galaxy-dev October 2013

galaxy-dev@lists.galaxyproject.org

112 participants
166 discussions

tool_dependencies.xml <action type="download_by_url"> regression?
by Peter Cock 22 Oct '13

22 Oct '13

This tools has been passing its nightly tests fine, http://testtoolshed.g2.bx.psu.edu/view/peterjc/nlstradamus However, there now appears to be a silent installation failure (the install hasn't worked but there was no install error): Automated tool test results Tool test results Automated test environment Tests that failed Tool id: nlstradamus Tool version: nlstradamus Test: test_tool_000000 (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterj…) Stderr: Fatal error: Exit code 127 () /bin/sh: 1: NLStradamus: not found Traceback: Traceback (most recent call last): File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 171, in test_tool self.do_it( td, shed_tool_id=shed_tool_id ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 102, in do_it self.verify_dataset_correctness( outfile, hid=elem_hid, maxseconds=testdef.maxseconds, attributes=attributes, shed_tool_id=shed_tool_id ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py", line 782, in verify_dataset_correctness self._assert_dataset_state( elem, 'ok' ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py", line 606, in _assert_dataset_state raise AssertionError( errmsg ) AssertionError: Expecting dataset state 'ok', but state is 'error'. Dataset blurb: error On the other hand, over on the main Tool Shed, with what should be the same tool configuration, the install works (although there is a new sniffer bug on the Galaxy side, see separate email): http://toolshed.g2.bx.psu.edu/view/peterjc/nlstradamus Here's the tool_dependencies.xml file, <?xml version="1.0"?> <tool_dependency> <package name="NLStradamus" version="1.8"> <install version="1.0"> <actions> <action type="download_by_url">http://www.moseslab.csb.utoronto.ca/NLStradamus/NLStradamus/NLStradamus.1.8…</action>  <action type="shell_command">g++ NLStradamus.cpp -o NLStradamus -O3</action> <action type="move_file"><source>NLStradamus</source><destination>$INSTALL_DIR/</destination></action> <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable> </action> </actions> </install> <readme> This downloads NLStradamus v1.8 from this folder, http://www.moseslab.csb.utoronto.ca/NLStradamus/NLStradamus/ The C++ tool is compiled as described in the README_C.txt file, using g++, and included in the $PATH. The older slower Perl implementation is not installed. </readme> </package> </tool_dependency> My hunch is a subtle regression in the <action type="download_by_url"> (note in this case the tarball does not contain a sub-folder). Peter

