- galaxy-dev - lists.galaxyproject.org

Error when uploading files (using Pulsar)
by Tiziano Flati 09 May '16

09 May '16

Hi all, I have succesfully setup a Galaxy-Pulsar architecture and I am able to run jobs over datasets* already uploaded on a history*. When I try to upload a new file to the history, though, the upload job fails with the following error: Traceback (most recent call last): > File "/home/flati/pulsar/files/staging/80/tool_files/upload.py", line > 18, in <module> > import galaxy.model # noqa > ImportError: No module named model Note: in job_conf.xml, Pulsar is the default destination: <destinations default="win_pulsar"> Does someone know what the problem is? I suspect that setting pulsar as the default destination causes the upload tool to run on Pulsar's side which, however, does not have access to Galaxy's lib directory (which contains the galaxy model module). Any help is very appreciated, Tiziano

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Planemo inside of Conda
by D K 06 May '16

06 May '16

Hi Galaxy-Devs I would like to have a single python / planemo environment that is portable across computers where I can use planemo test (which instantiates an instance of Galaxy). Currently, we're using conda on our current network. That way we have shared environments where the version of python and associated modules is consistent across network computers/users. This way, any user (including the galaxy system) can use exactly the same python version and modules which greatly simplifies management. I guess it's possible to manage dependencies through toolsheds, but we didn't want to do that. Although probably not optimal, what we do is to start a conda environment between the <command> tags in a tool's xml for python scripts, e.g.: <command> source activate pythonEnv; python Script.py $input1 > $output1 </command> The problem is that planemo is also installed in this environment, and since one cannot start a galaxy instance within a conda environment, planemo test now fails (since the environment doesn't get loaded correctly). I can get this to work in planemo 0.14, but not in the newer versions. Is there a workaround for this, a better setup, or must I stay with planemo 0.14? Thanks!

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file format of individual files within collections
by emanuele lapponi 06 May '16

06 May '16

Dear all, I am currently developing a tool that outputs an arbitrary number of files, using collections as described in the excellent tutorial by Steve Cassidy at https://web.science.mq.edu.au/~cassidy/2015/10/21/galaxy-tool-generating-da… . I am having a hard time figuring out how to make galaxy aware of the format of the individual files in the collection, as the two relevant admin help pages I found do not mention this ( https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax and https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files) I tried adding a format attribute to the collection tag in the tool description, similarly to ``normal'' single data outputs: <outputs> <collection type="list" format="foo"> <discover_datasets pattern="(?P<name>.*)" directory="bar" /> </collection> </outputs> ... but to no avail. I would be grateful for any helpful pointers! :) Best, Emanuele Lapponi

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Position Vacant - Galaxy and Language Research in Sydney
by Steve Cassidy 06 May '16

06 May '16

Hi all, I’d like to draw your attention to the following vacancy on our project in Sydney, Australia: https://goo.gl/6NcY3g This is on the Alveo project and I’m posting here because part of the platform is a Galaxy server with tools developed to work on language data (text and speech). The role would suit someone with knowledge of Galaxy and some exposure to general eResearch problems; knowledge of language research methods would obviously be a bonus. The ad mentions a part-time role for 6 months but in practice we have funding for longer than this and for a full time role for the right candidate. Please get in touch if you are interested in finding out about the post. International candidates are welcome to apply. Steve — Department of Computing, Macquarie University http://web.science.mq.edu.au/~cassidy

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Parallelism (job splitting) for ncbi_blast_plus running through CloudMan
by David Kovalic 05 May '16

05 May '16

Hello, We would like to split fasta query files and run multiple concurrent jobs to minimize our processing wall clock time for large jobs. After chatting with folks at GCC 2015 I understand this is possible, my problem is I cant find instructions on hos to configure CloudMan/ncbi_blast_plus to do this. For those of you who know me it probably goes without saying that I can't figure it out myself ;) Peter/Enis/others, can you help us out with this question? Thanks, David

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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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