[galaxy-dev] Password-Reset
Dear Galaxy Community, as we tried to establish the mail functionalities for our Galaxy instance, we managed to send email upon the I forgot my password user request. In the Email a Link is provided. Here two errors arise: 1. In the File galaxy/lib/galaxy/webapps/galaxy/controllers/user.pyc HTML Tags for this Email are generated, but the Email is send as plain/text, therefore the HTML Tags, as well as the (doubled) Link are visible for the user. 2. In our case, the provided link takes us to the normal user login page, where the user has no option of resetting his/her password. Can you provide me some assistance to tackle the problems? Kind Regards, Matthias Enders ___ 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/
[galaxy-dev] Error in Reset Password User Notification
Dear Galaxy Community, as we tried to establish the mail functionalities for our Galaxy instance, we managed to send email upon the I forgot my password user request. In the Email a Link is provided. Here two errors arise: 1. In the File galaxy/lib/galaxy/webapps/galaxy/controllers/user.pyc HTML Tags for this Email are generated, but the Email is send as plain/text, therefore the HTML Tags, as well as the (doubled) Link are visible for the user. 2. In our case, the provided link takes us to the normal user login page, where the user has no option of resetting his/her password. Can you provide me some assistance to tackle the problems? Kind Regards, Matthias Enders ___ 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/
Re: [galaxy-dev] Fatal Error while uploading a File with special Characters
Hi, MySQL: Server version: 5.5.44-0ubuntu0.14.04.1 (Ubuntu) MySQL-GalaxyDB Encoding: UTF8 Galaxy: Where can I find the current release und changeset of my Galaxy Instance? Mit freundlichen Grüßen Matthias Enders --- [cid:image001.png@01D03960.8254BEE0] GERMAN SEED ALLIANCE GmbH c/o Norddeutsche Pflanzenzucht Hans-Georg Lembke KG Hohenlieth, 24363 Holtsee Tel.: +49 (0)4351/ 736-189 Fax: + 49 (0)4351/ 736-271 Mobil: +49 (0)151/ 14247360 Email: m.end...@german-seed-alliance.de<mailto:m.end...@german-seed-alliance.de> Firmensitz Köln Amtsgericht Köln, HRB 73844 Von: Dannon Baker [mailto:dannon.ba...@gmail.com] Gesendet: Thursday, September 10, 2015 4:53 PM An: Matthias Enders <m.end...@german-seed-alliance.de> Cc: galaxy-dev@lists.galaxyproject.org Betreff: Re: [galaxy-dev] Fatal Error while uploading a File with special Characters Thanks. Can you specify exactly which release (or even the exact changeset) of the galaxy revision you're running, and what encoding the database is currently set to? I've reproduced the error with the latest galaxy release, mysql 5.6.26 (utf8 encoding) and will get a fix out shortly, but I want to make sure I'm testing your situation as well. On Thu, Sep 10, 2015 at 10:14 AM, Matthias Enders <m.end...@german-seed-alliance.de<mailto:m.end...@german-seed-alliance.de>> wrote: It was the name of the File: Blühzeitpunkt.txt (for example) Von: Dannon Baker [mailto:dannon.ba...@gmail.com<mailto:dannon.ba...@gmail.com>] Gesendet: Thursday, September 10, 2015 4:12 PM An: Matthias Enders <m.end...@german-seed-alliance.de<mailto:m.end...@german-seed-alliance.de>> Cc: galaxy-dev@lists.galaxyproject.org<mailto:galaxy-dev@lists.galaxyproject.org> Betreff: Re: [galaxy-dev] Fatal Error while uploading a File with special Characters You should definitely not have to purge a user to fix this (not that it should happen in the first place). Was it the file with special characters, or the name of the file? On Thu, Sep 10, 2015 at 2:28 AM, Matthias Enders <m.end...@german-seed-alliance.de<mailto:m.end...@german-seed-alliance.de>> wrote: Dear Galaxy Community, a User of our Galaxy Platform has produced a fatal error by uploading a file containing a German special character (ä / ü / ö / ß). This resulted in the following status (only for the given user): - Upload was canceled: Status was "Failed Internal Server Error (500)" - All Histories were corrupt stating: "An error was encountered while loading the contents." - Tools can´t be used an stating (in Traceback): " UnicodeDecodeError: 'utf8' codec can't decode byte 0xfc in position 5: invalid start byte" "Module weberror.evalexception.middleware:364 in respond" This totally destroyed to current user and we have had to purge him in order to get him back to work, even losing all his datasets & histories! We are using an MySQL database as a backend. Is the Encoding of this database the problem? If yes: Which encoding is used/supported by galaxy? Thanks in advance! Matthias ___ 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/
[galaxy-dev] Fatal Error while uploading a File with special Characters
Dear Galaxy Community, a User of our Galaxy Platform has produced a fatal error by uploading a file containing a German special character (ä / ü / ö / ß). This resulted in the following status (only for the given user): - Upload was canceled: Status was "Failed Internal Server Error (500)" - All Histories were corrupt stating: "An error was encountered while loading the contents." - Tools can´t be used an stating (in Traceback): " UnicodeDecodeError: 'utf8' codec can't decode byte 0xfc in position 5: invalid start byte" "Module weberror.evalexception.middleware:364 in respond" This totally destroyed to current user and we have had to purge him in order to get him back to work, even losing all his datasets & histories! We are using an MySQL database as a backend. Is the Encoding of this database the problem? If yes: Which encoding is used/supported by galaxy? Thanks in advance! Matthias ___ 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/
[galaxy-dev] This job is waiting to run - Issue after Update to 15.10
After some trying a college figured out, the Tools are working just fine, but all old datasets are not accessible by the tools via "redo the job". But I can Download them and so on. ___ 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/
[galaxy-dev] This job is waiting to run - Issue after Update to 15.10
Dear Galaxy Community, after updating my Galaxy instance to 15.10 via Git, I encountered a strange "This job is waiting to run" issue. When starting a new job, (even reloading a successfull one) the result dataset remains in the status "This job is waiting to run" The NCBI Blast+ tools as well as the chart tools (Boxplot, Barplot and so on) are not affected. Wheras all other tools are, including Filter, Sort and the other Build in tools as well as our own developed tools. A reload of the tool config via the admin console was successfull but did´t solve the problem. Can you give me a hint how to solve this? I´m using a Ubuntu 14.04 Server, if this is of interest. Many thanks in advance! ___ 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/
Re: [galaxy-dev] the future of trackster - was: galaxy-dev Digest, Vol 136, Issue 8
Hi Hans,
actually we are a company and the UCSC Genome Browser is not freely available
for us. As you pinpointed me to the website:
https://galaxyproject.org/visualization-setup/
There is an link to USCS utilities (for creating twobitfiles)
(http://hgdownload.cse.ucsc.edu/admin/exe/)
Actually this tools are also under license agreements, that permits free
commercial download or usage.
