- galaxy-dev - lists.galaxyproject.org

How to send a file from galaxy to an external URL
by Delphine Lariviere 23 Aug '13

23 Aug '13

Dear Galaxy developers, I am a beginner in galaxy development and I need to build a tool to send a file from galaxy to an external URL. I tried to work with the following tutorial : http://wiki.galaxyproject.org/ **Admin/Tools/External%**20Display%20Applications%**20Tutorial<http://wiki.galaxyproject.org/Admin/Tools/External%20Display%20Applications…> But I couldn't make it work and it doesn't seem to fit exactly to what I want to do. I would be grateful if someone could help me with this issue, Thank you everyone, Delphine -- Delphine Larivière Ph.D Student in Bioinformatics CIRAD Data Integration Team email: delphine.lariviere(a)cirad.fr

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How to retrieve the current job ID
by Peng Li 22 Aug '13

22 Aug '13

Hi All I am working on one galaxy tool that could output results to database and I want to link the data records with galaxy job table by job id. Is it possible to retrieve the current job id in the tools config or tools code? I read the wikis and manuals and only find one Deprecated tag <code> has some clues like exec_after_job()? Does anyone know how to achieve this? Best regards -lee

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Stopping jobs by deleting history via API
by Sytchev, Ilya 22 Aug '13

22 Aug '13

Hi, I was wondering if there are any near term plans to fix this issue? https://trello.com/c/Tbota8xG/992-deleting-history-using-the-api-does-not-d elete-stop-jobs Thanks, Ilya

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developing a tool which could encapsulate any tool
by Ketan Maheshwari 22 Aug '13

22 Aug '13

Hi All, I am trying to develop a generic Galaxy tool which could encapsulate any other Galaxy tool and run it. The motivation behind this development is to enable running ordinary Galaxy tools in parallel with multiple datasets and/or running ordinary tools on large-scale compute resources. I was wondering about the Galaxy-way of doing this. Is there a natural pattern I could adapt here for this work? Are there any existing examples which does this? Thanks, -- Ketan

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Passing user_email to a data source
by Anthony Bretaudeau 22 Aug '13

22 Aug '13

Hello, I'm trying to add a new data source to my Galaxy instance, using synchronous data depositing. The data source needs to know the email address of the user who tries to import data to the Galaxy server. I would have like to write something like that: <inputs action="https://example.com/my/data/source" check_values="false" method="get"> <display>Browse the XX data source $GALAXY_URL</display> <param name="user_email" type="hidden" value="$__user_email__" /> </inputs> Then Galaxy would have generated this url: https://example.com/my/data/source?GALAXY_URL=http....&user_email=test@exam… But this doesn't work, because the $__user_email__ seems to be available only in <command> tag. I end up with this url which is useless: https://example.com/my/data/source?GALAXY_URL=http....&user_email=$__user_e… Is there any way to do what I need to do? It would be great if variables were available in <param> tags too. Otherwise, maybe I could write a custom tool type to do this. Is there any guideline for this? I have seen someone talking about that a few months ago, but with no answer: http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-September/011258.html Thanks for your help Regards Anthony Bretaudeau

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Re: [galaxy-dev] Galaxy Release Cycle Length
by Leon Mei 22 Aug '13

22 Aug '13

Hi Dave, I am one of the requesters on a less frequent release. Certainly this does not need to replace the current release scheme in the development branch: Galaxy system users who prefer keeping their code up to date can still go there. It is just nice to have a separate branch with a less frequent stable release cycle with the support of fixing major bugs as Hans-Rudolf pointed out. This fixing support is only needed on the latest stable release. Regarding the frequency of such a release, I would say it is a bit dependent on the speed of introducing new major features in Galaxy. I wouldn't mind to have a 4 or 6 month release cycle in the stable branch if they synchronize better with the major milestones in Galaxy. Thanks, Leon Message: 3 Date: Wed, 21 Aug 2013 08:57:22 +0200 From: Hans-Rudolf Hotz <hrh(a)fmi.ch> To: Dave Clements <clements(a)galaxyproject.org> Cc: Galaxy Dev List <galaxy-dev(a)bx.psu.edu> Subject: Re: [galaxy-dev] Galaxy Release Cycle Length Message-ID: <521464D2.5010807(a)fmi.ch> Content-Type: text/plain; charset="ISO-8859-1"; format=flowed Hi Dave two months is a good time between releases. Much more important than the release cycle length is fixing identified bugs on the release branch as well. Regards, Hans-Rudolf On 08/20/2013 08:36 PM, Dave Clements wrote: > Hello all, > > At one of the GCC2013 Birds of a Feather sessions > <http://wiki.galaxyproject.org/Events/GCC2013/BoF/PublicGalaxyServers> the > group was very clear that they would like to see less frequent releases > of Galaxy. We're currently aiming to do a release every 2 months and > have been pretty successful at making that target. In the past, we have > tried doing releases more often and less often. > > Is there a sweet spot for the time between releases? > > Please reply to the group. We are interested in a discussion. > > Thanks, > > Dave C -- Hailiang (Leon) Mei Netherlands Bioinformatics Center BioAssist NGS Taskforce - http://ngs.nbic.nl<https://wiki.nbic.nl/index.php/Next_Generation_Sequencing> Skype: leon_mei Mobile: +31 6 41709231

