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Tool Development DELLY
by Marco Albuquerque 10 Jan '15

10 Jan '15

Hello Galaxy, I'm currently working on adding some tools and am having an issue with DELLY. So, I am under the impression that BAM indexing happens automatically when a BAM is uploaded. However there is no associated dataset_i.dat.bai file in the file location in my local instance of galaxy. There is however metadata which seems to be created but they are not being linked together. What I mean to say is DELLY errors with cannot find Bam Index. I was curious if there is a specific way developers are suppose to work around this? Basically we want to avoid having to provide both the BAM and BAM index and symbolically linking a new dataset because we know you have already created a better implementation, we just want to use it and don't know how. Any help is greatly appreciated, Marco

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Galaxy Bioblend option for importing dataset into a library?
by Dooley, Damion 09 Jan '15

09 Jan '15

I see Galaxy API has a feature to import a history dataset into the library (in copy_hda_to_ldda() fn from GCC2013 training day course). Is this available as well via Bioblend? Latest docs don't seem to include this feature. It would be the opposite of Bioblend's upload_dataset_from_library(history_id, lib_dataset_id) ) Objective is to get customized blast indexes into library that way for shared use. Or have them actually exist outside galaxy, and linked in. Regards, Damion Hsiao lab, BC Public Health Microbiology & Reference Laboratory, BC Centre for Disease Control 655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada

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How to test my functional tests?
by Jeltje van Baren 08 Jan '15

08 Jan '15

Hi, I'm trying to find out what the best way is to see if my functional tests work as expected, and I'm also wondering when these tests are (supposed to be) run. Here are the details: Following instructions at https://wiki.galaxyproject.org/Admin/Tools/AddToolTutorial, I created a little toolExample tool under galaxy-dist/tools/myTools. I also created test input and output in a test-data directory and added a test to the toolExample.xml file: <tests> <test> <param name="input" value="testinput.fa"/> <output name="out_file1" file="testoutput.txt"/> </test> </tests> And yes, the files are named correctly: tools/myTools/test-data/testinput.fa tools/myTools/test-data/testoutput.txt I added the new tool to config/tools_conf.xml AND to config/tools_conf.xml.sample. Question #1: Why is a .sample file used by run_functional_tests.sh? I thought with .sample extensions were meant as examples for creating your own versions, I'm really surprised that any script would want to access these. I restarted galaxy to verify that the new tool showed up, then checked that I could test it: ./run_functional_tests.sh -list | grep fa_gc_content_1 It shows up in the list of tools. So then I tested it: ./run_functional_tests.sh -id fa_gc_content_1 This gives IOError: [Errno 2] No such file or directory: '/inside/home/jeltje/exp/varscan2/programs/galaxy-dist/test-data/testinput.fa' So it looks like at some point the testinput should have been copied to galaxy-dist/test-data but wasn't. Question # 2: Is there some setting that makes this test input (and output) get copied to the correct location, or do I have to do this manually? I also tried testing by uploading the tool to the testtoolshed (as jtest1). I deliberatly put the wrong value in the testoutput.txt file because I'd like to see a test fail before I'll accept that it succeeds. It appears the testinput does not get tested on upload, because I got no automated test results, and no error messages anywhere. Is that expected behavior? I know the tools get tested every so often, I'm just surprised it doesn't happen on upload. The tool could then also be easily installed to my galaxy distribution, without errors in my log or on the browser pages. Question #3: At what point in creating or downloading a repository are these tests run? And lastly, #4: is either of these the best way to test my tests, or did I overlook something? Thank you! -Jeltje

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Mercurial is out of date for Toolshed
by Ryan G 08 Jan '15

08 Jan '15

I've been trying to track down why I can't get anything from the toolshed installed and finally have it figured out. Whenever I tried to install anything I always got an Error with no explanation of what the error was. After enabling Debug messages into the log file, I see the error is: tool_shed.util.hg_util DEBUG 2014-12-22 14:47:48,910 Error cloning repository: httpsconnection instance has no attribute '_set_hostport' I googled around and found out this is a known bug/issue with older version of Mercurial and was fixed in v3. I added a line to hg_util.py to see where it picks up hg. Its using version 2.2.3. Indeed, one of the eggs downloaded by Galaxy is mercurial-2.2.3. I have the newest version of mercurial installed in my site-packages folder but I guess that's not what galaxy wants. So my question is, how do I get Galaxy to use the latest version of Mercurial? And, Why did it download an older version?

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cluster queue job id?
by Anna Terry 08 Jan '15

08 Jan '15

Hi, Sorry if this is a stupid question, but is the job id and other queue info, for a job that has run on a cluster available from within galaxy? Both during and and after completion of the job. Many thanks Anna

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Text file busy
by Evan Bollig PhD 08 Jan '15

08 Jan '15

I get this error occasionally: "/bin/sh: 1: /opt/galaxy/web/database/job_working_directory/000/100/galaxy_100.sh: Text file busy" When this occurs, the step fails outright. Resubmitting the step resolves the issue and things run no problem. If this error appears early in a long workflow, I have to manually resubmit ALL dependent steps... what a pain! Perhaps this is something the Galaxy job scheduler can look out for, flush() the system, sleep() a second or two to let the file write and close, and then rerun. A more fault-tolerant way of running workflows without unnecessary human intervention. Cheers, -Evan Bollig Research Associate | Application Developer | User Support Consultant Minnesota Supercomputing Institute 599 Walter Library 612 624 1447 evan(a)msi.umn.edu boll0107(a)umn.edu

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The choice when I integrated slurm and galaxy in job_conf.xml
by xlwang 08 Jan '15

08 Jan '15

hi, Slurm is the DRM in my cluster. When I modified the job_conf.xml, which plugin should I use? slurm or drmaa?

