advertised? (Btw I'm seeing this in both 15.10 and 16.01.)
>
> Thanks for your help,
>
> Best wishes
>
> Peter
>
> --
> Peter Briggs peter.bri...@manchester.ac.uk
> Bioinformatics Core Facility University of Manchester
> B.1083 Michael Smith Bldg Tel: (0161) 2751482
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Re: [galaxy-dev] Please help fix toolshed repository: trtr

[Martin Čech]

Hi Lance,

it seems the whole .git/ folder got accidentally uploaded there and it
causes trouble. I recommend using the direct mercurial access (
https://toolshed.g2.bx.psu.edu/repos/mrvollger/trtr), delete the folder,
commit the change and push it to the TS repository.

Please let me know how it goes.

Martin

On Tue, Mar 15, 2016 at 4:54 PM Lance Parsons 
wrote:

> I was helping someone with their toolshed repository and we ran into an
> issue, there is an old folder "myTools" in the repository that we cannot
> delete. It has a second copy of the tool (inadvertently). However, when we
> upload a new version with Planemo, the directory remains. Attempts to
> delete it via the toolshed web interface result in internal server
> errors. Can an admin take a look?
>
> https://toolshed.g2.bx.psu.edu/view/mrvollger/trtr/13cad5d36301
>
>
> --
> Lance Parsons - Scientific Programmer
> Carl C. Icahn Laboratory - Room 136
> Lewis-Sigler Institute for Integrative Genomics
> Princeton University
>
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Re: [galaxy-dev] Galaxy Conference

[Martin Čech]

Hello Scott,

have you seen the schedule at https://gcc16.sched.org/ ?

The trainings are all listed, described, and categorized there, it should
help you decide what to attend.
>From my experience in addition to scientists there are many admins and
developers attending the conference so you should be able to find your
flock easily.

Plus we are all nice. :)

Best,
Martin

On Fri, Mar 4, 2016 at 11:32 AM Scott Szakonyi 
wrote:

> Hi all,
>
> I know this is not a technical question per se, but this seems my best
> option for getting better information.
>
> I am planning on attending the Galaxy Conference this year. I administrate
> the Galaxy server for VectorBase (vectorbase.org), but I'm a computer
> scientist, not a bioinformatics specialist. I'm uncertain what would be the
> most informative things for me to attend... for instance, I see there is a
> training day 1 and 2, but there's no real description on the site of what
> those are. If someone could offer some guidance, I would be most
> appreciative.
>
> Also, would the conference days be useful for someone in my position?
>
> Thanks!
>
> --
> Scott B. Szakonyi
> Research Programmer
>
> *Center for Research Computing*
> 107 Information Technology Center
> Notre Dame, IN 46556
> http://crc.nd.edu
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Re: [galaxy-dev] copy/import shared history

[Martin Čech]

Le-Shin,

'git clone https://github.com/galaxyproject/galaxy' command will get you on
the 'dev' branch of Galaxy. Unless you want to develop new features I
recommend you to use the latest Galaxy release, described here:
https://docs.galaxyproject.org/en/master/releases/15.10_announce.html

We are also tracking the bug you described on this ticket:
https://github.com/galaxyproject/galaxy/issues/1743

Best

Martin



On Tue, Feb 16, 2016 at 10:22 PM Le-Shin Wu <les...@gmail.com> wrote:

