galaxy-dev October 2016

galaxy-dev@lists.galaxyproject.org

43 participants
56 discussions

user email info
by Mohamed Kassam 20 Oct '16

20 Oct '16

Dear all, I would like to send as a parameter the name of the user (either user email or username). I tried in my xml file the option <inputs> <param name="user_email" type="hidden" value="$__user_email__" /> </inputs> But I have in results X__user_email__ Any clue ? Thanks in advance, Mohamed

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Tool.xml : correct way to define an environment_variable ?
by Pierre Lindenbaum 20 Oct '16

20 Oct '16

(cross-posted at https://biostar.usegalaxy.org/p/20220/ ) I'm trying to create some `tools.xml` that use java. Those tools need to download some library (*.jar) files from http://central.maven.org/ and I want to create a variable $MYTOOLCLASSPATH containing the jars. I've tried the following xml : <?xml version="1.0" encoding="UTF-8"?> <tool_dependency> <package name="mytool" version="0.0.1"> <install version="1.0"> <actions> <action type="shell_command">wget -P "$REPOSITORY_INSTALL_DIR" "http://central.maven.org/lib1.jar" "http://central.maven.org/lib2.jar"</action> <action type="set_environment"> <environment_variable name="MYTOOLCLASSPATH" action="set_to">$REPOSITORY_INSTALL_DIR/lib1.jar:$REPOSITORY_INSTALL_DIR/lib2.jar</environment_variable> </action> </actions> </install> </package> </tool_dependency> the base java command is defined as a token in macro.xml: (...) <token name="@MYJAVA@"> java -cp "\${MYTOOLCLASSPATH}" </token> (...) and called in my tool.xml: <command>@MYJAVA@ tool.Tool ${input} > ${out} </command> but It seems that $MYTOOLCLASSPATH is empty. I've also tried to create a set_environment under <tool_dependency>: <set_environment version="1.0"> <environment_variable name="MYTOOLCLASSPATH" action="set_to">$REPOSITORY_INSTALL_DIR/lib1.jar:$REPOSITORY_INSTALL_DIR/lib2.jar</environment_variable> </set_environment> same problem: the $MYTOOLCLASSPATH remains empty Where Am i wrong ? What's the correct way to define MYTOOLCLASSPATH ? Thanks, Pierre

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Perl module problem with vcftools in conda + new tool
by Peter van Heusden 20 Oct '16

20 Oct '16

Hi there I'm trying to add a wrapper for the vcftools vcf-consensus tool. There is an existing tool collection for vcftools in tools-devteam, so I'm add it there. Wrapper is at: https://github.com/pvanheus/tools-devteam/tree/master/tool_collections/vcft… I tested this using: planemo conda_install . planemo serve --conda_prefix /home/pvh/miniconda2 --con da_dependency_resolution When the tool executes I get the error: Fatal error: Exit code 2 () Can't locate Vcf.pm in @INC Which implies that the PERL5LIB is not being set correctly when the tool runs. Using planemo test gives me: No tests were executed - see Galaxy output for details. Strangely enough on the pull request the Travis test passes ( https://github.com/galaxyproject/tools-devteam/pull/402). Any idea how to fix this? Thanks! Peter

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dynamic runner and embed_metadata_in_job
by Laure QUINTRIC 20 Oct '16

20 Oct '16

Hi Galaxy users, As somebody try to run dynamic runner with the option embed_metadata_in_job set to False ? I notice that it works with drmaa runner but not with dynamic. Here is my job_conf.xmf : <destinations default="ifremer_conf"> <destination id="local" runner="local"/> <destination id="my_conf" runner="dynamic"> <param id="type">python</param> <param id="function">my_conf</param> <param id="embed_metadata_in_job">False</param> </destination> </destinations> I also set the this parameter in galaxy.ini retry_metadata_internally = True But I still have the set_metadata.py script in my jobs. Thanks for help. Regards, Laure

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KeyError: 'tool_panel_section' when installing a new tool
by Pierre Lindenbaum 19 Oct '16

19 Oct '16

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 <bjoern(a)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_revision…" "Mozilla/5.0 (X11; Ubuntu; Linux i686; rv:49.0) Gecko/20100101 Firefox/49.0" Error - <type 'exceptions.KeyError'>: '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] galaxy - prokka - tbl2asn
by Fernandez Edgar 19 Oct '16