If I understand it correctly the twobit-files are mandatory for trackster,
implicating that we have to buy licenses for using UCSC Genome Browser and/or
Trackster?
If yes: Are there any attempts to build in or rebuild this utilities, so the
full project with all parts "remains" compatible with AFL3 license?
Mit freundlichen Grüßen
Matthias Enders
---
GERMAN SEED ALLIANCE GmbH
c/o Norddeutsche Pflanzenzucht
Hans-Georg Lembke KG
Hohenlieth, 24363 Holtsee
Tel.: +49 (0)4351/ 736-189
Fax: + 49 (0)4351/ 736-271
Mobil: +49 (0)151/ 14247360
Email: m.end...@german-seed-alliance.de
Firmensitz Köln
Amtsgericht Köln, HRB 73844
-Ursprüngliche Nachricht-
Von: Hans-Rudolf Hotz [mailto:h...@fmi.ch]
Gesendet: Dienstag, 17. Oktober 2017 10:33
An: Matthias Enders <m.end...@german-seed-alliance.de>;
galaxy-dev@lists.galaxyproject.org
Betreff: the future of trackster - was: galaxy-dev Digest, Vol 136, Issue 8
Hi Matthias
We had a Birds of a Feather session about (the future of) Trackster at the
recent galaxy community conference in Montpellier. Though, as far as I know (I
might be wrong), this didn't result in any no active development on the
Trackster code.
What kind of functionality do you miss? It might be worth rising an issue on
github (https://github.com/galaxyproject/galaxy/issues) ?
Personally, I consider Trackster and the option to display data at the
UCSC genome browser as two different pairs of shoes:
- Trackster is a easy option to look at your data quickly. It is
particular useful, if you work with non-model organisms
- the display of your data at UCSC is handy, if you want to visually
compare it with all the available UCSC tracks. However, keep in mind,
unless you are using a local copy of the UCSC gemome browser, the data
will leave your local network.
WRT tutorial: Have you seen these pages:
https://galaxyproject.org/learn/visualization/
https://galaxyproject.org/visualization-setup/
Regards, Hans-Rudolf
PS: I took the freedom to change the subject line for easier searching
in the future
On 10/16/2017 03:50 PM, Matthias Enders wrote:
> Dear Galaxy Dev List,
>
> we currently searching for a good Genome Browser. As we run a local galaxy
> instance, we noticed the integrated GTB ("Galaxy Track Browser").
>
> So my question is: Is there a roadmap for further support / development of
> the GTB?
>
> Or will it perhaps get replaced/deprecated in the near future (we read a lot
> of UCSC Genome Browser - Galaxy - Integration)?
>
> Another question would be on good sources/tutorials/manuals for configuring
> and setup for the GTB.
>
> Mit freundlichen Grüßen
>
> Matthias Enders
> ---
>
>
> GERMAN SEED ALLIANCE GmbH
> c/o Norddeutsche Pflanzenzucht
> Hans-Georg Lembke KG
> Hohenlieth, 24363 Holtsee
> Tel.: +49 (0)4351/ 736-189
> Fax: + 49 (0)4351/ 736-271
> Mobil: +49 (0)151/ 14247360
>
> Email: m.end...@german-seed-alliance.de
>
> Firmensitz Köln
> Amtsgericht Köln, HRB 73844
> ___
> 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/
>
___
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/
Re: [galaxy-dev] the future of trackster - was: galaxy-dev Digest, Vol 136, Issue 8
Hi Hans,
your right, I´ve checked this. The utils are free and the folder on GITHub
contains the tools needed. Perhaps it´s an idea to change the link on the
website (https://galaxyproject.org/visualization-setup/) from here
("http://hgdownload.cse.ucsc.edu/admin/exe/;)
to github? ("https://github.com/ucscGenomeBrowser/kent/tree/master/src/utils;)
Mit freundlichen Grüßen
Matthias Enders
---
GERMAN SEED ALLIANCE GmbH
c/o Norddeutsche Pflanzenzucht
Hans-Georg Lembke KG
Hohenlieth, 24363 Holtsee
Tel.: +49 (0)4351/ 736-189
Fax: + 49 (0)4351/ 736-271
Mobil: +49 (0)151/ 14247360
Email: m.end...@german-seed-alliance.de
Firmensitz Köln
Amtsgericht Köln, HRB 73844
-Ursprüngliche Nachricht-
Von: Hans-Rudolf Hotz [mailto:h...@fmi.ch]
Gesendet: Dienstag, 17. Oktober 2017 16:50
An: Matthias Enders <m.end...@german-seed-alliance.de>;
galaxy-dev@lists.galaxyproject.org
Betreff: Re: AW: the future of trackster - was: galaxy-dev Digest, Vol 136,
Issue 8
Hi Matthias
No, the twobit-files are not mandatory for trackster. They are only required if
you want to zoom into the nucleotide level.