> Hi Martin,
>
> I used "git clone” to get the galaxy from github site, so I think our
> galaxy version should be the latest. I didn’t see any error from the JS
> console but I found if I didn’t use apache as the proxy, the "copy shared
> history” function seems working. I am not sure what went wrong for the
> apache proxy because I don’t have any other issue except this “copy shared
> history” function. Thanks for your information.
>
> Best
>
> Le-Shin
>
>
> On Feb 16, 2016, at 1:02 PM, Martin Čech <mar...@bx.psu.edu> wrote:
>
> Hi LW,
>
> 1) The described 'copy' feature works well for me on usegalaxy.org.
> However the 'view and import' activity does fail for me too. We will look
> into that. What version of Galaxy are you using? Do you see any errors in
> the JS console of your browser?
> 2) 'purge' does only remove all roles from the group, not the group
> itself. Galaxy does not delete entities, only marks them as deleted in the
> DB.
> 3) should be fixed after merge of
> https://github.com/galaxyproject/tools-iuc/pull/596
>
> Thank you for using Galaxy
>
> Martin
>
> On Tue, Feb 16, 2016 at 12:45 PM Le-Shin Wu <les...@gmail.com> wrote:
>
> Hi,
>>
>> I’ve recently installed a new galaxy server and I found some weird
>> behaviors of admin jobs.
>>
>> First, a shared history can not be copied as a new history. For example,
>> user A shared one of his history with user B. User B can see this shared
>> history through “histories shred with me” link, but when user B clicks
>> “copy” of this history nothing happened. However, user B can view this
>> history if he clicks “view” but if he then clicks “import history”, a new
>> galaxy home page will be displayed on the center panel (as shown in the
>> attached screenshot).
>>
>> Second, the administer can only delete groups but he can not purge those
>> deleted groups. In other words, when the administer clicks the “purge”
>> button of a deleted group, nothing will happen on this group. It still
>> shows on the table with status as “deleted”
>>
>> Third, when installed the “package_fontconfig_2_11_1” through tool shed,
>> the status of this package always shows as “installing tool dependencies”.
>> We restarted our galaxy server several times but this message never went
>> away (it always shows on the “monitor installing repositories” page).
>>
>> We really have no idea how to fix these strange behaviors and the web log
>> file also don’t have any error message. Any suggestion? Thank you.
>>
>> Best
>>
>> LW
>>
>> 
>>
> ___
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>
>
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Re: [galaxy-dev] bx-python issue with intersect and subtract tools

[Martin Čech]

Hello Richard,

this issue has been solved, if you update the tool it should work as
expected.
Details are available here: https://biostar.usegalaxy.org/p/15974/

Thank you for using Galaxy

Martin


On Tue, Dec 1, 2015 at 5:28 PM Poole, Richard  wrote:

> Hi all,
>
> I just used the subtract tool (installed under Operate on Genomic
> Intervals) on my own Galaxy server for the first time in a very long time
> and got this error message from the tool:
>
> Traceback (most recent call last):
>   File 
> "/Users/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/subtract/c19a2a29c561/subtract/gops_subtract.py",
>  line 16, in 
> from bx.intervals.io import GenomicInterval, NiceReaderWrapper
> ImportError: No module named bx.intervals.io
>
>
> So I uninstalled the intersect and subtract tools, plus the bx-python
> 0.7.1 package plus the galaxy-ops package and reinstalled both tools from
> the toolshed using the latest revisions of each from devteam. I now get
> this error message:
>
> /Users/galaxy/galaxy-dist/lib/galaxy/__init__.py:63: UserWarning: Module bx 
> was already imported from 
> /Users/galaxy/galaxy-dist/tool-dependencies/bx-python/0.7.1/devteam/package_bx_python_0_7/2d0c08728bca/venv/lib/python2.7/site-packages/bx/__init__.pyc,
>  but 
> /Users/galaxy/galaxy-dist/eggs/bx_python-0.7.2-py2.7-macosx-10.6-intel-ucs2.egg
>  is being added to sys.path
>   self.check_version_conflict()
> Traceback (most recent call last):
>   File 
> "/Users/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/subtract/c19a2a29c561/subtract/gops_subtract.py",
>  line 21, in 
> from utils.gff_util import GFFFeature, GFFReaderWrapper, 
> convert_bed_coords_to_gff
> ImportError: No module named utils.gff_util
>
> Does this suggest an incompatibility somehow with the the egg which is
> installed at startup and is versions 0.7.2 - I tried manually editing the
> egg file but could not switch that to 0.7.1
>
> I also then tried updating Galaxy to latest release 15.07 and even 15.10
> which appeared in the git tag list as I writing this email, but no fix
> there - my Galaxy is running on a Mac OS X 10.10.5 Yosemite.
>
> Any thoughts on how to resolve this problem?
>
> Cheers,
> Rich
>
>
>
>
> *Richard J Poole PhD*
> Wellcome Trust Fellow
> Department of Cell and Developmental Biology
> University College London
> 518 Rockefeller
> 21 University Street, London WC1E 6DE
> Office (518 Rockefeller): +44 20 7679 6577 (int. 46577)
> Lab (529 Rockefeller): +44 20 7679 6133 (int. 46133)
>
> ___
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Re: [galaxy-dev] Working on the admin interface: JS vs Mako

[Martin Čech]

Hi,

Galaxy is implementing frontend with the help of these libraries:
https://github.com/galaxyproject/galaxy/tree/dev/client/galaxy/scripts/libs

Notably the MV-paradigm is being implemented in Backbone.

