November 2015 - galaxy-dev - lists.galaxyproject.org

Trying to install GATK on up-to-date Galaxy install
by Dooley, Damion 04 Nov '15

04 Nov '15

I seem to run into a bottleneck with the .’package_pixman_0_32_4’. This seems to happen with both boris and devteam versions? The same error is preventing cairo from installing. libpng<http://salk.bccdc.med.ubc.ca/galaxylab/admin_toolshed/manage_repository_too…> 1.6.7 package Installed pixman<http://salk.bccdc.med.ubc.ca/galaxylab/admin_toolshed/manage_repository_too…> 0.32.4 package Error /usr/local/galaxy/shared/tool_dependency/libpng/1.6.7/boris/package_libpng_1_6_7/7de5acbf6c85/lib: file not recognized: Is a directory collect2: ld returned 1 exit status make[2]: *** [clip-test] Error 1 make[1]: *** [all-recursive] Error 1 make: *** [all] Error 2 I appreciate any pointers on this! Regards, Damion

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Planemo 0.19.0 testing tools that produce dataset collections
by Von Kuster, Greg 04 Nov '15

04 Nov '15

Hello Galaxy devs, I’m developing a tool that uses a multi-select list to accept any number of input datasets. The tool works fine when executing it within Galaxy, but when running it through planemo testing, it never passes, so I’m wondering if there are known issues with planemo testing tools that produce dataset collections. I’ve spent some time adding debugging log statements into the Galaxy framework for planemo test runs, but haven’t uncovered anything obvious. So if there are no known issues with planemo testing dataset_collections, I’m wondering if my tool config syntax is incorrect. Does anyone see anything obvious? Any insight is much appreciated! Here is the command line. Notice that I do not define any outputs since I am using a dataset collection. Is this causing a problem for planemo? <command> python $__tool_directory__/genetrack.py --input_format $input_format_cond.input_format #if str($input_format_cond.input_format) == "genetracktool": #for $i in $input_format_cond.input_genetracktool: --input "${i}" "${i.hid}" "${i.name}" #end for #elif str($input_format_cond.input_format) == "gff": #for $i in $input_format_cond.input_gff: --input "${i}" "${i.hid}" "${i.name}" #end for #end if --sigma $sigma --exclusion $exclusion --up_width $up_width --down_width $down_width --filter $filter --chromosome $chromosome --chunk_size $chunk_size --output_format $output_format </command> The input dataset parameter looks like this: <param name="input_gff" type="data" format="gff" multiple="True" label="Predict peaks on" /> The tool produces a list of outputs, so I’ve defined a collection like this: <outputs> <collection name="genetrack_output" type="list" label="Genetrack results on ${on_string}"> <discover_datasets pattern="(?P<designation>.*)" directory="output" ext="gff" visible="false" /> </collection> </outputs> I’m using planemo, version 0.19.0. Here is one of the tools’ functional test definitions. <test> <param name="input" value="genetrack_input_unsorted4.gff" ftype="gff" /> <param name="input_format" value="gff" /> <param name="sigma" value="5" /> <param name="exclusion" value="20" /> <param name="up_width" value="10" /> <param name="down_width" value="10" /> <param name="filter" value="3" /> <param name="chromosome" value="all" /> <param name="chunk_size" value="10" /> <param name="output_format" value="gff" /> <output_collection name="genetrack_output" type="list"> <element name="s5e20u10d10F3" file="genetrack_output4.gff" ftype="gff" /> </output_collection> </test> Here is the log from running the test with planemo. Genetrack ( genetrack ) > Test-3 ... requests.packages.urllib3.connectionpool INFO 2015-11-04 15:22:03,292 Starting new HTTP connection (1): localhost galaxy.web.framework.webapp INFO 2015-11-04 15:22:03,295 Session authenticated using Galaxy master api key requests.packages.urllib3.connectionpool DEBUG 2015-11-04 15:22:03,303 "GET /api/users?key=test_key HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2015-11-04 15:22:03,305 Starting new HTTP connection (1): localhost galaxy.web.framework.webapp INFO 2015-11-04 15:22:03,308 Session authenticated using Galaxy master api key requests.packages.urllib3.connectionpool DEBUG 2015-11-04 15:22:03,326 "POST /api/users/2891970512fa2d5a/api_key HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2015-11-04 15:22:03,328 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2015-11-04 15:22:03,418 "POST /api/histories HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2015-11-04 15:22:03,421 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2015-11-04 15:22:03,475 "POST /api/tools HTTP/1.1" 400 None ERROR ====================================================================== ERROR: Genetrack ( genetrack ) > Test-1 ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/gvk/work/git_workspace/galaxy/test/functional/test_toolbox.py", line 289, in test_tool self.do_it( td ) File "/Users/gvk/work/git_workspace/galaxy/test/functional/test_toolbox.py", line 58, in do_it raise e RunToolException: Error creating a job for these tool inputs - Unknown error occurred while processing request. -------------------- >> begin captured logging << -------------------- requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost galaxy.web.framework.webapp: INFO: Session authenticated using Galaxy master api key requests.packages.urllib3.connectionpool: DEBUG: "GET /api/users?key=test_key HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost galaxy.web.framework.webapp: INFO: Session authenticated using Galaxy master api key requests.packages.urllib3.connectionpool: DEBUG: "POST /api/users HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost galaxy.web.framework.webapp: INFO: Session authenticated using Galaxy master api key requests.packages.urllib3.connectionpool: DEBUG: "POST /api/users/2891970512fa2d5a/api_key HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool: DEBUG: "POST /api/histories HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool: DEBUG: "POST /api/tools HTTP/1.1" 400 None --------------------- >> end captured logging << —————————— Thanks very much, Greg Von Kuster

