galaxy-dev April 2016

galaxy-dev@lists.galaxyproject.org

47 participants
55 discussions

Data manager problem
by Scott Szakonyi 11 May '16

11 May '16

Hello, I'm having an odd problem after updating to the latest version of Galaxy. My users prepare data for analysis using data manager tools, such as "data_manager_bwa_mem_index_builder". When an attempt is made to run one of these tools, a pop up window opens stating "Tool request failed" and underneath "Uncaught error". I've pored over all the Galaxy system logs and can't find anything that might indicate what is happening. I've uninstalled and reinstalled the data manager tools, restarted both the Galaxy service and the server, to no avail. I get this same error with any installed data manager, yet all the standard tools are executing correctly and don't seem to be having any issues. If anyone can offer some insight or suggestions for resolving this issue, I'd be most appreciative. Best regards, -- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu

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a quick question about picard
by Beginner TI 09 May '16

09 May '16

Hi All, I wrote a very simple wrapper for one picard function. Here is the xml file: <tool name="CreateSequenceDictionary" id="picard_CreateSequenceDictionary" version="1.126.0"> <description>Create Sequence Dictionary</description> <requirements> <requirement type="package" version="1.126.0">picard</requirement> </requirements> <macros> <import>picard_macros.xml</import> </macros> <command> @java_options@ java -jar \$JAVA_JAR_PATH/picard.jar CreateSequenceDictionary R="${ref_file}" O="${dict_file}" </command> <inputs> <param format="fa" name="ref_file" type="data" label="Using reference genome" help="-R,--reference_sequence" /> </inputs> <outputs> <data format="txt" name="dict_file" /> </outputs> <help> **Purpose** Create Sequence Dictionary from fa file </help> </tool> It's ugly, I know. :-( Just want to finish a quick test...however when I tried to run a test, it always says something like: Exception in thread "main" picard.PicardException: /media/4tb-ext/galaxy-data-store/database/files/008/dataset_8757.dat already exists. Delete this file and try again, or specify a different output file When I looked at that file, it has a size 0, but even I remove that file, I'll still see the same thing. Galaxy terminal executes: galaxy.jobs.runners.local DEBUG 2016-04-29 13:55:51,423 (3189) executing: GALAXY_SLOTS="1"; export GALAXY_SLOTS; _JAVA_OPTIONS=${_JAVA_OPTIONS:-'-Xmx2048m -Xms256m'} && export _JAVA_OPTIONS && java -jar $JAVA_JAR_PATH/picard.jar CreateSequenceDictionary R="/media/mybook/GATK_galaxyWrapper/hg38.fa" O="/media/4tb-ext/galaxy-data-store/database/files/008/dataset_8757.dat" Seems it did the right thing, but why that set_meta set state to ERROR? Oh there was indeed a warning: WARNING:galaxy.datatypes.registry:Overriding conflicting datatype with extension 'eset', using datatype from /media/4tb-ext/galaxy-data-store/database/tmp/tmp_Uuw5Y. Have anyone seen this before? I'm quite confused since the same commandline runs smoothly in the terminal. Thanks, Rui

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Changing temporary directory for planemo
by D K 05 May '16

05 May '16

Hi Galaxy-Devs, Is it possible to change the temporary directory used by planemo test? The reason is that one of my xml tools uses ssh to connect to a machine specifically due to licensing requirements e.g.: <command> ssh address.com 'sh runCommand.sh $input' > $output </command> Unfortunately, when executing a planemo test, the input is copied into a local temporary directory (/tmp) which is of course different from the /tmp directory on the computer where the bash script is being executed. I've tried changing the TMP and TEMP environment variables to a location that is available to both machines but that hasn't worked. Is there a workaround? Thanks!