Good examples of applications/pieces that are written in JS are at
https://github.com/galaxyproject/galaxy/tree/dev/client/galaxy/scripts/mvc

The easiest one to look into is probably the shortest one: `citation`. If
you want to look into full backbone superpower check out `history`

Martin

On Mon, Feb 1, 2016 at 3:26 PM Ziphozakhe Mashologu 
wrote:

> Hi All
>
> In terms of the future, are we using or considering using any JS SPA
> frameworks or the route is plain JavaScript?
>
> I ask as we aim to satisfy our pursued RESTful architecture.
>
> Thanks
> Zipho
>
>
>
>
>
>
>
> On Mon, Feb 1, 2016 at 7:30 PM, Peter van Heusden  wrote:
>
>> Yeah I noticed that about the DependencyResolversView.
>>
>> In terms of writing JS - where's a good example to look at? I tried
>> digging around the client/ directories but couldn't make sense of how it
>> works.
>>
>> Thanks,
>> Peter
>>
>> On 1 February 2016 at 16:48, John Chilton  wrote:
>>
>>> Peter,
>>>
>>>   We would like to replace all the mako with JS, if I was going to put
>>> a bunch of effort into admin pages I'd start by reworking what was
>>> there to use JavaScript and the API. That is me however, I have lots
>>> of time to put into Galaxy fundamentals and refactoring. This is more
>>> work and I am happy to field PRs that modify mako for the time
>>> being.(https://github.com/galaxyproject/galaxy/pull/1632/files looks
>>> great for instance).
>>>
>>>   A middle ground between rewriting everything and still depending on
>>> mako is to dump dictionaries to JavaScript in the mako and render
>>> things in JS. This will make it easier to adapt your changes once the
>>> pages are ultimately rewritten to JavaScript SPAs. In the case 1632 -
>>> that DependencyResolversView class produces dictionaries that can be
>>> dumped as JSON easily into the page and JavaScript could be used to
>>> build up the tables in
>>> templates/webapps/tool_shed/repository/common.mako.
>>>
>>> -John
>>>
>>>
>>> On Mon, Feb 1, 2016 at 11:51 AM, Peter van Heusden 
>>> wrote:
>>> > Hi there
>>> >
>>> > Zipho and I'd would like to make some changes to the admin pages,
>>> including
>>> > the tool info page and the local data page. These are currently
>>> rendered
>>> > from mako templates - should we change these or is the interface going
>>> to be
>>> > rewritten in client side / javascript in the near(ish) future?
>>> >
>>> > Thanks,
>>> > Peter
>>> >
>>> > ___
>>> > Please keep all replies on the list by using "reply all"
>>> > in your mail client.  To manage your subscriptions to this
>>> > and other Galaxy lists, please use the interface at:
>>> >   https://lists.galaxyproject.org/
>>> >
>>> > To search Galaxy mailing lists use the unified search at:
>>> >   http://galaxyproject.org/search/mailinglists/
>>>
>>
>>
>> ___
>> Please keep all replies on the list by using "reply all"
>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>   https://lists.galaxyproject.org/
>>
>> To search Galaxy mailing lists use the unified search at:
>>   http://galaxyproject.org/search/mailinglists/
>>
>
> ___
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> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
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Re: [galaxy-dev] Get data via the cloud?

[Martin Čech]

Hi Scott,

Galaxy can retrieve data from any publicly available URL. Just paste the
URL into the upload modal using the 'paste/fetch data'.

This probably won't work with some of the services as they won't serve you
content without visiting their site. But it works with e.g. dropbox if you
add `dl=1` in the end of the shared url.

