Re: [galaxy-dev] Redirecting page after tool completes
Not that I am aware of, but given the run time of jobs is quite variable it seems confusing to have Galaxy suddenly switch focus - especially if I have another tool or visualisation open, or am looking at a particular datafile. However, if the user hasn't interacted with Galaxy since pressing the execute button (i.e. the job/workflow submitted page is still shown) then it would feel nice for Galaxy to auto- display the final history output when the job finishes? Peter On Mon, May 19, 2014 at 6:30 AM, neil.burd...@csiro.au wrote: Hi, I have a tool that generates some png files. These are viewed when you click on the eye symbol. I was wondering if there is a way to automatically redirect to this html page once the job completes without the user needing to click on the eye symbol? (as this could be a small part in a larger workflow) Thanks Neil ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] replacing XML fragments in mycustomtool.xml
This question was cross-posted on https://biostar.usegalaxy.org/p/7619/
Adding custom tools: resolving (external ) XML entities
I'd like to replace fragments of XML code in my custom tool declaration.
My first idea was to use XML entities but it seems that the XML engine
doesn't resolve them.
(BTW: I know I can replace/declare things in $PATH and
tool_dependencies.xml )
Another idea was to use macrostoken... but I cannot make it work
(see https://gist.github.com/lindenb/b2a04e0fefd4d295dba9 )
my macros definition:
?xml version=1.0?
macros
token
name=@JAVA_EXE@/usr/lib/jvm/jre-1.7.0-openjdk.x86_64/bin/java/token
token name=@JVM_OPTIONS@-Xmx500m/token
/macros my tool definition: as a test, I echoed the value of
@JAVA_EXE@ in /tmp/galaxy.txt (the macro was *not replaced* )
?xml version=1.0 encoding=UTF-8?
tool id=com_github_lindenb_jvarkit_tools_misc_VcfHead name=VcfHead
version=e098748b85acd5158a1ce612bd3d46e60948b9db hidden=false
descriptionPrint the first lines of a VCF/description
macros
importjvarkit_macros.xml/import
/macros
commandecho @JAVA_EXE@ gt; /tmp/galaxy.txt amp;amp; zcat -f
${input} | @JAVA_EXE@ @JVM_OPTIONS@ -cp
/commun/data/packages/htsjdk/dist/apache-ant-1.8.2-bzip2.jar:/commun/data/packages/htsjdk/dist/htsjdk-1.112.jar:/commun/data/packages/htsjdk/dist/commons-jexl-2.1.1.jar:/commun/data/packages/htsjdk/dist/commons-logging-1.1.1.jar:/commun/data/packages/jvarkit-git/vcfhead.jar
com.github.lindenb.jvarkit.tools.misc.VcfHead -n ${number} 2gt;
/dev/null gt; ${output}/command
inputs
param format=vcf name=input type=data label=Source VCF
optional=false/
param name=number type=integer value=10 label=Number of rows
optional=true/
/inputs
outputs
data format=input name=output metadata_source=input/
/outputs
helpsee https://github.com/lindenb/jvarkit/wiki/VcfHead/help
/tool the output of 'hg tip'
changeset: 9312:788cd3d06541
tag: tip
parent: 9310:19f6e62bd372
parent: 9311:d7f37a2fe690
user: Nate Coraor n...@bx.psu.edu
date: Mon Apr 08 12:30:08 2013 -0400
summary: Merged stable. what's wrong in my macros definition ? Thanks.
Pierre
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Re: [galaxy-dev] monitoring jobs start time
Il 2014-05-19 04:47 neil.burd...@csiro.au ha scritto: Hi, I am currently using the reports tool to see what jobs have been executed etc ... When you look at the information for each job it states the time the job was put on the queue (creation time) not the actual start time of the job. Do you know if the start time of the job is stored somewhere? Hi Neil, take a look at this pull request, which was merged recently in galaxy-central and will be available in the next Galaxy release: https://bitbucket.org/galaxy/galaxy-central/pull-request/352/implement-plugin-framework-and-plugins-for/diff Best, Nicola ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Get the user credentials from the tool.
Hello Dmitry,
Sorry the delayed response. It occurs to me that data source tools may
be an alternative I should have pointed you to right away -
https://wiki.galaxyproject.org/Admin/Internals/DataSources. I am not
sure they are a perfect fit but regular tools are not a perfect fit
either.