2 1

database I/O error
by Nikhil Joshi 22 Oct '13

22 Oct '13

Hi all, I have a client who is trying to run velvet on a small bacterial assembly in Galaxy. She is using our Core's custom Galaxy in the Amazon Cloud. It has had very few problems and we have been updating it and using it for years. However, after her assembly ran for a while, Galaxy crashed and now gives this error whenever you try to access it: Error Traceback: ⇝ OperationalError: (OperationalError) disk I/O error u'UPDATE galaxy_session SET update_time=?, is_valid=? WHERE galaxy_session.id = ?' ['2013-10-17 18:22:49.991937', 0, 110] URL: http://ec2-54-219-128-159.us-west-1.compute.amazonaws.com/user/logout Module weberror.evalexception.middleware:364 in respond view >> app_iter = self.application(environ, detect_start_response) Module paste.debug.prints:98 in __call__ view >> environ, self.app) Module paste.wsgilib:539 in intercept_output view >> app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ view >> return self.application(environ, start_response) Module paste.httpexceptions:632 in __call__ view >> return self.application(environ, start_response) Module galaxy.web.framework.base:132 in __call__ view >> return self.handle_request( environ, start_response ) Module galaxy.web.framework.base:185 in handle_request view >> body = method( trans, **kwargs ) Module galaxy.webapps.galaxy.controllers.user:509 in logout view >> trans.handle_user_logout( logout_all=logout_all ) Module galaxy.web.framework:713 in handle_user_logout view >> self.sa_session.flush() Module sqlalchemy.orm.scoping:127 in do view >> return getattr(self.registry(), name)(*args, **kwargs) Module sqlalchemy.orm.session:1356 in flush view >> self._flush(objects) Module sqlalchemy.orm.session:1434 in _flush view >> flush_context.execute() Module sqlalchemy.orm.unitofwork:261 in execute view >> UOWExecutor().execute(self, tasks) Module sqlalchemy.orm.unitofwork:753 in execute view >> self.execute_save_steps(trans, task) Module sqlalchemy.orm.unitofwork:768 in execute_save_steps view >> self.save_objects(trans, task) Module sqlalchemy.orm.unitofwork:759 in save_objects view >> task.mapper._save_obj(task.polymorphic_tosave_objects, trans) Module sqlalchemy.orm.mapper:1413 in _save_obj view >> c = connection.execute(statement.values(value_params), params) Module sqlalchemy.engine.base:824 in execute view >> return Connection.executors[c](self, object, multiparams, params) Module sqlalchemy.engine.base:874 in _execute_clauseelement view >> return self.__execute_context(context) Module sqlalchemy.engine.base:896 in __execute_context view >> self._cursor_execute(context.cursor, context.statement, context.parameters[0], context=context) Module sqlalchemy.engine.base:950 in _cursor_execute view >> self._handle_dbapi_exception(e, statement, parameters, cursor, context) Module sqlalchemy.engine.base:931 in _handle_dbapi_exception view >> raise exc.DBAPIError.instance(statement, parameters, e, connection_invalidated=is_disconnect) OperationalError: (OperationalError) disk I/O error u'UPDATE galaxy_session SET update_time=?, is_valid=? WHERE galaxy_session.id = ?' ['2013-10-17 18:22:49.991937', 0, 110] I will be getting more information from her soon, but I just wanted to post this to see if anybody had any suggestions about what might be going on and perhaps how to fix it? Any help would be highly appreciated. Thanks! - Nik. -- Nikhil Joshi Bioinformatics Analyst/Programmer UC Davis Bioinformatics Core http://bioinformatics.ucdavis.edu/ najoshi -at- ucdavis -dot- edu 530.752.2698 (w)

2 1

Uploads stalling on local Galaxy installation
by Tim Booth 22 Oct '13

22 Oct '13

Hi All, Some of the developers will know me already but it's my first time being properly on this list as I'm now working concertedly on Galaxy. I'm responsible for Bio-Linux which currently ships with an out-of-date and slightly flakey galaxy, but I'm working to fix that. I've hit a problem. This may or may not be the same as the issue seen by Luobin Yang. When uploading a file, no job appears in the right-hand panel. If I click refresh I might see a job but it stays in the blue "Dataset is uploading" state forever. I'm working on packaging Galaxy for Debian/Ubuntu/Bio-Linux, specifically Ubuntu 12.04 LTS (python 2.7.3). To rearrange Galaxy into something that resembles a Debian package takes a lot of tinkering and I've patched a few bits of the code, so when uploads started freezing like this I assumed it was something I'd done and started reverting patches. But it turns out I can trigger this problem on a pristine download of the latest server release (20130926 from Bitbucket). All I do is: grab and unpack latest version python ./scripts/fetch_eggs.py -c universe_wsgi.ini.sample python ./scripts/fetch_eggs.py -c universe_wsgi.ini.sample -e psycopg2 (note - I'm not actually using Posgres in this case and I'm assuming this is irrelevant but reporting for completenes) mkdir eggs-cache ; export PYTHON_EGG_CACHE=`pwd`/eggs-cache ./run.sh (wait for SQLite DB to build) Ctrl-C, ./run.sh, test, Ctrl-C, ./run.sh, test, etc... After a few restarts the problem occurs. Failing that, it seems I can make failure more likely by tarring up the whole directory and untarring it again. I suspect all this is doing is affecting the disk cache timing and thus triggering some underlying race condition. Once the server is started, behaviour is apparently consistent - ie. all uploads either fail or all work. Other tasks seem to work, so long as they don't depend on the stalled uploads, but I've only tried a couple of these (just a basic "select first lines"). I'm now convinced there is some sort of race condition on start-up that is responsible. On my DEB package it fails like this all the time, but an issue is clearly there in the unmolested code, just rarer. I don't mind getting into the code to try and debug this but I don't know where to start, even with the source code docs and my rapidly increasing Python-fu. Trying to fathom the interactions between the threads and the browser and the SQLAlchemy layer I either need a good outline document or a developer to hold my hand for a bit. Can someone help me out with this one? Thanks in advance, TIM -- Tim Booth <tbooth(a)ceh.ac.uk> NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://nebc.nerc.ac.uk +44 1491 69 2705