Martin

On Mon, Feb 1, 2016 at 4:14 PM Scott Szakonyi 
wrote:

> Hi all,
>
> Of course, we need to upload large data files. I understand that the
> common way to achieve this is with an FTP server, but due to our situation
> setting one up is problematic. Does Galaxy have any mechanism for
> retrieving data from cloud resources such as Dropbox, Box, or Google Drive?
>
> Thanks in advance,
>
> --
> Scott B. Szakonyi
> Research Programmer
>
> *Center for Research Computing*
> 107 Information Technology Center
> Notre Dame, IN 46556
> http://crc.nd.edu
> ___
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> and other Galaxy lists, please use the interface at:
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>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
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Re: [galaxy-dev] Loading or Upload Large datasets into Galaxy History

[Martin Čech]

Hi Amos,

what Galaxy are you using and where are you seeing these messages?

thanks

Martin

On Thu, Jan 28, 2016 at 2:56 PM Raphenya, Amogelang 
wrote:

> Hi All,
>
> Is there a faster way to upload or load large datasets into galaxy history
> without using FTP?
>
> I tried *Upload_local_file* (*to current history*) and it doesn’t upload
> *.gz* files correctly as compared to when using* Upload_file *(*from your
> computer*).
>
> Cheers.
>
>
> *Amos Raphenya *
> *Bioinformatics Software Developer*
> *Department of Biochemistry & Biomedical Sciences*
> *McMaster University, MDCL **2317*
> *p: (905) 525-9140 **ext: **22787*
> *a: 1280 Main St W.,Hamilton, Ontario, Canada L8S 4K1*
> *e:  raphe...@mcmaster.ca  *
> *skype: amos_raphenya*
>
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
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Re: [galaxy-dev] errors installing tool dependencies...

[Martin Čech]

Hi Edgar,

I am not sure about this one. Please try setting 'new_file_path' in your
galaxy.ini to an absolute path, try again and check whether something
changes.

Martin

On Mon, Jan 25, 2016 at 9:23 AM Fernandez Edgar <
edgar.fernan...@umontreal.ca> wrote:

> Hello Martin,
>
>
>
> Thank you!
>
> Your instructions for my problem with Perl package worked.
>
> For the URL of hmmer, it is wrong and I will report it like you suggested
> it.
>
>
>
> Finally, a new error occurred for bowtie.
>
> Would you please take a look?
>
>
>
> My Sincere Salutations,
>
>
>
> *Edgar Fernandez*
>
> System Administrator (Linux)
>
> Direction Générale des Technologies de l'Information et de la Communication
>
> *Université de Montréal*
>
>
>
> PAVILLON ROGER-GAUDRY, bureau X-210
>
> (  Bur. : *1-514-343-6111 poste 16568*
>
>
>
>
>
> *From:* Martin Čech [mailto:mar...@bx.psu.edu]
> *Sent:* January-22-16 2:34 PM
> *To:* Fernandez Edgar <edgar.fernan...@umontreal.ca>;
> galaxy-...@bx.psu.edu
> *Subject:* Re: [galaxy-dev] errors installing tool dependencies...
>
>
>
> Hi Edgar,
>
> for the package_perl issue please try installing updates to the
> dependencies (package_gnu_coreutils and package_perl in their respective
> versions) and then return to this screen and click the 'repository action'
> button and then 'manage dependencies' from the menu. Uninstall both
> dependencies (gnu_coreutil and perl) and then install them again.
>
> That should pick up the newest versions and you should be set.
>
>
>
> Regarding the hmmer that is a more prosaic problem, at the time of the
> installation the software was not available at the given URL. Check the
> machine's internet connection and if it is ok try downloading the file
> manually. If it succeeds the problem might have been on their side and is
> ok now. If it does not the problem can still be on their side and in that
> case either wait a bit and try again or report the issue at
> https://github.com/galaxyproject/tools-iuc/issues
>
>
>
> thank you for using Galaxy.
>
>
>
> Martin
>
> On Fri, Jan 22, 2016 at 2:24 PM Fernandez Edgar <
> edgar.fernan...@umontreal.ca> wrote:
>
> Hello guys,
>
>
>
> Happy new year everyone!
>
> Wish you all the best!
>
>
>
> I have a couple of small problems I’ve attached as pictures…
>
> Can you please help me?
>
>
>
> INFO: My galaxy installation and database is updated today!
>
>
>
> My sincere salutations,
>
>
>
> *Edgar Fernandez*
>
> System Administrator (Linux)
>
> Direction Générale des Technologies de l'Information et de la Communication
>
> *Université de Montréal*
>
>
>
> PAVILLON ROGER-GAUDRY, bureau X-210
>
> (  Bur. : *1-514-343-6111 poste 16568 *
>
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
>
>
___
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Re: [galaxy-dev] errors installing tool dependencies...