On Tue, May 6, 2014 at 4:26 AM, Dmitry redmi...@list.ru wrote:
Hello John,
If it is at all possible to send the data to the web service instead ...
Unfortunately, I cannot push the data to the web service, because this is
the BES one and the interface is defined in the spec.
As far as I understand reading the mailing list there is no way to pull data
through FTP (only upload).
This is correct.
The API key looks interesting even I do not completely understand it.
Is it possible to manipulate the key(s) programmatically?
It would be great to generate a temporal key, execute the service and remove
the key after that.
When you phrase the problem like this it occurs to me I recently added
this functionality to Galaxy. The LWR (a tool to remotely execute
Galaxy tools) can now be configured to pull files from and send files
to Galaxy with single purpose keys tied to particular jobs. The
details are outlined in the following pull request
(https://bitbucket.org/galaxy/galaxy-central/pull-request/327/implement-job-files-api/diff).
Piggy backing on this is probably the right way to go because you
don't have to worry about whether user's have API keys defined - jobs
have implicit keys not users.
If you wanted to go down this road - you will need to throw Galaxy's
job object or at least the id into the context Galaxy uses to evaluate
tool xml files. This patch
https://gist.github.com/jmchilton/ddec237d2ad63821addc for instances
SHOULD give tools access to a $__job_id__ variable (haven't tested
it).
Then you should be able to construct URLs inside of your Galaxy XML
for your inputs and outputs as follows:
#set $encode_job_id = ${__app__.security.encode_id( $__job_id__ )}
#set $job_key = ${__app__.security.encode_id( $__job_id__, kind=jobs_files ) }
#set $input_path = str($input)
--url
http://mygalaxy.com/api/files/$encode_job_id/files?job_key=$job_keypath=$input_pathfile_type=input;
#set $encode_job_id = ${__app__.security.encode_id( $__job_id__ )}
#set $job_key = ${__app__.security.encode_id( $__job_id__, kind=jobs_files ) }
#set $output_path = str($output)
--output_url
http://mygalaxy.com/api/files/$encode_job_id/files?job_key=$job_keypath=$output_pathfile_type=output;
This API endpoint I believe will respond to GETs for the inputs and
POSTs for the output.
There are probably some syntax errors in above tool/cheetah snipplets
(Galaxy doesn't formally support this, I am just giving you some
informal advice on how one might proceed).
In general I would discourage this because it is difficult to do in a
generic way ...
I understand that the problem is when Galaxy is behind a proxy. In my case I
control the URL for the galaxy.
${ __app__.model.User.get( $__user_id__ ).api_keys[0].key }
Again, wouldn't need this if you are using the newer job files API endpoint.
Obviously this e-mail is very informal and hand-wavy because I am
likely too busy to walk through and verify all of these steps. But I
have created a Trello card (https://trello.com/c/JjIF9l4h) to keep
track of this feature request and outline this approach, I will try to
find some time to think about this use case some more in the future.
Sorry I don't have more time to give you a more complete response.
Galaxy is generally very focused on wrapping command-line utilities
for analysis and it doesn't necessarily target web services like this
very well.
-John
I absolutely lost here...
should I know $__user_id__ or this is a variable already known to the tool?
Thank you very much for the help,
Dmitry
On 5/6/2014 4:39 AM, John Chilton wrote:
Hello Dmitry,
This use case isn't really addressed by Galaxy currently.
There is not a generic way of doing grabbing the users credentials
like this or producing URLs from inside the tool. This depends on a
lot of different things - how Galaxy's proxy is configured, etc... so
in many (all?) cases Galaxy would not be able to fetch the users raw
credentials. Your best bet is going to be to use the Galaxy's API -
tools can fetch a user's API key and you can use Galaxy's API to build
a URL that includes this key.
Your users will all need API keys set to use the tool. There have been
some other galaxy-dev discussions about using the API from tools -
http://osdir.com/ml/galaxy-development-source-control/2013-12/msg00105.html.
In general I would discourage this because it is difficult to do in a
generic way - for instance there is no way for the tool to accurately
determine what the URL of Galaxy should be - but it should be possible
to tailor something to your setup if absolutely needed.