5 9

Test Toolshed Biopython package dependency & NumPy
by Peter Cock 22 Oct '13

22 Oct '13

On Sun, Sep 29, 2013 at 1:17 PM, Björn Grüning wrote: > I updated R, numpy, scipy, scikit and removed the atlas dependency. It > seems to work fine for the ChemicalToolBox. I do not remove the lapack > dependency, because I did not get any complains until now. I'm seeing problems on the Test Tool Shed with NumPy :( The updated no-ATLAS numpy is revision f0490401cfff http://testtoolshed.g2.bx.psu.edu/view/iuc/package_numpy_1_7 My tools using NumPy via Biopython 1.62 do seem to be picking up this new NumPy package, which is good. However, the install of NumPy seems to be failing in strange and *different* ways - which I suspect points to a Tool Shed test framework bug, perhaps in sharing the dependencies between tools? ---------------------- http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id /9e9e3b860aa0 Looks like partial NumPy install? Installation errors - no functional tests were run for any tools in this changeset revision Tool dependencies TypeNameVersion biopython package 1.62 Error Traceback (most recent call last): File "setup.py", line 463, in <module> setup(**setup_args) File "/usr/lib/python2.7/distutils/core.py", line 152, in setup dist.run_commands() File "/usr/lib/python2.7/distutils/dist.py", line 953, in run_commands self.run_command(cmd) File "/usr/lib/python2.7/distutils/dist.py", line 972, in run_command cmd_obj.run() File "setup.py", line 216, in run if check_dependencies_once(): File "setup.py", line 123, in check_dependencies_once _CHECKED = check_dependencies() File "setup.py", line 163, in check_dependencies if is_Numpy_installed(): File "setup.py", line 282, in is_Numpy_installed return bool(can_import("numpy")) File "setup.py", line 274, in can_import return __import__(module_name) File "/ToolDependencies/numpy/1.7.1/iuc/package_numpy_1_7/f0490401cfff/lib/python/numpy/__init__.py", line 137, in <module> import add_newdocs File "/ToolDependencies/numpy/1.7.1/iuc/package_numpy_1_7/f0490401cfff/lib/python/numpy/add_newdocs.py", line 9, in <module> from numpy.lib import add_newdoc File "/ToolDependencies/numpy/1.7.1/iuc/package_numpy_1_7/f0490401cfff/lib/python/numpy/lib/__init__.py", line 13, in <module> from polynomial import * File "/ToolDependencies/numpy/1.7.1/iuc/package_numpy_1_7/f0490401cfff/lib/python/numpy/lib/polynomial.py", line 11, in <module> import numpy.core.numeric as NX AttributeError: 'module' object has no attribute 'core' ---------------------- http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id/9e9e3b860aa0 Apparently the same error: Installation errors - no functional tests were run for any tools in this changeset revision Tool dependencies TypeNameVersion biopython package 1.62 Error Traceback (most recent call last): File "setup.py", line 463, in <module> setup(**setup_args) File "/usr/lib/python2.7/distutils/core.py", line 152, in setup dist.run_commands() File "/usr/lib/python2.7/distutils/dist.py", line 953, in run_commands self.run_command(cmd) File "/usr/lib/python2.7/distutils/dist.py", line 972, in run_command cmd_obj.run() File "setup.py", line 216, in run if check_dependencies_once(): File "setup.py", line 123, in check_dependencies_once _CHECKED = check_dependencies() File "setup.py", line 163, in check_dependencies if is_Numpy_installed(): File "setup.py", line 282, in is_Numpy_installed return bool(can_import("numpy")) File "setup.py", line 274, in can_import return __import__(module_name) File "/ToolDependencies/numpy/1.7.1/iuc/package_numpy_1_7/f0490401cfff/lib/python/numpy/__init__.py", line 137, in <module> import add_newdocs File "/ToolDependencies/numpy/1.7.1/iuc/package_numpy_1_7/f0490401cfff/lib/python/numpy/add_newdocs.py", line 9, in <module> from numpy.lib import add_newdoc File "/ToolDependencies/numpy/1.7.1/iuc/package_numpy_1_7/f0490401cfff/lib/python/numpy/lib/__init__.py", line 13, in <module> from polynomial import * File "/ToolDependencies/numpy/1.7.1/iuc/package_numpy_1_7/f0490401cfff/lib/python/numpy/lib/polynomial.py", line 11, in <module> import numpy.core.numeric as NX AttributeError: 'module' object has no attribute 'core' ---------------------- http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename/d08767ae73ce Looks like a different partial NumPy install? Installation errors - no functional tests were run for any tools in this changeset revision Tool dependencies TypeNameVersion biopython package 1.62 Error Traceback (most recent call last): File "setup.py", line 393, in <module> if is_Numpy_installed(): File "setup.py", line 282, in is_Numpy_installed return bool(can_import("numpy")) File "setup.py", line 274, in can_import return __import__(module_name) File "/ToolDependencies/numpy/1.7.1/iuc/package_numpy_1_7/f0490401cfff/lib/python/numpy/__init__.py", line 137, in <module> import add_newdocs File "/ToolDependencies/numpy/1.7.1/iuc/package_numpy_1_7/f0490401cfff/lib/python/numpy/add_newdocs.py", line 9, in <module> from numpy.lib import add_newdoc File "/ToolDependencies/numpy/1.7.1/iuc/package_numpy_1_7/f0490401cfff/lib/python/numpy/lib/__init__.py", line 4, in <module> from type_check import * File "/ToolDependencies/numpy/1.7.1/iuc/package_numpy_1_7/f0490401cfff/lib/python/numpy/lib/type_check.py", line 8, in <module> import numpy.core.numeric as _nx File "/ToolDependencies/numpy/1.7.1/iuc/package_numpy_1_7/f0490401cfff/lib/python/numpy/core/__init__.py", line 42, in <module> __all__ += shape_base.__all__ AttributeError: 'module' object has no attribute '__all__' ---------------------- http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_primer_clip/834cf6618a14 Looks like yet another different partial NumPy install? Installation errors - no functional tests were run for any tools in this changeset revision Tool dependencies TypeNameVersion biopython package 1.62 Error Bio/Cluster/clustermodule.c: In function ‘py_median’: Bio/Cluster/clustermodule.c:2164:31: error: ‘PyArray_NOTYPE’ undeclared (first use in this function) Bio/Cluster/clustermodule.c:2164:31: note: each undeclared identifier is reported only once for each function it appears in Bio/Cluster/clustermodule.c: In function ‘py_mean’: Bio/Cluster/clustermodule.c:2230:31: error: ‘PyArray_NOTYPE’ undeclared (first use in this function) error: command 'x86_64-linux-gnu-gcc' failed with exit status 1 ---------------------- http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss/308ec20faefb My old favourite, listed under "Latest revision: failing tool tests" but with no visible test results or install failure - but as this also depends on Biopython and NumPy so it probably failed installation too. Regards, Peter