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Dataset deletion / database update after user purge
by Nicolas Lapalu 08 Jan '15

08 Jan '15

Hi Galaxy team, We performed a database and datasets purge of our Galaxy server. We decided to delete and purge few user accounts. We supposed that the purge of a user would trigger cascade deletions in database. So we used the web interface to delete and to purge these accounts. Then we launched cleanup_dataset.py in several ways: python scripts/cleanup_datasets/cleanup_datasets.py universe_wsgi.ini -d 1 -1 -r > cleanup_1.log python scripts/cleanup_datasets/cleanup_datasets.py universe_wsgi.ini -d 1 -2 -r > cleanup_2.log python scripts/cleanup_datasets/cleanup_datasets.py universe_wsgi.ini -d 1 -3 -r > cleanup_3.log python scripts/cleanup_datasets/cleanup_datasets.py universe_wsgi.ini -d 1 -5 -r > cleanup_5.log python scripts/cleanup_datasets/cleanup_datasets.py universe_wsgi.ini -d 1 -4 -r > cleanup_4.log python scripts/cleanup_datasets/cleanup_datasets.py universe_wsgi.ini -d 1 -6 -r > cleanup_6.log After a simple control, I can see that some datasets belonging to (and only to) purged user accounts are still present with a status : deleted = t and purged = f. Moreover, some datasets (not shared with other users or linked to a library) have the status deleted = f and purged = f. When I look at the history status associated with the dataset, I can obtain deleted = t and purged = f. So, the purge of a user account don't change the status of his histories and datasets. Do you thing that I can change the history status 'deleted = f to deleted = t, and purged = f to purged = t' for all purged users ? I expect that the cleanup script launches the cascade purge ! below the sql command: // all datasets belonging to at least one purged user (shared or not) select D.id as "dataset id",U.email, D.deleted as "dataset deleted", D.purged as "dataset purged" , H.deleted as "history deleted" ,H.purged as "history purged" from galaxy_user U,history H ,history_dataset_association A, dataset D where A.dataset_id=D.id and H.id=A.history_id and U.id=H.user_id and D.id in (select D.id from galaxy_user U,history H ,history_dataset_association A, dataset D where A.dataset_id=D.id and H.id=A.history_id and U.id=H.user_id and U.deleted = 't' and U.purged = 't') order by D.id;

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GCC2015 Training Day Topic Nominations are Open through January 6
by Dave Clements 06 Jan '15

06 Jan '15

Hello all, GCC2015 Training Day <http://gcc2015.tsl.ac.uk/training-day/> topics are nominated by you <http://bit.ly/gcc2015tdnom>, the Galaxy Community. Please take a few minutes to nominate a topic. Any topic of interest to the Galaxy Community can be nominated and you are encouraged to nominate more than one. If you are looking for ideas, see the topics nominated in 2013 <http://bit.ly/1i2j1gN> and 2014 <http://bit.ly/1s6NtMN>, and the Events <https://wiki.galaxyproject.org/Events> and the Events Archives <https://wiki.galaxyproject.org/Events/Archive> pages. Nominated topics will be published on the Training Day <http://gcc2015.tsl.ac.uk/training-day/> page as they come in. *Nominations close 6 January*. Topics will be compiled into a uniform list by the GCC2015 Organising Committee <http://gcc2015.tsl.ac.uk/organisers>, and topics will be voted on by the Galaxy Community 12-23 January. Topics will then be selected and scheduled based on topic interest, and the organisers' ability to confirm instructors for each session. Some very popular sessions may be scheduled more than once. The final schedule will be posted before registration opens. Cheers, GCC2015 Organising Committee <http://gcc2015.tsl.ac.uk/organisers> -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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Problem with Biopython
by Alfredo Guilherme Silva Souza 06 Jan '15

06 Jan '15

Has anyone used the Biopython in Galaxy ? *Traceback (most recent call last):* * File "/home/steve/galaxy-dist/tools/molecular_dynamics/gromacs.py", line 10, in <module>* * import Bio.PDB.PDBParser* *ImportError: No module named Bio.PDB.PDBParser* Researching I saw that I have to work with eggs in the Galaxy. Has anyone done this with Biopython? Is it really necessary? Thanks -- *Alfredo Guilherme da Silva Souza* Distributed Systems and Computer Networks Federal University of São Carlos - UFSCar Contact +55 16 9115-3035 | alfredo.bioinformatics(a)gmail.com <contato(a)gilsonleite.com.br>

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