Also, though, I am not sure, and I recommend to check this with your legal
department, but I have been under the impression that the tool 'faToTwoBit' can
be built from the "kent/src/utils" source code directory, which is freely
available for all uses, isn't-it?
Regards, Hans-Rudolf
On 10/17/2017 04:29 PM, Matthias Enders wrote:
> Hi Hans,
>
> actually we are a company and the UCSC Genome Browser is not freely
> available for us. As you pinpointed me to the website:
> https://galaxyproject.org/visualization-setup/
>
> There is an link to USCS utilities (for creating twobitfiles)
> (http://hgdownload.cse.ucsc.edu/admin/exe/)
> Actually this tools are also under license agreements, that permits free
> commercial download or usage.
>
> If I understand it correctly the twobit-files are mandatory for trackster,
> implicating that we have to buy licenses for using UCSC Genome Browser and/or
> Trackster?
>
> If yes: Are there any attempts to build in or rebuild this utilities, so the
> full project with all parts "remains" compatible with AFL3 license?
>
> Mit freundlichen Grüßen
>
> Matthias Enders
> --
> -
>
>
> GERMAN SEED ALLIANCE GmbH
> c/o Norddeutsche Pflanzenzucht
> Hans-Georg Lembke KG
> Hohenlieth, 24363 Holtsee
> Tel.: +49 (0)4351/ 736-189
> Fax: + 49 (0)4351/ 736-271
> Mobil: +49 (0)151/ 14247360
>
> Email: m.end...@german-seed-alliance.de
>
> Firmensitz Köln
> Amtsgericht Köln, HRB 73844
>
> -Ursprüngliche Nachricht-
> Von: Hans-Rudolf Hotz [mailto:h...@fmi.ch]
> Gesendet: Dienstag, 17. Oktober 2017 10:33
> An: Matthias Enders <m.end...@german-seed-alliance.de>;
> galaxy-dev@lists.galaxyproject.org
> Betreff: the future of trackster - was: galaxy-dev Digest, Vol 136,
> Issue 8
>
> Hi Matthias
>
> We had a Birds of a Feather session about (the future of) Trackster at the
> recent galaxy community conference in Montpellier. Though, as far as I know
> (I might be wrong), this didn't result in any no active development on the
> Trackster code.
>
> What kind of functionality do you miss? It might be worth rising an issue on
> github (https://github.com/galaxyproject/galaxy/issues) ?
>
>
> Personally, I consider Trackster and the option to display data at the
> UCSC genome browser as two different pairs of shoes:
>
>- Trackster is a easy option to look at your data quickly. It is
> particular useful, if you work with non-model organisms
>
>- the display of your data at UCSC is handy, if you want to
> visually compare it with all the available UCSC tracks. However, keep
> in mind, unless you are using a local copy of the UCSC gemome browser,
> the data will leave your local network.
>
>
>
> WRT tutorial: Have you seen these pages:
>
> https://galaxyproject.org/learn/visualization/
> https://galaxyproject.org/visualization-setup/
>
>
> Regards, Hans-Rudolf
>
>
> PS: I took the freedom to change the subject line for easier searching
> in the future
>
>
>
>
>
>
> On 10/16/2017 03:50 PM, Matthias Enders wrote:
>> Dear Galaxy Dev List,
>>
>> we currently searching for a good Genome Browser. As we run a local galaxy
>> instance, we noticed the integrated GTB ("Galaxy Track Browser").
>>
>> So my question is: Is there a roadmap for further support / development of
>> the GTB?
>>
>> Or will it perhaps get replaced/deprecated in the near future (we read a lot
>> of U
Re: [galaxy-dev] galaxy-dev Digest, Vol 136, Issue 8
Dear Galaxy Dev List,
we currently searching for a good Genome Browser. As we run a local galaxy
instance, we noticed the integrated GTB ("Galaxy Track Browser").
So my question is: Is there a roadmap for further support / development of the
GTB?
Or will it perhaps get replaced/deprecated in the near future (we read a lot of
UCSC Genome Browser - Galaxy - Integration)?
Another question would be on good sources/tutorials/manuals for configuring and
setup for the GTB.