4 18

RFC: Streamlined Uploading
by John Chilton 22 Oct '13

22 Oct '13

This question is vaguely related to the following pull request put together by Gert Hulselmans. https://bitbucket.org/galaxy/galaxy-central/pull-request/171/avoid-corrupti… I think it makes sense to add this option. But I also I think the upload form is getting quite complicated and it only promises to get more complicated (looking ahead to things like advanced handling of compressed datasets or dataset collections). So I have the outline of a plan that could potentially address some of this that I would be interested in feedback on: 1) We merge this pull request. 2) Rename (or re-describe I guess): "Upload File from your computer" to "Advanced Upload Tool" (still with id upload1 to keep things as simple as possible). 3) We then create several news tools, which would appear before "Advanced Upload Tool" in the "Get Data" section: "Upload file from your computer" "Import files from the web via URLs" "Import FTP uploaded files" "Paste file contents" Each of these has just the form element they need (upload box, textbox, or FTP selector) as well for genome selection box. They also have a checkbox conditional for advanced options for "Convert tabs to spaces", the new "Posix lines", and perhaps "File format" (we could default to *auto* and make specification an advanced option). More thought should be given to what is considered a advanced option in each of these cases. If you are pasting content, you do not need the new "posix lines" option, but replace spaces with tabs might be a very common option. Whereas for uploaded files the inverse is sort of true. 4) To further streamline things, we could replace "Your history is empty. Click 'Get Data' on the left pane to start" in the empty history section with something with links: "Your history is empty. To get started, import data from [your computer], [web links], [your clipboard], [FTP], or by choosing an external data source from the 'Get Data' section in the left panel". I kind of find the big upload form daunting and I consider myself something of a Galaxy expert, I assume new users must find it even more so. I have no data to back this however, so let me know if you think I am way off base here. I would be really interested for perspectives from people who work closely with new users. Also it is potentially confusing that to upload data via URLs for instance you click a link that says "Upload File from your computer". This could simplify that as well. Thoughts? Thanks for your time, -John