19 Oct '16

Hey Guys, I’ve fixed this problem by bypassing the system perl and compiling my own with all the right modules. So I don’t get any more perl errors. Also, I’ve realized that the latest prokka package (Revision: f5e44aad6498) has a dependency with the package_tbl2_asn_24_3 (Revision 41764d6a6a3c). However, when you execute prokka, tbl2asn gives you the following error: [tbl2asn] This copy of tbl2asn is more than a year old. Please download the current version. What would you suggest I do? 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.soranzo@gmail.com] On Behalf Of Nicola Soranzo Sent: October-07-16 3:14 PM To: Fernandez Edgar <edgar.fernandez(a)umontreal.ca>; galaxy-dev(a)bx.psu.edu Subject: Re: [galaxy-dev] galaxy - bioperl - prokka Hi Edgar, presently the Prokka wrapper requires some dependencies (in particular some Perl modules) to be installed separetely, see the README file at https://toolshed.g2.bx.psu.edu/view/crs4/prokka/ We are planning to release an updated Prokka wrapper which will use Conda dependencies, you can track the progress at: https://github.com/galaxyproject/tools-iuc/pull/985 Cheers, Nicola On 07/10/16 15:06, Fernandez Edgar wrote: Hello, I have installed prokka, perl and bioperl in my Galaxy’s ToolShed. However, my users are getting this error during execution of prokka: Can't locate Bio/Root/Version.pm in @INC (@INC contains: /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at /home/galaxy/galaxy-prod/tool-data/toolshed.dependency.dir/prokka/1.11/crs4/prokka/f5e44aad6498/bin/prokka line 29. BEGIN failed--compilation aborted at /home/galaxy/galaxy-prod/tool-data/toolshed.dependency.dir/prokka/1.11/crs4/prokka/f5e44aad6498/bin/prokka line 29. I was under the impression that the galaxy’s tools will use the internal perl. Do I just need to install Bio::Root:Version on my system installation of perl? Please give me whatever information you can on this issue. Regards, 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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Python ValueError: too many values to unpack
by Matthias De Smet 18 Oct '16

18 Oct '16

Hi all, I’m trying to develop a tool that lets you select a file on the server. I’m using the dynamic_options setting to let Galaxy render a dropdown list of available file. However, when I try to test the tool in its current form, I get the following error: <pre> galaxy.web.framework.decorators ERROR 2016-01-26 13:08:35,649 Uncaught exception in exposed API method: Traceback (most recent call last): File "lib/galaxy/web/framework/decorators.py", line 260, in decorator rval = func( self, trans, *args, **kwargs) File "lib/galaxy/webapps/galaxy/api/tools.py", line 98, in build return tool.to_json(trans, kwd.get('inputs', kwd)) File "lib/galaxy/tools/__init__.py", line 2602, in to_json populate_state(trans, self.inputs, state_inputs, state_errors, params.__dict__) File "lib/galaxy/tools/__init__.py", line 2471, in populate_state state[input.name] = input.get_initial_value(trans, context, history=history) File "lib/galaxy/tools/parameters/basic.py", line 984, in get_initial_value value = [ optval for _, optval, selected in options if selected ] ValueError: too many values to unpack </pre> My tool xml looks like this: <pre> <tool id="archivetolibrary" name="Copy files" version="0.1.0"> <description>from the archive to a data library</description> <code file="list_files.py"/> <command interpreter="bash"> test.sh > $log </command> <inputs> <param name="archive_source" type="select" display="radio" label="Choose source archive"> <options from_file="archives.loc"> <column name="name" index="0"/> <column name="value" index="1"/> </options> </param> <param name="query" type="text" label="Search for files"/> <param name="selected_file" type="select" label="Choose your file" dynamic_options="list_files(archive_source,query)"/> </inputs> <outputs> <data name="log" format="txt" label="${tool.name} on ${on_string}"></data> </outputs> <tests> <test> </test> </tests> <help> This tool copies data from and archive folder to your history. Keep in mind this folder MUST be readable by Galaxy in order for this tool to work. </help> </tool> </pre> and the script called in the “code” tag looks like this <pre> def list_files(dir,query): listing=[] for fname in listdir(dir): fullpath = path.join(dir, fname) #only select datafiles, not md5 checksums if path.isfile(fullpath) and not fullpath.endswith(".md5"): listing.append( fname ) return listing </pre> This script should return a list with filenames that should be displayed in the dropdown list. I’m tracking Galaxy release 15.10, running on a Ubuntu 14.04.3 server Thanks for your help! Matthias