If you are really keen to use the Galaxy API to do this and you
understand the
Re: [galaxy-dev] user specific access/options
Hi Emma Have a look at https://wiki.galaxyproject.org/Admin/Config/Access%20Control and https://wiki.galaxyproject.org/UserDefinedToolboxFilters as an alternative you could also do a bad hack using dynamic_options Regards, Hans-Rudolf On 05/19/2014 10:38 AM, Emma Prudent wrote: Hi, I am currently an intern and I work on galaxy, particularly on this acces problem. So I am very interested in the answers that could be given to this question. Thanks to you, Emma Prudent Hi Petr, I am going to forward your email to the galaxy-dev list so that the development community can offer comments/suggestions. Best, Jen Galaxy team On 8/30/11 2:27 AM, Petr Novak wrote: / Hi everybody, // I am developing the application on Galaxy server. One of the requirement // is to create user specific list of options. Is it possible to access // somehow $__user_email__ in options tag or in conditional ?. I did // not found documentation how to used cheetah in galaxy tool xml files but // from files provided with galaxy, cheetah is used only in command and // config tag. Is that rigth? If it can be used in any part of xml // definition file it would make much easier to generate xml dynamicaly // based on the $__user_email__ // Does anybody have an idea how to manage this problem? // Petr Novak/ ___ 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: http://lists.bx.psu.edu/ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] ToolShed: Uploaded archives can only include regular directories and files
Hi Greg, Dave, I just tried to upload an updated tar-ball to the Test ToolShed and got a red error message: quote Uploaded archives can only include regular directories and files (no symbolic links, devices, etc). Offender: /quote Note no offending files were listed. When I double checked I had prepared my tar-ball from the wrong source directory and it did contain symlinks, but the Tool Shed error message failed to list these. Regards, 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] workflow delete cancelled but workflows are still deleted
I am working in the galaxy-dist stable branch. I select a workflow and select Delete. An alert pops up asking if I'm sure I want to do that. I press Cancel and the alert disappears, along with the workflow. This shouldn't happen. Cheers, -Evan Bollig Research Associate | Application Developer | User Support Consultant Minnesota Supercomputing Institute 599 Walter Library 612 624 1447 e...@msi.umn.edu boll0...@umn.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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Fwd: InvalidVersionError: 103 is not 105
Hey Dannon, I managed to resolve this on my own. The postgres version is 9.1, and I'm on Ubuntu 12.04. The instance is an OpenStack VM. It turned out that the dir contained files that were outdated from a previous version of galaxy-dist. After I realized that they were part of hgignore, I ran hg clean --all to make sure I was working with a fresh install. Cheers, -E -Evan Bollig Research Associate | Application Developer | User Support Consultant Minnesota Supercomputing Institute 599 Walter Library 612 624 1447 e...@msi.umn.edu boll0...@umn.edu On Fri, May 16, 2014 at 2:39 PM, Dannon Baker dannon.ba...@gmail.com wrote: On Fri, May 16, 2014 at 3:33 PM, Evan Bollig boll0...@umn.edu wrote: InvalidVersionError: 103 is not 105 This would indicate to me that migration script 104 failed. My question is: why can't the manage_db.sh upgrade step be included automatically when the initial DB build fails? It is, in a sense, hence all the other migration steps. Can you provide more details about your configuration? Postgres version, whether you're using a virtualenv (or not), or anything else you think seems relevant? -Dannon ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Fwd: InvalidVersionError: 103 is not 105
Ok, great, glad you're up and running! I'll scratch this one off the list of things to think about. On Mon, May 19, 2014 at 4:00 PM, Evan Bollig boll0...@umn.edu wrote: Hey Dannon, I managed to resolve this on my own. The postgres version is 9.1, and I'm on Ubuntu 12.04. The instance is an OpenStack VM. It turned out that the dir contained files that were outdated from a previous version of galaxy-dist. After I realized that they were part of hgignore, I ran hg clean --all to make sure I was working with a fresh install. Cheers, -E -Evan Bollig Research Associate | Application Developer | User Support Consultant Minnesota Supercomputing Institute 599 Walter Library 612 624 1447 e...@msi.umn.edu boll0...@umn.edu On Fri, May 16, 2014 at 2:39 PM, Dannon Baker dannon.ba...@gmail.com wrote: On Fri, May 16, 2014 at 3:33 PM, Evan Bollig boll0...@umn.edu wrote: InvalidVersionError: 103 is not 105 This would indicate to me that migration script 104 failed. My question is: why can't the manage_db.sh upgrade step be included automatically when the initial DB build fails? It is, in a sense, hence all the other migration steps. Can you provide more details about your configuration? Postgres version, whether you're using a virtualenv (or not), or anything else you think seems relevant? -Dannon ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Get the user credentials from the tool.