Mit freundlichen Grüßen
Matthias Enders
---
GERMAN SEED ALLIANCE GmbH
c/o Norddeutsche Pflanzenzucht
Hans-Georg Lembke KG
Hohenlieth, 24363 Holtsee
Tel.: +49 (0)4351/ 736-189
Fax: + 49 (0)4351/ 736-271
Mobil: +49 (0)151/ 14247360
Email: m.end...@german-seed-alliance.de
Firmensitz Köln
Amtsgericht Köln, HRB 73844
___
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/
[galaxy-dev] Problem with dependencies: Conda/freebayes
Following the suggestion from Devon Ryan @ https://biostar.usegalaxy.org/p/26197/ Our IT-people re-do the installation several times, until it works out. So it works on occasion.. Mit freundlichen Grüßen Matthias Enders --- GERMAN SEED ALLIANCE GmbH c/o Norddeutsche Pflanzenzucht Hans-Georg Lembke KG Hohenlieth, 24363 Holtsee Tel.: +49 (0)4351/ 736-189 Fax: + 49 (0)4351/ 736-271 Mobil: +49 (0)151/ 14247360 Email: m.end...@german-seed-alliance.de Firmensitz Köln Amtsgericht Köln, HRB 73844 -Ursprüngliche Nachricht- Von: galaxy-dev [mailto:galaxy-dev-boun...@lists.galaxyproject.org] Im Auftrag von galaxy-dev-requ...@lists.galaxyproject.org Gesendet: Donnerstag, 11. Januar 2018 18:00 An: galaxy-dev@lists.galaxyproject.org Betreff: galaxy-dev Digest, Vol 139, Issue 4 Priorität: Hoch Send galaxy-dev mailing list submissions to galaxy-dev@lists.galaxyproject.org To subscribe or unsubscribe via the World Wide Web, visit https://lists.galaxyproject.org/listinfo/galaxy-dev or, via email, send a message with subject or body 'help' to galaxy-dev-requ...@lists.galaxyproject.org You can reach the person managing the list at galaxy-dev-ow...@lists.galaxyproject.org When replying, please edit your Subject line so it is more specific than "Re: Contents of galaxy-dev digest..." HEY! This is important! If you reply to a thread in a digest, please 1. Change the subject of your response from "Galaxy-dev Digest Vol ..." to the original subject for the thread. 2. Strip out everything else in the digest that is not part of the thread you are responding to. Why? 1. This will keep the subject meaningful. People will have some idea from the subject line if they should read it or not. 2. Not doing this greatly increases the number of emails that match search queries, but that aren't actually informative. Today's Topics: 1. Re: Problem with dependencies: Conda/freebayes (Björn Grüning) 2. Re: Problem with dependencies: Conda/freebayes (Devon Ryan) 3. Re: Problems installing conda dependencies for seq2hlatool (Peter Briggs) 4. Re: Problem with dependencies: Conda/freebayes (Jennifer Hillman-Jackson) -- Message: 1 Date: Thu, 11 Jan 2018 09:44:10 +0100 From: Björn Grüning <bjoern.gruen...@gmail.com> To: Matthias Enders <m.end...@german-seed-alliance.de>, "galaxy-dev@lists.galaxyproject.org" <galaxy-dev@lists.galaxyproject.org> Cc: Fabian Kaiser <f.kai...@npz-innovation.de> Subject: Re: [galaxy-dev] Problem with dependencies: Conda/freebayes Message-ID: <2b047e78-2a48-02e2-b413-8c597d0d5...@gmail.com> Content-Type: text/plain; charset=utf-8; format=flowed Hi Matthias, sorry for answering so late! Do you have any error message from the logs during installation? What means it is not recognised by Galaxy? Do you see the conda environment in /tool_deps/_conda/ ? Is freebayes crashing? Ciao, Bjoern > Dear Galaxy Dev Mailing List, > > We encountered a problem while installing freebayes and its via Tool > Shed. > > Galaxy installed correctly freebayes (1.1.0.46); samtools (0.1.19); > gawk (4.1.3) (all have the Current Installation Status "Installed > through Conda") but then failed on the last dependency "parallel". > (Status: "Not Installed") > > The strange thing is: parallel was installed correctly. Its callable > from the command line, (e.g. parallel --help works fine) and installed > with the latest version. But it's not recognized by Galaxy. > > We are using the Galaxy - Docker image in Version 17.09. > > Can you please assist us in resolving this? > > Mit freundlichen Grüßen > > Matthias Enders > -- > - > > > > GERMAN SEED ALLIANCE GmbH c/o Norddeutsche Pflanzenzucht Hans-Georg > Lembke KG Hohenlieth, 24363 Holtsee Tel.: +49 (0)4351/ 736-189 Fax: + > 49 (0)4351/ 736-271 Mobil: +49 (0)151/ 14247360 > > Email: m.end...@german-seed-alliance.de > > Firmensitz Köln Amtsgericht Köln, HRB 73844 > > -Ursprüngliche Nachricht- Von: galaxy-dev > [mailto:galaxy-dev-boun...@lists.galaxyproject.org] Im Auftrag von > galaxy-dev-requ...@lists.galaxyproject.org Gesendet: Donnerstag, 21. > Dezember 2017 18:00 An: galaxy-dev@lists.galaxyproject.org Betreff: > galaxy-dev Digest, Vol 138, Issue 9 > > Send galaxy-dev mailing list submissions to > galaxy-dev@lists.galaxyproject.org > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.galaxyproject.org/listinfo/galaxy-dev or, via email, > send a message with subject or body 'help' to > galaxy-dev-requ
[galaxy-dev] Archive of Histories