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Kallisto tool wrapper?
by Lance Parsons 02 May '16

02 May '16

I've had requests from users to install Kallisto as Galaxy tool. I didn't see any wrappers or evidence of wrappers in my searching, but I thought I'd ask here to see if anyone is working on or interested in working on such a thing. -- Lance Parsons - Scientific Programmer Carl C. Icahn Laboratory - Room 136 Lewis-Sigler Institute for Integrative Genomics Princeton University

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May 2016 Galaxy News: GCC2016 DEADLINES Approaching
by Dave Clements 29 Apr '16

29 Apr '16

Hi All, The *May Galaxy News* <https://wiki.galaxyproject.org/GalaxyUpdates/2016_05> is out and the lead news is *GCC2016 deadlines! <https://wiki.galaxyproject.org/GalaxyUpdates/2016_05#Deadlines.21>* - Poster and demo abstracts are due May 20 - Early registration closes May 20 as well. - The application deadline for scholarships is May 1. *So get moving! * There's also lots of other news too. Check it out <https://wiki.galaxyproject.org/GalaxyUpdates/2016_05>. Don't miss those deadlines(!), and *see you in June* <https://gcc2016.iu.edu/>, Dave Clements and the Galaxy Team <https://wiki.galaxyproject.org/GalaxyTeam> -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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local toolshed not working
by Vincent Cahais 28 Apr '16

28 Apr '16

Hi everyone, I'm trying to set up a new local toolshed with a fresh install of galaxy. I can run the server, create repositories and upload files. But when I try to install a tool in galaxy it fail with a server error. In the tool_shed_webapp.log I have the following error : ---------------------------------------- Exception happened during processing of request from ('**.**.**.**', 41026) Traceback (most recent call last): File "/home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py", line 1085, in process_request_in_thread self.finish_request(request, client_address) File "/usr/lib/python2.7/SocketServer.py", line 331, in finish_request self.RequestHandlerClass(request, client_address, self) File "/usr/lib/python2.7/SocketServer.py", line 652, in __init__ self.handle() File "/home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py", line 459, in handle BaseHTTPRequestHandler.handle(self) File "/usr/lib/python2.7/BaseHTTPServer.py", line 340, in handle self.handle_one_request() File "/home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py", line 454, in handle_one_request self.wsgi_execute() File "/home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py", line 304, in wsgi_execute self.wsgi_start_response) File "/home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/paste/urlmap.py", line 216, in __call__ return app(environ, start_response) File "/home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/paste/debug/prints.py", line 107, in __call__ environ, self.app) File "/home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/paste/wsgilib.py", line 547, in intercept_output if data[0] is None: IndexError: list index out of range ---------------------------------------- Removing PID file tool_shed_webapp.pid Cheers,

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Problem with DRMAA and Pbs Pro
by Tiziano Flati 28 Apr '16

28 Apr '16

Hi all, I am trying to use the pbs-drmaa library to let Galaxy "see" our cluster. We have PBS Pro, so I followed the instructions found here: http://apps.man.poznan.pl/trac/pbs-drmaa - I installed the library through: ./configure --with-pbs=$PBS_HOME --prefix=$HOME make make install where PBS_HOME points to the local pbs installation folder (the one with bin, etc, lib folders and so on) and $HOME points to my user's home dir. - I have set the DRMAA_LIBRARY_PATH env variable: env | grep DRMAA_LIBRARY_PATH DRMAA_LIBRARY_PATH=$HOME/lib/libdrmaa.so Here is my job_conf.xml: <?xml version="1.0"?> <job_conf> <plugins> <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner"/> <plugin id="drmaa" type="runner" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner"/> </plugins> <handlers> <handler id="main"/> </handlers> <destinations default="queue"> <destination id="local" runner="local"/> <destination id="queue" runner="drmaa"> <param id="nativeSpecification">-A cin_galaxy</param> </destination> </destinations> </job_conf> But when I use the nativeSpecification parameter (with -A account parameter), I receive the following error, with no further specification of what the error can be (it says "Illegal attribute or resource value" without saying which one triggered the error): galaxy.jobs.runners.drmaa DEBUG 2016-04-27 12:18:26,782 (15) native specification is: -A cin_galaxy galaxy.jobs.runners.drmaa ERROR 2016-04-27 12:18:26,784 (15) drmaa.Session.runJob() failed unconditionally Traceback (most recent call last): File "$GALAXY_DIR/lib/galaxy/jobs/runners/drmaa.py", line 179, in queue_job external_job_id = self.ds.runJob(jt) File "$GALAXY_DIR/.venv/lib/python2.6/site-packages/drmaa/session.py", line 314, in runJob c(drmaa_run_job, jid, sizeof(jid), jobTemplate) File "$GALAXY_DIR/.venv/lib/python2.6/site-packages/drmaa/helpers.py", line 299, in c return f(*(args + (error_buffer, sizeof(error_buffer)))) File "$GALAXY_DIR/.venv/lib/python2.6/site-packages/drmaa/errors.py", line 151, in error_check raise _ERRORS[code - 1](error_string) *InvalidAttributeValueException: code 14: Illegal attribute or resource value: Illegal attribute or resource value* Can you please help me understanding the cause of the problem? Any help would be most appreciated! Thank you very much! Tiziano Flati