Hello John,
Thank you very much for the very extended response.
It seems I have enough reading to be calm for a month :-).
Thank you again,
Dmitry
On 5/19/2014 4:42 PM, John Chilton wrote:
Hello Dmitry,
Sorry the delayed response. It occurs to me that data source tools may
be an alternative I should have pointed you to right away -
https://wiki.galaxyproject.org/Admin/Internals/DataSources. I am not
sure they are a perfect fit but regular tools are not a perfect fit
either.
On Tue, May 6, 2014 at 4:26 AM, Dmitry redmi...@list.ru wrote:
Hello John,
If it is at all possible to send the data to the web service instead ...
Unfortunately, I cannot push the data to the web service, because this is
the BES one and the interface is defined in the spec.
As far as I understand reading the mailing list there is no way to pull data
through FTP (only upload).
This is correct.
The API key looks interesting even I do not completely understand it.
Is it possible to manipulate the key(s) programmatically?
It would be great to generate a temporal key, execute the service and remove
the key after that.
When you phrase the problem like this it occurs to me I recently added
this functionality to Galaxy. The LWR (a tool to remotely execute
Galaxy tools) can now be configured to pull files from and send files
to Galaxy with single purpose keys tied to particular jobs. The
details are outlined in the following pull request
(https://bitbucket.org/galaxy/galaxy-central/pull-request/327/implement-job-files-api/diff).
Piggy backing on this is probably the right way to go because you
don't have to worry about whether user's have API keys defined - jobs
have implicit keys not users.
If you wanted to go down this road - you will need to throw Galaxy's
job object or at least the id into the context Galaxy uses to evaluate
tool xml files. This patch
https://gist.github.com/jmchilton/ddec237d2ad63821addc for instances
SHOULD give tools access to a $__job_id__ variable (haven't tested
it).
Then you should be able to construct URLs inside of your Galaxy XML
for your inputs and outputs as follows:
#set $encode_job_id = ${__app__.security.encode_id( $__job_id__ )}
#set $job_key = ${__app__.security.encode_id( $__job_id__, kind=jobs_files ) }
#set $input_path = str($input)
--url
http://mygalaxy.com/api/files/$encode_job_id/files?job_key=$job_keypath=$input_pathfile_type=input;
#set $encode_job_id = ${__app__.security.encode_id( $__job_id__ )}
#set $job_key = ${__app__.security.encode_id( $__job_id__, kind=jobs_files ) }
#set $output_path = str($output)
--output_url
http://mygalaxy.com/api/files/$encode_job_id/files?job_key=$job_keypath=$output_pathfile_type=output;
This API endpoint I believe will respond to GETs for the inputs and
POSTs for the output.
There are probably some syntax errors in above tool/cheetah snipplets
(Galaxy doesn't formally support this, I am just giving you some
informal advice on how one might proceed).
In general I would discourage this because it is difficult to do in a
generic way ...
I understand that the problem is when Galaxy is behind a proxy. In my case I
control the URL for the galaxy.
${ __app__.model.User.get( $__user_id__ ).api_keys[0].key }
Again, wouldn't need this if you are using the newer job files API endpoint.
Obviously this e-mail is very informal and hand-wavy because I am
likely too busy to walk through and verify all of these steps. But I
have created a Trello card (https://trello.com/c/JjIF9l4h) to keep
track of this feature request and outline this approach, I will try to
find some time to think about this use case some more in the future.
Sorry I don't have more time to give you a more complete response.
Galaxy is generally very focused on wrapping command-line utilities
for analysis and it doesn't necessarily target web services like this
very well.
-John
I absolutely lost here...
should I know $__user_id__ or this is a variable already known to the tool?
Thank you very much for the help,
Dmitry
On 5/6/2014 4:39 AM, John Chilton wrote:
Hello Dmitry,
This use case isn't really addressed by Galaxy currently.
There is not a generic way of doing grabbing the users credentials
like this or producing URLs from inside the tool. This depends on a
lot of different things - how Galaxy's proxy is configured, etc... so
in many (all?) cases Galaxy would not be able to fetch the users raw
credentials. Your best bet is going to be to use the Galaxy's API -
tools can fetch a user's API key and you can use Galaxy's API to build
a URL that includes this key.