Dear Dev Mailing List, is there any possibility build into galaxy to "archive" histories? By "archive" I mean not deleting them, but hiding them from the normal views? Many thanks in advance! Mit freundlichen Grüßen Matthias Enders --- GERMAN SEED ALLIANCE GmbH c/o Norddeutsche Pflanzenzucht Hans-Georg Lembke KG Hohenlieth, 24363 Holtsee Tel.: +49 (0)4351/ 736-189 Fax: + 49 (0)4351/ 736-271 Mobil: +49 (0)151/ 14247360 Email: m.end...@german-seed-alliance.de Firmensitz Köln Amtsgericht Köln, HRB 73844 -Ursprüngliche Nachricht- Von: galaxy-dev [mailto:galaxy-dev-boun...@lists.galaxyproject.org] Im Auftrag von galaxy-dev-requ...@lists.galaxyproject.org Gesendet: Dienstag, 23. Januar 2018 18:00 An: galaxy-dev@lists.galaxyproject.org Betreff: galaxy-dev Digest, Vol 139, Issue 12 Send galaxy-dev mailing list submissions to galaxy-dev@lists.galaxyproject.org To subscribe or unsubscribe via the World Wide Web, visit https://lists.galaxyproject.org/listinfo/galaxy-dev or, via email, send a message with subject or body 'help' to galaxy-dev-requ...@lists.galaxyproject.org You can reach the person managing the list at galaxy-dev-ow...@lists.galaxyproject.org When replying, please edit your Subject line so it is more specific than "Re: Contents of galaxy-dev digest..." HEY! This is important! If you reply to a thread in a digest, please 1. Change the subject of your response from "Galaxy-dev Digest Vol ..." to the original subject for the thread. 2. Strip out everything else in the digest that is not part of the thread you are responding to. Why? 1. This will keep the subject meaningful. People will have some idea from the subject line if they should read it or not. 2. Not doing this greatly increases the number of emails that match search queries, but that aren't actually informative. Today's Topics: 1. GCCBOSC 2018 Training Topic Voting is now open (Dave Clements) -- Message: 1 Date: Mon, 22 Jan 2018 11:06:01 -0800 From: Dave Clements <cleme...@galaxyproject.org> To: Galaxy Dev List <galaxy-dev@lists.galaxyproject.org>, Galaxy Announcements List <galaxy-annou...@lists.galaxyproject.org> Cc: GCCBOSC 2018 Organizers <gccbosc2018-...@lists.galaxyproject.org> Subject: [galaxy-dev] GCCBOSC 2018 Training Topic Voting is now open Message-ID: <CA+He-X_e7frd_nT8dK0-XieKdZ+q0fOSgqJdv32TsK1MFcD=v...@mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hello all, Voting is now open <http://bit.ly/gccbosc2018-vote> on what training topics <https://galaxyproject.org/events/gccbosc2018/training/> will be offered at GCCBOSC 2018 <https://gccbosc2018.sched.com/>. Your vote <http://bit.ly/gccbosc2018-vote> will determine the topics that are offered, which topics should be offered more than once, and which ones should not be scheduled at the same time. Your vote matters. *Topic voting closes January 31.* The Training schedule, including instructors, will be published before early registration opens. GCCBOSC2018 <https://gccbosc2018.sched.com/> will be held 25-30 June in Portland, Oregon, United States. It will feature two days of training: the second of which is multi-track and will feature content for both the BOSC and Galaxy communities. Workshops will be hands-on and participants will be strongly encouraged to bring a laptop and follow along. If you work in data-intensive biomedical research, there is no better place than GCCBOSC 2018 to present your work and to learn from others. Thanks, and see you in Portland! The GCCBOSC 2018 Organizers <https://galaxyproject.org/events/gccbosc2018/organizers> -- https://galaxyproject.org/ https://usegalaxy.org/ -- next part -- An HTML attachment was scrubbed... URL: <https://lists.galaxyproject.org/pipermail/galaxy-dev/attachments/20180122/31486ca7/attachment-0001.html> -- Subject: Digest Footer ___ galaxy-dev mailing list galaxy-dev@lists.galaxyproject.org https://lists.galaxyproject.org/listinfo/galaxy-dev To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- End of galaxy-dev Digest, Vol 139, Issue 12 *** ___ 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/
[galaxy-dev] Problem with dependencies: Conda/freebayes
Dear Galaxy Dev Mailing List, We encountered a problem while installing freebayes and its via Tool Shed. Galaxy installed correctly freebayes (1.1.0.46); samtools (0.1.19); gawk (4.1.3) (all have the Current Installation Status "Installed through Conda") but then failed on the last dependency "parallel". (Status: "Not Installed") The strange thing is: parallel was installed correctly. Its callable from the command line, (e.g. parallel --help works fine) and installed with the latest version. But it's not recognized by Galaxy. We are using the Galaxy - Docker image in Version 17.09. Can you please assist us in resolving this? Mit freundlichen Grüßen Matthias Enders --- GERMAN SEED ALLIANCE GmbH c/o Norddeutsche Pflanzenzucht Hans-Georg Lembke KG Hohenlieth, 24363 Holtsee Tel.: +49 (0)4351/ 736-189 Fax: + 49 (0)4351/ 736-271 Mobil: +49 (0)151/ 14247360 Email: m.end...