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Problem uploading multigigabyte files via API
by Sytchev, Ilya 27 Apr '16

27 Apr '16

Hi, I'm running Galaxy 16.01 behind Nginx 1.4.6 on Ubuntu 14.04 and I came across an issue where uploading files larger than ~3GB via the API into histories and libraries fails. Steps to reproduce (using BioBlend 0.7.0): from bioblend.galaxy.objects import GalaxyInstance gi = GalaxyInstance("galaxy-dev", "api_key") h = gi.histories.create() h.upload_dataset('/path/to/multigigabytefile') Observed results: ConnectionError: Unexpected response from galaxy: 504: <html> <head><title>504 Gateway Time-out</title></head> <body bgcolor="white"> <center><h1>504 Gateway Time-out</h1></center> <hr><center>nginx/1.4.6 (Ubuntu)</center> </body> </html> It looks like Nginx is accepting the full incoming data transfer over the network and saving it to disk successfully, and the error occurs during the subsequent forwarding of the request to Galaxy. There doesn't seem to be a particular threshold for file size (for example, 2GB and 2.7GB file can be uploaded successfully). Also, large file uploads do work when Galaxy is not running behind Nginx. Relevant log entries and config details are attached. I'd appreciate any help. Thanks, Ilya

1 0

output datasets
by Ryan G 27 Apr '16

27 Apr '16

I'm playing around with creating a Galaxy wrapper for custom tool I've created. My tool takes a single parameter, and SRA ID. In command block, I have something like this: <command> ${GALAXY_ROOT_DIR}/tools/mycustomtools/doSomething.pl --sra $sraid </command> <inputs> <param name="sraid" ... /> </inputs> <outputs> <data format="txt", name="out1", from_work_dir="${sraid}.data" /> <data format="txt", name="out2", from_work_dir="${sraid}.txt" /> </outputs> Galaxy doesn't like thr $sraid in the output. I see from the docs I need to use discover_datasets. It would be nice to use a parameter such as what I have to name output file as my script names output files use an input parameter as the base.

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PSU Meet and Greet this Saturday
by Suderman Keith 23 Apr '16

23 Apr '16

Sorry for spamming the list, but I thought this would be the easiest/quickest way to reach out to any interested people in State College. I had to make a short-notice trip to meet with colleagues in Pittsburgh and I will be driving home to NY Saturday. Since I am driving right by State College I thought it would be silly, if not downright rude, if I didn’t at least ask if anyone is up for a quick meet and greet somewhere? I should be passing by around 1-2PM. I would like to put some faces to the names I see on the list and you guys might be interested in learning more about what the NLP community is doing with Galaxy. Cheers, Keith ------------------------------ Research Associate Department of Computer Science Vassar College Poughkeepsie, NY

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galaxy-dev April 2016