Your users will all need API keys set to use the tool. There have been
some other galaxy-dev discussions about using the API from tools -
http://osdir.com/ml/galaxy-development-source-control/2013-12/msg00105.html.
In general I would discourage this because it is difficult to do in a
generic way - for instance there is no way for the tool to accurately
determine what the URL of Galaxy should be - but it should
[galaxy-dev] GCC2014 Early Registration closes this Friday, May 23
Hello all, This just a reminder that early registrationhttps://wiki.galaxyproject.org/Events/GCC2014/Register for the 2014 Galaxy Community Conference (GCC2014)https://wiki.galaxyproject.org/Events/GCC2014 *closes this Friday, May 23* Register early and *avoid paying 70% more for regular registration costs.* Early registration is downright affordable, with combined registration (Training Dayhttps://wiki.galaxyproject.org/Events/GCC2014/TrainingDay + main meeting) starting at $140 for post-docs and students. Registering early assures you a place at the conference and also a spot in the Training Day workshopshttps://wiki.galaxyproject.org/Events/GCC2014/TrainingDayyou want to attend. And ... - The program https://wiki.galaxyproject.org/Events/GCC2014/Program , and abstracts https://wiki.galaxyproject.org/Events/GCC2014/Abstracts for all accepted talks are now available. - Registration for the GCC2014 hackathonhttps://wiki.galaxyproject.org/Events/GCC2014/Hackathon is also open (and also has limited capacity - register for that now toohttps://wiki.galaxyproject.org/Events/GCC2014/Hackathon ) - We are pleased to have Penguin Computinghttp://www.penguincomputing.com/as a Silver Sponsor for GCC2014 You are strongly encouraged to register this week. Registration is capped this year at 250 participants, *and we expect to hit that limit*. Thanks a bunch, and hope to see you in Baltimore! Dave C -- http://galaxyproject.org/GCC2014 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/ ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] The main Tool Shed is now tracking the next-stable branch in preparation for the upcoming Galaxy release
Hello all, The upcoming Galaxy release is currently scheduled for Monday, June 2. In preparation for this release, the main Galaxy Tool Shed is now tracking the next-stable branch and is currently running changeset 13542:11403745e7ce. The main Tool Shed will be regularly updated with any additions made to the next-stable branch between now and the upcoming Galaxy release. Please let us know if you encounter any issues. Thanks very much, Greg Von Kuster ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] error: flexbar dependency is not installed by the toolshed
Hi Guys, I tried to install flexbar from toolshed, but upon running, error said it could not find it. I checked and found idtoolshed.g2.bx.psu.edu/repos/jtilman/flexbar/flexbar/2.4/id in the config file, but this path does not exist. Is it that I need to install the dependency on my own? I had the impression that toolshed will do it for me. Please correct me if I'm wrong. 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Redirecting page after tool completes
Yes. I'm looking to auto display the final history output when the job finishes. It's pretty traightforward to get the URL to display i.e. http://'servername'/capaibl/datasets/5a1cff6882ddb5b2/display/?preview=True. However, I don't know how to use the URL to set it on the galaxy webpage. i.e. do I need to call something like h.url_for or something similar passing the target=galaxy_main. can i do this from my tool? Any help much appreciated Neil From: Peter Cock [p.j.a.c...@googlemail.com] Sent: Monday, May 19, 2014 6:25 PM To: Burdett, Neil (CCI, Herston - RBWH) Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Redirecting page after tool completes Not that I am aware of, but given the run time of jobs is quite variable it seems confusing to have Galaxy suddenly switch focus - especially if I have another tool or visualisation open, or am looking at a particular datafile. However, if the user hasn't interacted with Galaxy since pressing the execute button (i.e. the job/workflow submitted page is still shown) then it would feel nice for Galaxy to auto- display the final history output when the job finishes? Peter On Mon, May 19, 2014 at 6:30 AM, neil.burd...@csiro.au wrote: Hi, I have a tool that generates some png files. These are viewed when you click on the eye symbol. I was wondering if there is a way to automatically redirect to this html page once the job completes without the user needing to click on the eye symbol? (as this could be a small part in a larger workflow) Thanks Neil ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