[Martin Čech]

That was my second guess, I wasn't sure whether it should create that dir
structure. Are you installing this package at this revision? And what
system are you installing it on?

https://toolshed.g2.bx.psu.edu/view/iuc/package_bowtie_2_2_6/0d9cd7487cc9

M.

On Mon, Jan 25, 2016 at 11:17 AM Fernandez Edgar <
edgar.fernan...@umontreal.ca> wrote:

> No wait my mistake: the path doesn’t exists:
>
>
> [Errno 2] No such file or directory: 
> '/home/galaxy/galaxy-prod/database/tmp/tmp-toolshed-mtdb6vbEI/bowtie2-2.2.6/bowtie2-2.2.6/'
>
> Because you have twice "bowtie2-2.2.6" in the full path…
>
> Is that normal?
>
>
>
> *Edgar Fernandez*
>
> System Administrator (Linux)
>
> Direction Générale des Technologies de l'Information et de la Communication
>
> *Université de Montréal*
>
>
>
> PAVILLON ROGER-GAUDRY, bureau X-210
>
> (  Bur. : *1-514-343-6111 poste 16568*
>
>
>
>
>
> *From:* Fernandez Edgar
> *Sent:* January-25-16 11:11 AM
> *To:* 'Martin Čech' <mar...@bx.psu.edu>; galaxy-...@bx.psu.edu
> *Subject:* RE: [galaxy-dev] errors installing tool dependencies...
>
>
>
> Hello Martin.
>
>
>
> I changed the setting “new_file_path” like you said and the same error
> occurs (with the full path obviously).
>
> I check that the full path exists. And is rwx for the galaxy user.
>
> Any other ideas I could try?
>
>
>
> *Edgar Fernandez*
>
> System Administrator (Linux)
>
> Direction Générale des Technologies de l'Information et de la Communication
>
> *Université de Montréal*
>
>
>
> PAVILLON ROGER-GAUDRY, bureau X-210
>
> (  Bur. : *1-514-343-6111 poste 16568*
>
>
>
>
>
> *From:* Martin Čech [mailto:mar...@bx.psu.edu <mar...@bx.psu.edu>]
> *Sent:* January-25-16 9:33 AM
>
>
> *To:* Fernandez Edgar <edgar.fernan...@umontreal.ca>;
> galaxy-...@bx.psu.edu
> *Subject:* Re: [galaxy-dev] errors installing tool dependencies...
>
>
>
> Hi Edgar,
>
>
>
> I am not sure about this one. Please try setting 'new_file_path' in your
> galaxy.ini to an absolute path, try again and check whether something
> changes.
>
>
>
> Martin
>
>
>
> On Mon, Jan 25, 2016 at 9:23 AM Fernandez Edgar <
> edgar.fernan...@umontreal.ca> wrote:
>
> Hello Martin,
>
>
>
> Thank you!
>
> Your instructions for my problem with Perl package worked.
>
> For the URL of hmmer, it is wrong and I will report it like you suggested
> it.
>
>
>
> Finally, a new error occurred for bowtie.
>
> Would you please take a look?
>
>
>
> My Sincere Salutations,
>
>
>
> *Edgar Fernandez*
>
> System Administrator (Linux)
>
> Direction Générale des Technologies de l'Information et de la Communication
>
> *Université de Montréal*
>
>
>
> PAVILLON ROGER-GAUDRY, bureau X-210
>
> (  Bur. : *1-514-343-6111 poste 16568*
>
>
>
>
>
> *From:* Martin Čech [mailto:mar...@bx.psu.edu]
> *Sent:* January-22-16 2:34 PM
> *To:* Fernandez Edgar <edgar.fernan...@umontreal.ca>;
> galaxy-...@bx.psu.edu
> *Subject:* Re: [galaxy-dev] errors installing tool dependencies...
>
>
>
> Hi Edgar,
>
> for the package_perl issue please try installing updates to the
> dependencies (package_gnu_coreutils and package_perl in their respective
> versions) and then return to this screen and click the 'repository action'
> button and then 'manage dependencies' from the menu. Uninstall both
> dependencies (gnu_coreutil and perl) and then install them again.
>
> That should pick up the newest versions and you should be set.
>
>
>
> Regarding the hmmer that is a more prosaic problem, at the time of the
> installation the software was not available at the given URL. Check the
> machine's internet connection and if it is ok try downloading the file
> manually. If it succeeds the problem might have been on their side and is
> ok now. If it does not the problem can still be on their side and in that
> case either wait a bit and try again or report the issue at
> https://github.com/galaxyproject/tools-iuc/issues
>
>
>
> thank you for using Galaxy.
>
>
>
> Martin
>
> On Fri, Jan 22, 2016 at 2:24 PM Fernandez Edgar <
> edgar.fernan...@umontreal.ca> wrote:
>
> Hello guys,
>
>
>
> Happy new year everyone!
>
> Wish you all the best!
>
>
>
> I have a couple of small problems I’ve attached as pictures…
>
> Can you please help me?
>
>
>
> INFO: My galaxy installation and database is updated today!
>
>
>
> My sincere salutations,
>
>
>
> *Edgar Fernandez*
>
> System Administrator (Linux)
>