3 2

display at third party tools error
by TerryYeh＠NARL 22 Oct '13

22 Oct '13

I have a question about sending a bed to Ensembl or bam to IGV through Galaxy. I have setup a galaxy on my own pccluster. Everything is fine. But when I want to display the bam file to IGV, I got the error message about error loading files. "Error loading http://xxx.xx.xxx/galaxy/display_application/xxxxxxxxxx/data/galaxy_xxxxx.ba m: An error occurred while accessing: http://xxx.xx.xxx/galaxy/display_application/xxxxxxxxxx/data/galaxy_xxxxx.ba m Read error; BinaryCode in readmode; streamed file (filename not available)" When I use the url to get the file directly, it can be successfully downloaded. I meet the same situation when I send the bed file to display at Ensembl. The tract will not be shown on Ensembl. When I want to send the bed manually through url, I also get the error message about loading files. "Unable to access file. Server response: 500 read timeout" Does anyone know how to solve the problem?? Thanks a lot!! Best Regards, Terry Yeh

1 0

Share workflows for all users
by Anatoliy Pandorin 22 Oct '13

22 Oct '13

For a long time I used release_2013.01.13. And to share workflows for all users galaxy used a simple link to workflow (exp: <url>/workflow/run?id=cbbbf59e8f08c98c ) This was done by my simple script. (copied links to "welcome" page) Moving on release_2013.08.12 this method does not work anymore. You first need add users to "Share Workflow with Individual Users". It is without a doubt correct. But: As now distribute(Share) workflow for all users at once? Maybe I do not understand that. Pardon Best regards, Anatoly

2 1

Workflow step dependencies
by Eric Rasche 21 Oct '13

21 Oct '13

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hello all, At my organisation's instance of galaxy, we have some connectors to talk to chado (inserting/removing GenBank & GFF files, etc). However, for one of the workflows we plan to use, there is a script which must be run which has no input files and no output files (gmod_add_organism.pl, for those curious). This script *must* be run before another script is run (gmod_bulk_load_gff3.pl), or the database insert will fail So my question is: Is there an easy way to specify dependencies when they depend on external factors, rather than just input/output files? If there isn't a generalised mechanism to do this, should I just list input and output files that are never actually created or removed? Cheers, Eric - -- Eric Rasche Programmer II Center for Phage Technology Texas A&M University College Station, TX 77843 404-692-2048 esr(a)tamu.edu rasche.eric(a)yandex.ru -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.11 (GNU/Linux) Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/ iQIcBAEBAgAGBQJSZWA0AAoJEMqDXdrsMcpVGBUP/izaBVdCMR8ezm+5GNDpbsiZ CohkkFFZluewd14a08Mmgv42atmqAD10YiJAr1p5xu2eDB5OQJSH7dqXEbAS3IaL IhmfCkZdyd/+FUbOHwcS1AQ/XGWCQlahoME3sPsNOJM0Ru1jwA/Z4w7+CwZ0VSmy ooqExkS87S3wLzzflivqBnu40de1vWt33mIIbPRUDukPHQRPZMDNRPtAhUE2mL52 nkuUfhgcSNjyIYnCEqCNq5xd+sACepLB5F3LtszdmMgd9jjAJVcXqeXugiN4TSeI arMlzmPq2uIhDNKqx/ljsA9GqgrsLI+WJ2EvbTirAAvbcPVZDUCEMuRc7tMluSfp J8wU4wu2h2J3KvTIbOYiP0eudTTzDdfBvkNV4Zdvygv9WdNutFbLvwiNMt7FiUVI gq3/Mq95J74UahL9NeuG02vpMCRChigMG6cXjCaZfAlnubjbdLZ56XF/XVQeRaoz MnW35R7Y3ER46eFzSq6hU1Xlsjq2I5Esm4yx2O5Rs7Ieu4MSHdz7SV6qkGX32dVC ajSfue/zPd4DEj83mFrZjcjpax7YNF006CrWyBftC5dPKWfftuqy1Uhl2EZuscPI I8dliTrT0DIHJX5GqhqoMuX4iq5rN1WhSVB0N+HQZDt1nhHyiWyO/7zb0n6sHPv/ E9D2qOO7jYL++b6oTIT9 =RQ0Y -----END PGP SIGNATURE-----