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installable revisions for repository suite definitions
by Aaron Petkau 04 Nov '15

04 Nov '15

Hello, I'm running into some issues with maintaining multiple installable revisions for a repository suite and I'm not sure if there's something I've missed. I have a local toolshed where I'm maintaining my tools, and I have a repository suite definition, defining a number of dependencies. So, I have: suite_X (mercurial revision 0): Dependency A Dependency B I updated "suite_X" and changed the dependencies: suite_X (mercurial revision 1): Dependency A Dependency B Dependency C I would like to have both mercurial revision 0 and 1 installable in Galaxy, but only revision 1 (the latest) is showing up as installable. I found documentation at https://wiki.galaxyproject.org/RepositoryRevisions but this seems to only cover a repository containing a single tool, not a suite of tools. Is there something I'm doing wrong or some setting I have to change here? My toolshed is running with Galaxy tag "v15.07". Thanks, Aaron

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GCC2016 Training Topic Voting CLOSES THIS FRIDAY
by Dave Clements 04 Nov '15

04 Nov '15

Hello all, *Voting <http://bit.ly/gcc2016vote>* on what training topics <https://wiki.galaxyproject.org/Events/GCC2016/Training> are offered at GCC2016 Training <https://wiki.galaxyproject.org/Events/GCC2016/Training> *closes this Friday*. Please vote <http://bit.ly/gcc2016vote> in the next two days! > As always, please let us know if you have any questions. Thanks, The GCC2016 Exec <https://wiki.galaxyproject.org/Events/GCC2016/Organizers> http://bit.ly/gcc2016vote > There are nominated topics > <https://wiki.galaxyproject.org/Events/GCC2016/Training> spanning from > basic usage to advanced deployment. No matter what you do with Galaxy, > there are topics for you to choose from. Your vote > <http://bit.ly/gcc2016vote> will determine the topics that are offered, > which topics should be offered more than once, and which ones should not be > scheduled at the same time. Your vote matters. *Topic voting closes November 6.* The Training schedule, including > instructors, will be published before early registration opens. *About GCC2016 Training > <https://wiki.galaxyproject.org/Events/GCC2016/Training>:* The 2016 Galaxy Community Conference (GCC2016) > <https://wiki.galaxyproject.org/Events/GCC2016> will be held June 25-29 > at Indiana University <http://indiana.edu/> in Bloomington, Indiana, > United States. GCC2016 features two full days of training on June 26-27 > <https://wiki.galaxyproject.org/Events/GCC2016/Training>. Each day will > have multiple tracks, with each track featuring several sessions throughout > the day. Workshops will be hands-on and participants will be strongly encouraged to > bring a laptop and follow along. If you work in data-intensive biomedical research, there is no better place > than GCC2016 to present your work and to learn from others. > -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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support for newer versions of Torque
by Malcolm Tobias 04 Nov '15