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Galaxy Release Cycle Length
by Dave Clements 22 Aug '13

22 Aug '13

Hello all, At one of the GCC2013 Birds of a Feather sessions<http://wiki.galaxyproject.org/Events/GCC2013/BoF/PublicGalaxyServers> the group was very clear that they would like to see less frequent releases of Galaxy. We're currently aiming to do a release every 2 months and have been pretty successful at making that target. In the past, we have tried doing releases more often and less often. Is there a sweet spot for the time between releases? Please reply to the group. We are interested in a discussion. Thanks, Dave C -- http://galaxyproject.org/GCC2013 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

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error installing dependency for tool shed repository.
by Curt Palm 22 Aug '13

22 Aug '13

I've just created a repository in the sandbox and have been trying to test the installation of a dependency my tool needs. The tool needs the python module "requests" and I've written code. I get an error: STDERR python: can't open file 'setup.py': [Errno 2] No such file or directory I've modeled my code on examples I've found in the tool shed. I've replaced the requests module with other python modules and these are installed ok. I can also download and manually install requests with "python setup.py install" Any suggestions as to what I may be doing wrong? tool_dependencies.xml: <?xml version="1.0"?> <tool_dependency> <package name="requests" version="1.2.3"> <install version="1.0"> <actions> <action type="download_by_url">http://pypi.python.org/packages/source/r/requests/requests-1.2.3.tar.gz</action> <action type="make_directory">$INSTALL_DIR/lib/python</action> <action type="make_directory">$INSTALL_DIR/bin</action> <action type="set_environment"> <environment_variable name="PYTHONPATH" action="append_to">$INSTALL_DIR/lib/python</environment_variable> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> </action> <action type="shell_command">python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action> </actions> </install> <readme> </readme> </package> </tool_dependency> ingTest.xml: <tool id="ingTest" name="ingTest" version="1.0"> <description>Testing Tool Shed</description> <requirements> <requirement type="package" version="1.2.3">requests</requirement> </requirements> <command interpreter="python"> </command> <inputs> </inputs> <outputs> </outputs> <help> .. class:: infomark </help> </tool> Thanks, -Curt Curt Palm Data Engineer ________________________________________ INGENUITY SYSTEMS | www.ingenuity.com 1700 Seaport Blvd., 3rd Floor | Redwood City, CA 94063 650.381.5084

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Bismark issue
by Shane Sturrock 21 Aug '13

21 Aug '13

I've had a bit of a time trying to get Bismark working on our Galaxy instance. The install doesn't work because of the dependency on samtools 0.1.18 but in fact it requires samtools 0.1.19. I have a build of that installed as standard on our system so putting a symlink to that in the place of the samtools built for the bismark wrapper makes it work - I was seeing issues where the BAM file wasn't created and noticed in Bjoern's readme.rst that said it required samtools 0.1.19 or later. Shane -- For urgent cases, contact support(a)biomatters.com Dr Shane Sturrock shane.sturrock(a)biomatters.com Senior Scientist Tel: +64 (0) 9 379 5064 76 Anzac Ave Auckland New Zealand

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Action type 'template_command' on galaxy-dist?
by Peter Cock 21 Aug '13

21 Aug '13

Hi all, I'm currently trying out installation of tools from the Tool Shed on a secondary Galaxy server (not our production server nor my development setup). This is running galaxy-dist, current latest stable I believe: $ sudo -u galaxy hg heads changeset: 10201:ebe87051fadf tag: tip parent: 10199:8bf64d933704 user: Dannon Baker <dannonbaker(a)me.com> date: Tue Jul 02 10:48:31 2013 -0400 summary: Fix two more downgrade invocations to accept the migrate_engine parameter changeset: 10200:fd4113962c32 branch: stable parent: 10198:0a06df7da177 user: Dannon Baker <dannonbaker(a)me.com> date: Tue Jul 02 10:48:31 2013 -0400 summary: Fix two more downgrade invocations to accept the migrate_engine parameter I'm having some problems, e.g. Tool shed repository 'package_numpy_1_7' tool dependencies Name Version Type Status Error atlas 3.10.1 package Error Error installing tool dependency atlas version 3.10.1: [Errno 2] No such file or directory: u'/opt/galaxy-dist-shed-tools/atlas/3.10.1/iuc/package_atlas_3_10/597c0e54eded/env.sh' lapack 3.4.2 package Error Error installing tool dependency lapack version 3.4.2: [Errno 2] No such file or directory: u'/opt/galaxy-dist-shed-tools/lapack/3.4.2/iuc/package_lapack_3_4/98a7d116c15f/env.sh' numpy 1.7.1 package Error Error installing tool dependency numpy version 1.7.1: Unsupported action type 'template_command' in tool dependency definition. Is this due to to galaxy-dist being too old for Tool Shed tools whose XML installation scripts use action template_command? e.g. http://toolshed.g2.bx.psu.edu/view/iuc/package_numpy_1_7/c75482be1d3a One way to catch this kind of error would be if the nightly Tool Shed tests included attempting to install package repositories (e.g. the new "Tool dependency definition") explicitly. (I think I've suggested this before - but it is worth reiterating) Thanks, Peter

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