Re: [galaxy-dev] Want to Contribute in galaxy project

[Martin Čech]

Hi Manish,

thank you very much for your interest in Galaxy project!

I would first look here to check the beginner's dev overview:
https://wiki.galaxyproject.org/Develop/GettingStarted

And once you feel somewhat comfortable you can check the beginner friendly
issues on GitHub here:
https://github.com/galaxyproject/galaxy/issues?q=is%3Aopen+is%3Aissue+label%3Afriendliness%2Fbeginner

Don't be afraid of starting the resolution of any issue with public
discussion on GitHub on how to tackle it. We will do our best to help.

Please ask any questions here or on any other channel we use. Notably we
use #galaxyproject IRC channel on freenode (
https://wiki.galaxyproject.org/Support/IRC)

Thanks again for being interested in Galaxy.

Martin







On Mon, Jan 25, 2016 at 12:09 PM Manish Bisht 
wrote:

> Hello Developers,
>
> I am Manish Bisht. I am in second year of my engineering in information
> technology. I want to provide the code for Galaxy Project. I have created
> many projects outside of my college projects. You can see all at https://
> github.com
> / 
> manishbisht . I am familiar with many
> languages some of them are HTML, CSS, JavaScript, PHP, C/C++, Java, and I am
> currently learning Python also.
>
> Also apart from my college hours i have also started my own startup with
> Run4Offers (http://www.run4offers.com/)
>
> I have also interested in Graphics Designing also. I have the knowledge of
> AdobePhotoshop, Adobe Illustrator and Adobe In Design. I have created many
> images of various festivals for my College Entrepreneurship Cell(TOPAZ).
>
> This is all about about me.
>
> I am new to open source communities. I want to work on the projects
> that can make world wide impact. So I have selected Galaxy Project and
> want to start contributing to it. Can anyone please help me in contributing
> to Galaxy Project. From where I can start contributing to Galaxy Project.
>
> Waiting for all the useful suggestions.
>
> Thanks :)
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
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Re: [galaxy-dev] errors installing tool dependencies...