@german-seed-alliance.de Firmensitz Köln Amtsgericht Köln, HRB 73844 -Ursprüngliche Nachricht- Von: galaxy-dev [mailto:galaxy-dev-boun...@lists.galaxyproject.org] Im Auftrag von galaxy-dev-requ...@lists.galaxyproject.org Gesendet: Donnerstag, 21. Dezember 2017 18:00 An: galaxy-dev@lists.galaxyproject.org Betreff: galaxy-dev Digest, Vol 138, Issue 9 Send galaxy-dev mailing list submissions to galaxy-dev@lists.galaxyproject.org To subscribe or unsubscribe via the World Wide Web, visit https://lists.galaxyproject.org/listinfo/galaxy-dev or, via email, send a message with subject or body 'help' to galaxy-dev-requ...@lists.galaxyproject.org You can reach the person managing the list at galaxy-dev-ow...@lists.galaxyproject.org When replying, please edit your Subject line so it is more specific than "Re: Contents of galaxy-dev digest..." HEY! This is important! If you reply to a thread in a digest, please 1. Change the subject of your response from "Galaxy-dev Digest Vol ..." to the original subject for the thread. 2. Strip out everything else in the digest that is not part of the thread you are responding to. Why? 1. This will keep the subject meaningful. People will have some idea from the subject line if they should read it or not. 2. Not doing this greatly increases the number of emails that match search queries, but that aren't actually informative. Today's Topics: 1. Re: Galaxy v17.09 impersonation doesn't work (Ping Luo) -- Message: 1 Date: Wed, 20 Dec 2017 13:52:45 -0600 From: Ping Luo <luop0...@gmail.com> To: Hans-Rudolf Hotz <h...@fmi.ch> Cc: galaxy-dev <galaxy-dev@lists.galaxyproject.org> Subject: Re: [galaxy-dev] Galaxy v17.09 impersonation doesn't work Message-ID: <CA+58tPaRSi0OPWPE9-YqZJr_o+LY7szbdY3sLz3PkKXY=ad...@mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hans-Rudolf, I just started a brand new galaxy with the default internal database. I did the minimal change to galaxy.ini so that I could use CAS authentication. Still, impersonation failed. Ping On Wed, Dec 20, 2017 at 3:02 AM, Hans-Rudolf Hotz <h...@fmi.ch> wrote: > Hi Ping > > > Does it work with a fresh installation ( v17.09) staring with an empty > PostgrSQL database? > > > Hans-Rudolf > > On 12/19/2017 03:41 PM, Ping Luo wrote: > >> Hans-Rudolf, >> >> Yes, I have set the flag to be true >> >> # Allow administrators to log in as other users (useful for >> debugging) >> allow_user_impersonation = True >> >> We use CAS authentication and our database is Postgresql. Our current >> Galaxy is v15.07 and impersonation works well. I have tried v16.10 >> before and impersonation didn't work either. >> >> Thanks, >> >> Ping >> >> On Tue, Dec 19, 2017 at 5:12 AM, Hans-Rudolf Hotz <h...@fmi.ch >> <mailto:h...@fmi.ch>> wrote: >> >> Hi Ping >> >> The 'impersonate a user' function works for me with v17.09. >> >> >> I assume, you have set: "allow_user_impersonation = True" in the >> galaxy.ini file? >> >> >> Do you encounter this problem, for the first time, i.e did it work >> before using (v17.05 or earlier) and you only have the issues after >> upgrading? >> >> What database do you use? >> >> Do you use external authentication? >> >> >> Regards, Hans-Rudolf >> >> >> >> >> >> >> On 12/18/2017 05:22 PM, Ping Luo wrote: >> >> The impersonation feature in Galaxy v17.09 doesn't work as >> expected. >> >> After clickin
Re: [galaxy-dev] Expose Command Line in Galaxy
Dear all, finally a restart of the container solved the issue with the database/blast. Regarding the problem with the command line: For other tools, the command line showed up, but not for blastn, as the wrapper encountered the error before creating the command line (this is my interpretation). So the error: "An invalid option was selected for database, 'myCoolDatabaseName', please verify." Was produced by the wrapper, which did not find the new database before restarting the galaxy container. So the real issue here is perhaps more on "How could blast+ be made aware of new integrated databases, without restarting"? Mit freundlichen Grüßen Matthias Enders --- GERMAN SEED ALLIANCE GmbH c/o Norddeutsche Pflanzenzucht Hans-Georg Lembke KG Hohenlieth, 24363 Holtsee Tel.: +49 (0)4351/ 736-189 Fax: + 49 (0)4351/ 736-271 Mobil: +49 (0)151/ 14247360 Email: m.end...