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Storing data in the user session
by Steve Cassidy 18 Oct '16

18 Oct '16

Hi again, I’m looking for the right way to store some user credentials in the galaxy session so that tools can work on behalf of the user with our repository. Currently users have an API key and they need to upload it as a data item to that is then passed to each tool that needs it as input. This doesn’t seem like the right solution since the API key becomes part of the history and so would be shared if the history were shared. What would be better would be a way of storing the API key in the user session and then being able to pass that into a tool. I note that there are a few user session variables available in the tool xml file: __user__, __user_email__, __user_name__ and __user_id__. There is also a user preferences page where they can fill out a few details. However, I can’t see a mechanism to extend this in any way and have extra properties in the preferences pane that would then be available to tools via the template file. I can see that the standard practice for the data sources on usegalaxy.org<http://usegalaxy.org> is to send the user off to a repository website to find data that is then posted back to the galaxy server. This isn’t appropriate for us since the interaction with the repository is not just for downloading a single dataset - tools will query the repository, download various kinds of data and possibly upload new data, so we need to store user credentials in some way. Is there already a good way to achieve this or is this an enhancement to Galaxy? Thanks, Steve — Department of Computing, Macquarie University http://web.science.mq.edu.au/~cassidy

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Paste/Fetch data, indicate filename before download data (default = Pasted Entry)
by Floreline TOUCHARD 17 Oct '16

17 Oct '16

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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Galaxy Admin Training: November 7-11, Salt Lake City
by Dave Clements 16 Oct '16

16 Oct '16

Hello all, *Early registration <https://wiki.galaxyproject.org/Events/AdminTraining2016/Registration> for Galaxy Admin Training 2016 <https://wiki.galaxyproject.org/Events/AdminTraining2016> ends in one week, on Monday, September 19.* Galaxy Admin Training 2016 <https://wiki.galaxyproject.org/Events/AdminTraining2016> is a weeklong event offering basic and advanced sessions. It will be held in Salt Lake City, Utah, November 7-11, 2016, the week before Supercomputing 16 (SC16) <http://sc16.supercomputing.org/> meets in Salt Lake. These workshops are aimed at admins from organizations and labs that are installing, upgrading, or prototyping Galaxy instances. *Basics Session: November 7-8* <https://wiki.galaxyproject.org/Events/AdminTraining2016/BasicsSession> This two day basics session <https://wiki.galaxyproject.org/Events/AdminTraining2016/BasicsSession> will introduce participants to what you need to know to get a Galaxy server up and running on a standalone server. You'll also learn how to extend your Galaxy with your own tools and tools from the community, and how to define reference data in your server. *Advanced Session: November 9-11* <https://wiki.galaxyproject.org/Events/AdminTraining2016/AdvancedSession> The three day advanced session <https://wiki.galaxyproject.org/Events/AdminTraining2016/AdvancedSession> will build on topics covered in the basics section <https://wiki.galaxyproject.org/Events/AdminTraining2016/BasicsSession>. This session both extends those topics, such as tool definition, and adds new ones, such as working with compute clusters and heterogeneous resources. The goal of the advanced workshop is to enable Galaxy administrators to create robust, high-performance Galaxy instances that take full advantage of available tools and compute and storage resources. Galaxy Admin Training 2016 is hosted by the University of Utah Center for High Performance Computing (CHPC) <http://www.chpc.utah.edu/>, the USTAR Center for Genetic Discovery (UCGD) <http://ucgd.genetics.utah.edu/>, Department of Biomedical Informatics <http://medicine.utah.edu/dbmi/> and the Clinical & Translational Science Biomedical Informatics Core (CCTS BMIC) <http://medicine.utah.edu/ccts/bmic/> at the University of Utah <http://utah.edu/>. We hope to see you in Salt Lake! The Galaxy Team <https://wiki.galaxyproject.org/GalaxyTeam> PS: Please share this flier <https://wiki.galaxyproject.org/Events/AdminTraining2016/Publicity> with any individuals or groups who might be interested in this event. -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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galaxy-dev October 2016