[Martin Čech]

Edgar,

check 'How to migrate a Galaxy instance from Mercurial Bitbucket to Git
GitHub' at https://wiki.galaxyproject.org/Develop/SourceCode

Thanks

M.
On Mon, Jan 25, 2016 at 12:29 PM Fernandez Edgar <
edgar.fernan...@umontreal.ca> wrote:

> How would I safely make the transition from mercurial to github without my
> installation?
>
>
>
> *Edgar Fernandez*
>
> System Administrator (Linux)
>
> Direction Générale des Technologies de l'Information et de la Communication
>
> *Université de Montréal*
>
>
>
> PAVILLON ROGER-GAUDRY, bureau X-210
>
> (  Bur. : *1-514-343-6111 poste 16568*
>
>
>
>
>
> *From:* Nicola Soranzo [mailto:nicola.sora...@gmail.com] *On Behalf Of *Nicola
> Soranzo
> *Sent:* January-25-16 12:22 PM
> *To:* Fernandez Edgar <edgar.fernan...@umontreal.ca>;
> galaxy-dev@lists.galaxyproject.org
>
>
> *Subject:* Re: [galaxy-dev] errors installing tool dependencies...
>
>
>
> Hi Edgar,
> indeed your bug was fixed long ago, please see
> http://dev.list.galaxyproject.org/Bismark-installation-dependencies-error-td4668186.html
>
> You should really move to the GitHub repository and update to the latest
> 15.07 or (better) to 15.10 .
>
> Cheers,
> Nicola
>
> On 25/01/16 17:09, Fernandez Edgar wrote:
>
> [galaxy@galaxy_sever galaxy-prod]$ hg id -i
>
> f6683935f81a+
>
>
>
> *Edgar Fernandez*
>
> System Administrator (Linux)
>
> Direction Générale des Technologies de l'Information et de la Communication
>
> *Université de Montréal*
>
>
>
> PAVILLON ROGER-GAUDRY, bureau X-210
>
> (  Bur. : *1-514-343-6111 poste 16568*
>
>
>
>
>
> *From:* Nicola Soranzo [mailto:nicola.sora...@gmail.com
> <nicola.sora...@gmail.com>] *On Behalf Of *Nicola Soranzo
> *Sent:* January-25-16 12:05 PM
> *To:* Fernandez Edgar <edgar.fernan...@umontreal.ca>
> <edgar.fernan...@umontreal.ca>; Martin Čech <mar...@bx.psu.edu>
> <mar...@bx.psu.edu>; galaxy-...@bx.psu.edu
> *Subject:* Re: [galaxy-dev] errors installing tool dependencies...
>
>
>
> Hi Edgar,
> this smells like an old fixed bug, what version of Galaxy are you running?
>
> Cheers,
> Nicola
>
> On 25/01/16 14:22, Fernandez Edgar wrote:
>
> Hello Martin,
>
>
>
> Thank you!
>
> Your instructions for my problem with Perl package worked.
>
> For the URL of hmmer, it is wrong and I will report it like you suggested
> it.
>
>
>
> Finally, a new error occurred for bowtie.
>
> Would you please take a look?
>
>
>
> My Sincere Salutations,
>
>
>
> *Edgar Fernandez*
>
> System Administrator (Linux)
>
> Direction Générale des Technologies de l'Information et de la Communication
>
> *Université de Montréal*
>
>
>
> PAVILLON ROGER-GAUDRY, bureau X-210
>
> (  Bur. : *1-514-343-6111 poste 16568*
>
>
>
>
>
> *From:* Martin Čech [mailto:mar...@bx.psu.edu <mar...@bx.psu.edu>]
> *Sent:* January-22-16 2:34 PM
> *To:* Fernandez Edgar <edgar.fernan...@umontreal.ca>
> <edgar.fernan...@umontreal.ca>; galaxy-...@bx.psu.edu
> *Subject:* Re: [galaxy-dev] errors installing tool dependencies...
>
>
>
> Hi Edgar,
>
> for the package_perl issue please try installing updates to the
> dependencies (package_gnu_coreutils and package_perl in their respective
> versions) and then return to this screen and click the 'repository action'
> button and then 'manage dependencies' from the menu. Uninstall both
> dependencies (gnu_coreutil and perl) and then install them again.
>
> That should pick up the newest versions and you should be set.
>
>
>
> Regarding the hmmer that is a more prosaic problem, at the time of the
> installation the software was not available at the given URL. Check the
> machine's internet connection and if it is ok try downloading the file
> manually. If it succeeds the problem might have been on their side and is
> ok now. If it does not the problem can still be on their side and in that
> case either wait a bit and try again or report the issue at
> https://github.com/galaxyproject/tools-iuc/issues
>
>
>
> thank you for using Galaxy.
>
>
>
> Martin
>
> On Fri, Jan 22, 2016 at 2:24 PM Fernandez Edgar <
> edgar.fernan...@umontreal.ca> wrote:
>
> Hello guys,
>
>
>
> Happy new year everyone!
>
> Wish you all the best!
>
>
>
> I have a couple of small problems I’ve attached as pictures…
>
> Can you please help me?
>
>
>
> INFO: My galaxy installation and database is updated today!
>
>
>
> My sincere salutations,
>
>
>
&g