@german-seed-alliance.de Firmensitz Köln Amtsgericht Köln, HRB 73844 -Ursprüngliche Nachricht- Von: Peter Cock Gesendet: Dienstag, 10. Juli 2018 12:11 An: Matthias Enders Cc: Björn Grüning ; galaxy-dev@lists.galaxyproject.org Betreff: Re: [galaxy-dev] Expose Command Line in Galaxy There is a setting to enable showing the command line string and full paths on disk via the "i" icon from a history entry, see https://docs.galaxyproject.org/en/master/admin/options.html#expose-dataset-path # This option allows users to see the full path of datasets via the # "View Details" option in the history. This option also exposes the # command line to non-administrative users. Administrators can always # see dataset paths. #expose_dataset_path: false https://github.com/galaxyproject/galaxy/blob/release_18.05/config/galaxy.yml.sample#L1495 It existed in galaxy.ini too, which has since be replaced by galaxy.yml Peter On Tue, Jul 10, 2018 at 8:19 AM, Matthias Enders wrote: > Dear Björn, > > thanks for the very fast reply. Unfortunately, this part is not visible in > our instance. (see screenshot). As you can see in the topmost bar, this is > done, while being loged in as admin. > > Mit freundlichen Grüßen > > Matthias Enders > -- > - > > > GERMAN SEED ALLIANCE GmbH > c/o Norddeutsche Pflanzenzucht > Hans-Georg Lembke KG > Hohenlieth, 24363 Holtsee > Tel.: +49 (0)4351/ 736-189 > Fax: + 49 (0)4351/ 736-271 > Mobil: +49 (0)151/ 14247360 > > Email: m.end...@german-seed-alliance.de > > Firmensitz Köln > Amtsgericht Köln, HRB 73844 > > -Ursprüngliche Nachricht- > Von: Björn Grüning > Gesendet: Dienstag, 10. Juli 2018 09:15 > An: Matthias Enders ; > galaxy-dev@lists.galaxyproject.org > Betreff: Re: [galaxy-dev] Expose Command Line in Galaxy > Priorität: Hoch > > Hi Matthias, > > please have a look at the attached screenshot. Given that you are an admin > and click on the info-symbol of the dataset you should see the commandline. > > This is with a 18.05 Docker. > Cheers, > Bjoern > > Am 10.07.2018 um 08:58 schrieb Matthias Enders: >> Dear Galaxy Community, >> >> is there any possibility to expose the command line call, generated >> within galaxy? >> >> We searched the net and found this discussions: >> https://github.com/galaxyproject/galaxy/issues/3252 >> https://github.com/galaxyproject/galaxy/issues/2954 >> >> But both are on the exposure to non-admin users. Within our instance >> we see the command line call nor for admin, neither for normal users! >> >> ... ___ 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/
[galaxy-dev] Expose Command Line in Galaxy
Dear Galaxy Community, is there any possibility to expose the command line call, generated within galaxy? We searched the net and found this discussions: https://github.com/galaxyproject/galaxy/issues/3252 https://github.com/galaxyproject/galaxy/issues/2954 But both are on the exposure to non-admin users. Within our instance we see the command line call nor for admin, neither for normal users! The problem, behind the question is the error message: "An invalid option was selected for database, 'myCoolDatabaseName', please verify." In Blast (toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.2.01) Local (directly from command line, without Galaxy in between) the blast works fine. We are using the 18.05 Docker Galaxy Version. Thanks in advance! Mit freundlichen Grüßen Matthias Enders --- GERMAN SEED ALLIANCE GmbH c/o Norddeutsche Pflanzenzucht Hans-Georg Lembke KG Hohenlieth, 24363 Holtsee Tel.: +49 (0)4351/ 736-189 Fax: + 49 (0)4351/ 736-271 Mobil: +49 (0)151/ 14247360 Email: m.end...@german-seed-alliance.de Firmensitz Köln Amtsgericht Köln, HRB 73844 -Ursprüngliche Nachricht- Von: galaxy-dev Im Auftrag von galaxy-dev-requ...@lists.galaxyproject.org Gesendet: Montag, 9. Juli 2018 18:00 An: galaxy-dev@lists.galaxyproject.org Betreff: galaxy-dev Digest, Vol 145, Issue 3 Send galaxy-dev mailing list submissions to galaxy-dev@lists.galaxyproject.org To subscribe or unsubscribe via the World Wide Web, visit https://lists.galaxyproject.org/listinfo/galaxy-dev or, via email, send a message with subject or body 'help' to galaxy-dev-requ...@lists.galaxyproject.org You can reach the person managing the list at galaxy-dev-ow...@lists.galaxyproject.org When replying, please edit your Subject line so it is more specific than "Re: Contents of galaxy-dev digest..." HEY! This is important! If you reply to a thread in a digest, please 1. Change the subject of your response from "Galaxy-dev Digest Vol ..." to the original subject for the thread. 2. Strip out everything else in the digest that is not part of the thread you are responding to. Why? 1. This will keep the subject meaningful. People will have some idea from the subject line if they should read it or not. 2. Not doing this greatly increases the number of emails that match search queries, but that aren't actually informative. Today's Topics: 1. From Paste to uWSGI (Jochen Bick) 2. Re: From Paste to uWSGI (Peter Briggs) 3. Re: From Paste to uWSGI (Martin Čech) -- Message: 1 Date: Mon, 9 Jul 2018 13:49:23 +0200 From: Jochen Bick To: "galaxy-dev@lists.galaxyproject.org" Subject: [galaxy-dev] From Paste to uWSGI Message-ID: <1a0f33ad-938c-64d5-8db8-28914a5ca...@usys.ethz.ch> Content-Type: text/plain; charset="utf-8"; format=flowed Hi all, we would like to update to 18.05 and thereby also update our Paste Server. https://docs.galaxyproject.org/en/latest/admin/scaling.html Is there any tutorial on how to update from Paste to uWSGI? Cheers Jochen -- ETH Zurich *Jochen Bick* Animal Physiology Institute of Agricultural Sciences Postal address: Universitätstrasse 2 / LFW B 58.1 8092 Zurich, Switzerland Office: Eschikon 27 8315 Lindau, Switzerland Phone +41 52 354 92 06 jochen.b...@usys.ethz.ch <mailto:jochen.b...@usys.ethz.ch> www.ap.ethz.ch -- Message: 2 Date: Mon, 9 Jul 2018 15:31:16 + From: Peter Briggs To: Jochen Bick , "galaxy-dev@lists.galaxyproject.org" Subject: Re: [galaxy-dev] From Paste to uWSGI Message-ID: Content-Type: text/plain; charset="iso-8859-1" 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