2 2

Main tool shed is running the next-stable branch
by Greg Von Kuster 21 Oct '13

21 Oct '13

FYI: The Main Tool Shed is now running the next-stable branch and all metadata has been reset on all repositories. The tentative date of the next Galaxy relesase is currently November 4. The Main Tool Shed will be updated to the stable branch at the time of the release. Greg Von Kuster

1 0

Installation on cluster
by Jurgens de Bruin 21 Oct '13

21 Oct '13

Hi, I am struggling to get galaxy to submit job to a cluster, I am using Torque and Maui. This is my universe_wsgi.ini ----- Handler Definitions ------------------------------------------------- [server:web0] use = egg:Paste#http port = 8181 host = 127.0.0.1 use_threadpool = true threadpool_workers = 7 [server:web1] use = egg:Paste#http port = 8182 host = 127.0.0.1 use_threadpool = true threadpool_workers = 7 [server:handler0] use = egg:Paste#http port = 8090 host = 127.0.0.1 use_threadpool = true threadpool_workers = 5 [server:handler1] use = egg:Paste#http port = 8091 host = 127.0.0.1 use_threadpool = true threadpool_workers = 5 # ------ Handler Definitions ------------------------------------------------- This is job_conf.xml *<?xml version="1.0"?>  <job_conf> <plugins workers="4"> <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="2"/> <plugin id="pbs" type="runner" load="galaxy.jobs.runners.pbs:PBSJobRunner" workers="6"/> </plugins> <handlers default="handlers"> <handler id="handler0" tags="handlers"/> <handler id="handler1" tags="handlers"/> </handlers> <destinations default="regularjobs"> <destination id="local" runner="local"/> <destination id="regularjobs" runner="pbs" tags="cluster"> <param id="Resource_List">walltime=24:00:00</param> <param id="galaxy_external_runjob_script">scripts/drmaa_external_runner.py</param> <param id="galaxy_external_killjob_script">scripts/drmaa_external_killer.py</param> <param id="galaxy_external_chown_script">scripts/external_chown_script.py</param> </destination> <destination id="real_user_cluster" runner="pbs"> <param id="galaxy_external_runjob_script">scripts/drmaa_external_runner.py</param> <param id="galaxy_external_killjob_script">scripts/drmaa_external_killer.py</param> <param id="galaxy_external_chown_script">scripts/external_chown_script.py</param> </destination> <destination id="dynamic" runner="dynamic">  <param id="type">python</param> <param id="function">interactiveOrCluster</param> </destination> </destinations> </job_conf><?xml version="1.0"?>  <job_conf> <plugins workers="4"> <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="2"/> <plugin id="pbs" type="runner" load="galaxy.jobs.runners.pbs:PBSJobRunner" workers="6"/> </plugins> <handlers default="handlers"> <handler id="handler0" tags="handlers"/> <handler id="handler1" tags="handlers"/> </handlers> <destinations default="regularjobs"> <destination id="local" runner="local"/> <destination id="regularjobs" runner="pbs" tags="cluster"> <param id="Resource_List">walltime=24:00:00</param> <param id="galaxy_external_runjob_script">scripts/drmaa_external_runner.py</param> <param id="galaxy_external_killjob_script">scripts/drmaa_external_killer.py</param> <param id="galaxy_external_chown_script">scripts/external_chown_script.py</param> </destination> <destination id="real_user_cluster" runner="pbs"> <param id="galaxy_external_runjob_script">scripts/drmaa_external_runner.py</param> <param id="galaxy_external_killjob_script">scripts/drmaa_external_killer.py</param> <param id="galaxy_external_chown_script">scripts/external_chown_script.py</param> </destination> <destination id="dynamic" runner="dynamic">  <param id="type">python</param> <param id="function">interactiveOrCluster</param> </destination> </destinations> </job_conf>* I can submit jobs to the cluster so I know that part is working. Any help would be appreciated. -- Regards/Groete/Mit freundlichen Grüßen/recuerdos/meilleures salutations/ distinti saluti/siong/duì yú/привет Jurgens de Bruin

2 1

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galaxy-dev October 2013