04 Nov '15

I'm having trouble "scrambling my eggs". I'm trying to build PBS support into Galaxy on a cluster running Torque >5.0. The problem seems to be with pbs_python 4.4.0 which doesn't build against newer versions of Torque. I was able to download 4.6.0 and was able to build it from: ftp://ftp.surfsara.nl/pub/outgoing/pbs_python.tar.gz but I'm not sure how to integrate that build with Galaxy. It seems if 4.6.0 was available from: http://eggs.galaxyproject.org/pbs_python/ I'd have a chance. Any thoughts? Cheers, Malcolm -- Malcolm Tobias 314.362.1594

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FASTQ Groomer tool
by Fernandez Edgar 04 Nov '15

04 Nov '15

Hello gents, I just installed "FASTQ Groomer tool" for the teachers to try it out and I've been getting the following error than I do not understand: galaxy.jobs DEBUG 2015-11-04 08:16:19,957 (756) Working directory for job is: /home/galaxy/galaxy-prod/database/job_working_directory/000/756 galaxy.jobs.handler WARNING 2015-11-04 08:16:19,958 (756) Tool 'toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.0.4' removed from tool config, unable to run job galaxy.jobs.handler ERROR 2015-11-04 08:16:20,159 failure running job 756 Traceback (most recent call last): File "/home/galaxy/galaxy-prod/lib/galaxy/jobs/handler.py", line 273, in __monitor_step job_state = self.__check_job_state( job ) File "/home/galaxy/galaxy-prod/lib/galaxy/jobs/handler.py", line 342, in __check_job_state state, job_destination = self.__verify_job_ready( job, job_wrapper ) File "/home/galaxy/galaxy-prod/lib/galaxy/jobs/handler.py", line 362, in __verify_job_ready job_wrapper.fail( e ) File "/home/galaxy/galaxy-prod/lib/galaxy/jobs/__init__.py", line 984, in fail self.sa_session.flush() File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/scoping.py", line 150, in do return getattr(self.registry(), name)(*args, **kwargs) File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/session.py", line 2004, in flush self._flush(objects) File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/session.py", line 2122, in _flush transaction.rollback(_capture_exception=True) File "build/bdist.linux-x86_64/egg/sqlalchemy/util/langhelpers.py", line 60, in __exit__ compat.reraise(exc_type, exc_value, exc_tb) File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/session.py", line 2086, in _flush flush_context.execute() File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/unitofwork.py", line 373, in execute rec.execute(self) File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/unitofwork.py", line 532, in execute uow File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/persistence.py", line 170, in save_obj mapper, table, update) File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/persistence.py", line 673, in _emit_update_statements execute(statement, multiparams) File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line 914, in execute return meth(self, multiparams, params) File "build/bdist.linux-x86_64/egg/sqlalchemy/sql/elements.py", line 323, in _execute_on_connection return connection._execute_clauseelement(self, multiparams, params) File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line 1010, in _execute_clauseelement compiled_sql, distilled_params File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line 1146, in _execute_context context) File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line 1332, in _handle_dbapi_exception exc_info File "build/bdist.linux-x86_64/egg/sqlalchemy/util/compat.py", line 199, in raise_from_cause reraise(type(exception), exception, tb=exc_tb) File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line 1139, in _execute_context context) File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/default.py", line 442, in do_execute cursor.execute(statement, parameters) File "build/bdist.linux-x86_64-ucs4/egg/MySQLdb/cursors.py", line 173, in execute self.errorhandler(self, exc, value) File "build/bdist.linux-x86_64-ucs4/egg/MySQLdb/connections.py", line 36, in defaulterrorhandler raise errorclass, errorvalue ProgrammingError: (_mysql_exceptions.ProgrammingError) (1064, "You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near '), blurb='tool error' WHERE history_dataset_association.id = 1498' at line 1") [SQL: u'UPDATE history_dataset_association SET update_time=%s, info=%s, blurb=%s WHERE history_dataset_association.id = %s'] [parameters: (datetime.datetime(2015, 11, 4, 13, 16, 20, 153739), ('This tool was disabled before the job completed. Please contact your Galaxy administrator.',), 'tool error', 1498L)] According to the tool shed repo, fastq_groomer is installed properly. Mysql is at its latest for oracle linux 6: [0]# mysql --version mysql Ver 14.14 Distrib 5.1.73, for redhat-linux-gnu (x86_64) using readline 5.1 [0]# rpm -qa | grep -i mysql mysql-5.1.73-5.el6_6.x86_64 The only thing I have not done is update galaxy for the last 6 months because they're students using it and I do not want to change anything while it's in production. I'm a little bit lost: Would you please indicate what I should check next? Cordialement / Regards, Edgar Fernandez System Administrator (Linux) Direction Générale des Technologies de l'Information et de la Communication * Bur. : 1-514-343-6111 poste 16568 Université de Montréal PAVILLON ROGER-GAUDRY, bureau X-218