Re: [galaxy-dev] Expose Command Line in Galaxy
Dear Peter, up to our galaxy admin, we make use of the Data Manager, so this seems not to be the issue here?: [cid:image001.jpg@01D41868.AAB17910] Mit freundlichen Grüßen Matthias Enders --- GERMAN SEED ALLIANCE GmbH c/o Norddeutsche Pflanzenzucht Hans-Georg Lembke KG Hohenlieth, 24363 Holtsee Tel.: +49 (0)4351/ 736-189 Fax: + 49 (0)4351/ 736-271 Mobil: +49 (0)151/ 14247360 Email: m.end...@german-seed-alliance.de Firmensitz Köln Amtsgericht Köln, HRB 73844 -Ursprüngliche Nachricht- Von: Peter Cock Gesendet: Dienstag, 10. Juli 2018 13:27 An: Matthias Enders Cc: Björn Grüning ; galaxy-dev@lists.galaxyproject.org Betreff: Re: [galaxy-dev] Expose Command Line in Galaxy Priorität: Hoch Thanks for getting back to us - this was actually my guess from the original email - that it was not a blastn error message, but a Galaxy message before ever calling BLAST. My guess is you are seeing this issue, or something like it, with having to restart Galaxy to reload the *.loc files? https://github.com/galaxyproject/galaxy/issues/3171 Peter On Tue, Jul 10, 2018 at 12:22 PM, Matthias Enders mailto:m.end...@german-seed-alliance.de>> wrote: > Dear all, > > finally a restart of the container solved the issue with the database/blast. > > Regarding the problem with the command line: > For other tools, the command line showed up, but not for blastn, as the > wrapper encountered the error before creating the command line (this is my > interpretation). > > So the error: "An invalid option was selected for database, > 'myCoolDatabaseName', please verify." Was produced by the wrapper, which did > not find the new database before restarting the galaxy container. > > So the real issue here is perhaps more on "How could blast+ be made aware of > new integrated databases, without restarting"? > > Mit freundlichen Grüßen > > Matthias Enders ___ 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/
Re: [galaxy-dev] Expose Command Line in Galaxy
Dear Peter, the reloading of the blast *.loc files did not solve the Problem. Actually only a complete restart of the container solved the problem for us. Mit freundlichen Grüßen Matthias Enders --- [cid:image001.png@01D03960.8254BEE0] GERMAN SEED ALLIANCE GmbH c/o Norddeutsche Pflanzenzucht Hans-Georg Lembke KG Hohenlieth, 24363 Holtsee Tel.: +49 (0)4351/ 736-189 Fax: + 49 (0)4351/ 736-271 Mobil: +49 (0)151/ 14247360 Email: m.end...@german-seed-alliance.de<mailto:m.end...@german-seed-alliance.de> Firmensitz Köln Amtsgericht Köln, HRB 73844 Von: Peter Cock Gesendet: Mittwoch, 11. Juli 2018 16:12 An: Matthias Enders Cc: Björn Grüning ; galaxy-dev@lists.galaxyproject.org; f.kai...@npz.de Betreff: Re: [galaxy-dev] Expose Command Line in Galaxy Good. So is everything resolved now? Peter On Wed, Jul 11, 2018 at 3:08 PM, Matthias Enders mailto:m.end...@german-seed-alliance.de>> wrote: Dear Peter, yes we did reload the Blast *.loc files using the admin interface. Our Version is 18.05 (based on the Galaxy – Docker image). Mit freundlichen Grüßen Matthias Enders ___ 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/
Re: [galaxy-dev] Expose Command Line in Galaxy
Dear Peter, we will re-create this problem with a new database in our instance, (to be sure on the reproducibility) and then raise an issue. Mit freundlichen Grüßen Matthias Enders --- [cid:image001.png@01D03960.8254BEE0] GERMAN SEED ALLIANCE GmbH c/o Norddeutsche Pflanzenzucht Hans-Georg Lembke KG Hohenlieth, 24363 Holtsee Tel.: +49 (0)4351/ 736-189 Fax: + 49 (0)4351/ 736-271 Mobil: +49 (0)151/ 14247360 Email: m.end...@german-seed-alliance.de<mailto:m.end...@german-seed-alliance.de> Firmensitz Köln Amtsgericht Köln, HRB 73844 Von: Peter Cock Gesendet: Mittwoch, 11. Juli 2018 16:42 An: Matthias Enders Cc: Björn Grüning ; galaxy-dev@lists.galaxyproject.org; f.kai...@npz.de Betreff: Re: [galaxy-dev] Expose Command Line in Galaxy You may have found a new Galaxy bug then :( Could you log an issue here: https://github.com/galaxyproject/galaxy/issues (From what you've said, I don't think that this is a problem in the BLAST+ wrappers themselves) Peter On Wed, Jul 11, 2018 at 3:20 PM, Matthias Enders mailto:m.end...@german-seed-alliance.de>> wrote: Dear Peter, the reloading of the blast *.loc files did not solve the Problem. Actually only a complete restart of the container solved the problem for us. Mit freundlichen Grüßen Matthias Enders ___ 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/
