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Workflow Execution Files
by Katherine Beaulieu 24 Oct '16

24 Oct '16

Hi Everyone, Does anyone know what files workflow execution goes through? I had assumed it just went through the same files as individual jobs for each step but I don't think that's the case. I was looking at tool-form.js but it doesn't seem to be executing that file. Thanks! Katherine

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Tool needs a particular file extension
by Steve Cassidy 24 Oct '16

24 Oct '16

Hi, I’m wrapping a tool that needs it’s input to have a known file extension (an audio file, eg. .wav). Since Galaxy stores all data as .dat files the tool is falling over since it doesn’t know what .dat is. I thought I’d be able to get around this by hard linking the .dat file to the same name with a .wav extension (dataset_1.dat.wav), this works when I try it with the tool on the command line but within Galaxy it fails, here’s my <command>: ln $signal ${signal}.wav & /home/maus/maus OUTFORMAT=TextGrid LANGUAGE=$language BPF=$bpf INSKANTEXTGRID=$inskantextgrid INSORTTEXTGRID=$insorttextgrid MODUS=$modus MAUSSHIFT=$mausshift MINPAUSLEN=$minpauslen WEIGHT=$weight INSPROB=$insprob NOINITIALFINALSILENCE=$noinitialfinalsilence OUTSYMBOL=$outsymbol OUT=$output SIGNAL=${signal}.wav resulting in the job command line: ln /tmp/tmp7AZvx7/files/000/dataset_2.dat /tmp/tmp7AZvx7/files/000/dataset_2.dat.wav & /home/maus/maus OUTFORMAT=TextGrid LANGUAGE=aus BPF=/tmp/tmp7AZvx7/files/000/dataset_1.dat INSKANTEXTGRID=false INSORTTEXTGRID=false MODUS=standard MAUSSHIFT=10 MINPAUSLEN=5 WEIGHT=7.0 INSPROB=0.0 NOINITIALFINALSILENCE=no OUTSYMBOL=sampa OUT=/tmp/tmp7AZvx7/files/000/dataset_3.dat SIGNAL=/tmp/tmp7AZvx7/files/000/dataset_2.dat.wav I’m getting an error message from the tool: sox FAIL formats: can't open input file `/tmp/tmp7AZvx7/files/000/dataset_2.dat.wav': WAVE: RIFF header not found this suggests that the hard link didn’t get made. I tried copying the file instead but got the same result. I could go in and patch the tool script to be more forgiving but it would be good to find a solution that didn’t require that if possible. Any pointers appreciated. Steve — Department of Computing, Macquarie University http://web.science.mq.edu.au/~cassidy

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question about galaxy supported datastore
by Beginner TI 24 Oct '16

24 Oct '16

Hi, A couple days ago, I was having problem with uploading data to Galaxy. I had no clue why this happened. Seems some kind of validator didn't pass. Here is the message: You will need to reselect the file you specified I searched and found this error message is in galaxy release before, but not in this release: <validator type="expression" message="You will need to reselect the file you specified (%s)." substitute_value_in_message="True">not ( ( isinstance( value, unicode ) or isinstance( value, str ) ) and value != "" )</validator>  My understanding of this comment is that user needs to select a file as the input file. It could not be set due to security reasons. I didn't get it...still confused. However, today I found that we are using an external 8tb drive that is physically attached on another host as the data store. Seems postgresql takes it well, but galaxy doesn't. The file system is CIFS. When I looked at the permissions, there is a + at the end, but when I use getfacl, I don't see anything besides the regular user/group/other. In ths past we have used external drives directly connected to the galaxy instance and it always worked. So...does galaxy not support disks not physically attached?? I feel this is less likely, maybe what I'm seeing is a coincidence? What exactly caused this? Any input will be greatly appreciated. :-) Thanks, Rui

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Changing Tool Shed URL
by Youssef GHORBAL 21 Oct '16

21 Oct '16

Hello, I’m wondering if there is any way to change an established Tool Shed URL. I have a Galaxy instance and a Tool Shed instance (http://mytoolshed.url/xxx) A lot of tools have beed installed from that Tool Shed inside Galaxy (tools referenced inside workflows etc) I want to change the Tool Shed URL from http://mytoolshed.url/xxx to http://mytoolshed2.url/yyyy. Galaxy and Tool Shed seems to use parts of the URL as a guid for tools. Tool Shed does not seem to bother to be called by either URLs (it generates guids with the new URLs scheam for new tools though) Galaxy does not seem to handle it, I changed the tool_sheds_conf.xml to point to new URL, but when I update a tool on the Tool Shed, Galaxy gets the new version but it generates buggy tool panel (the tool is cited twice) I also tried to mess around with the shed_tool_conf.xml apdapting the guids and the <tool_shed> items with no luck. Can someone point me to the right direction ? How the matching is done between shed_tool_conf.xml entries, the tool_version and tool_shed_repository tables. Thank you for your help. Youssef Ghorbal Institut Pasteur

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Data Library Import "Click this to start analyzing it." requires relogin
by D K 21 Oct '16

21 Oct '16

Hi Galaxy-devs, On my local instance of Galaxy (v16.07) when a user imports a shared data library file into their history and clicks on the "Selected datasets imported into history. Click this to start analyzing it." popup, they get directed back to the Galaxy log in page regardless if they are already logged in. Does this have to do with my settings in galaxy.ini? This behavior does not occur on usegalaxy.org. Any suggestions would be appreciated. Thanks! DK

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Wrapper for the MISO programs
by evan clark 20 Oct '16

20 Oct '16

I am currently working to create a wrapper for the MISO tools and wanted to see if anyone has previously developed a functional or semi-functional wrapper for it.

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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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