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tool-shed delete problem
by Kucukural, Alper 03 Nov '15

03 Nov '15

Hi, Could you help me to delete crisprseek from https://toolshed.g2.bx.psu.edu/? I am the owner but cannot delete. I got “Internal Server Error”. Thanks, Alper

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netcdf 4.3 error
by Olivier CLAUDE 03 Nov '15

03 Nov '15

Hello, I have found something strange while trying to install netcdf 4.3 : The error message: <urlopen error ftp : [Errno ftp error] 550 Failed to change directory> the link: ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4.3.1.1.tar.gz Which is now located here: ftp://ftp.unidata.ucar.edu/pub/netcdf/ <ftp://ftp.unidata.ucar.edu/pub/netcdf/old/netcdf-4.3.1.1.tar.gz> old/netcdf-4.3.1.1.tar.gz What can I do to override this? Thank you, M Olivier CLAUDE- PhD Student INSERM/UPMC UMRS ICAN 1166 Equipe 2 Faculté de médecine Pitié-Salpêtrière 91, bld de l'Hôpital - 3ème étage - Porte 305 75013 Paris - FRANCE

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Developing package wrappers
by Tiago Rodrigues Antao 02 Nov '15

02 Nov '15

Hi, I am afraid that I might be overlooking something obvious but... I am trying to add a few tools to the RAD-Seq portfolio of Galaxy. For that effect I am designing a few package wrappers. My problem is to understand the best practice to develop wrappers for dependencies of external tools. For normal tools, that is quite easy: one uses the galaxy/tool/XXX to do all development and testing. But for dependency wrappers, the only solution that I have found is to upload the wrapper to a toolshed and installing it via the admin interface... This is cumbersome. Is there any way to test/develop a package wrapper so that I can test tool_dependencies.xml without uploading it to a toolshed and installing it from there? Thanks, Tiago

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November Galactic News: New papers, events, jobs, servers, and more
by Dave Clements 02 Nov '15

02 Nov '15

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