Re: [galaxy-dev] configuration management, tool shed and tool revisions

[Martin Čech]

Hello Steve,

Galaxy project's efforts in automating tool installations are mostly
represented by the following Ansible playbook (
https://github.com/afgane/galaxy-tools-playbook) and a role (
https://github.com/galaxyproject/ansible-galaxy-tools).
We plan on improving that tracked at:
https://github.com/galaxyproject/galaxy/issues/1115

The install_tool_shed_repositories.py script should install the latest
revision when no revision is specified (and owner and repo name is
present). This feature was added on May 14, 2014 (
https://github.com/galaxyproject/galaxy/commit/2d5c37a73f90931e03291d5c4ad6057a0e41a712
).

Please let us know how it works for you.

Thank you for using Galaxy.

Martin Cech

On Sun, Jan 24, 2016 at 7:02 PM  wrote:

> Hi,
>
>
>
> We are using Puppet to manage the configuration for VMs for our
> development and production Galaxy instances.  We would like to be able to
> specify tool shed tools and their revisions and have Puppet ensure that
> they are installed.  Our Puppet code makes use of the
> “install_tool_shed_repositories.py” script and a script based on that which
> checks to see whether a particular tool and revision is installed.
>
>
>
> We are finding that if we don’t specify the latest revision of a tool that
> the “install_tool_shed_repositories.py” script fails.  Is this what others
> experience?
>
>
>
> I know other sites are doing configuration management with Ansible.  What
> approach are these sites taking for ensuring tools are installed or are
> these sites doing the tool installations outside of configuration
> management?
>
>
>
> Regards.
>
>
>
> *Steve McMahon*
> Solution Architect and Senior System Administrator | Scientific Computing
> *Information Management and Technology*
> CSIRO
>
> T +61 2 6214 2968 Alt +61 4 0077 9318
> *steve.mcma...@csiro.au * | www.csiro.au
> 1 Wilf Crane Crescent, Yarralumla ACT 2600
>
> *PLEASE NOTE*
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>
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>
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Re: [galaxy-dev] Sample tracking / external services - still supported?

[Martin Čech]

Hello Matthias,

As you correctly identified the original implementation, in spite of being
present in the Galaxy distribution, is treated as deprecated.
However I know about three sample tracking implementation based on Galaxy's
old sample tracking.


   - *TRON Mainz*
   http://bioinformatics.oxfordjournals.org/content/29/9/1233.longsource
   here: https://bitbucket.org/jelle/galaxy-central-tron-lims
   - *Massachusetts General Hospital *
   
http://bcbio.wordpress.com/2011/01/11/next-generation-sequencing-information-management-and-analysis-system-for-galaxy/
source here:https://bitbucket.org/chapmanb/galaxy-central
   - https://github.com/specimentracking


I am not sure about the current state of the first two but the last one is
being used in a pilot project for tracking using smartphones and QR codes
here at PSU and is under our somewhat active development.

Let me know if you have more questions.
Thanks for using Galaxy.

Martin

On Wed, Jan 20, 2016 at 3:06 AM Matthias De Smet 
wrote:

> Hi all,
>
> Is there still any support out there for sample tracking / data transfers
> from sequencer / external services? Or is this part of Galaxy completely
> abandoned/deprecated? All the info in the wiki or other sources is at least
> 5 years old or refers to files and code that isn’t there anymore.
>
> Any help?
>
> Thanks!
>
> Matthias
>
>
>
> ___
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>
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>   http://galaxyproject.org/search/mailinglists/
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