June 2012 - galaxy-dev - lists.galaxyproject.org

Citations for tools
by Clare Sloggett 21 Jun '12

21 Jun '12

Hi all, I'd like to suggest, or request, a feature - I think that posting to galaxy-dev is the right place to start? After I've done an analysis, it would be useful to be given a list of references for all the tools I used in that history, which I could use to cite the appropriate papers. At the moment, it seems that most tool developers add a "please cite the following paper" note to the <help> tag in the wrapper so that it displays on the tool screen before you run it. I'd like to suggest: * adding a <cite> tag to the tool wrappers xml, * adding a feature to the history UI which will list all the references to cite for the a history. I think this would encourage people to cite the tools they use properly and hence encourage developers to put their tools into the toolshed! With the standard tools moving into the toolshed it will be really important for tool wrappers to be maintained. Any thoughts? Clare -- Clare Sloggett Research Fellow / Bioinformatician Life Sciences Computation Centre Victorian Life Sciences Computation Initiative University of Melbourne, Parkville Campus 187 Grattan Street, Carlton, Melbourne Victoria 3010, Australia Ph: 03 903 53357 M: 0414 854 759

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Do input and output files get modified in Galaxy?
by Ciara Ledero 20 Jun '12

20 Jun '12

Hi all, This is going to be a very long message, so please bear with me. Anyway... I have been asked by my colleagues to integrate modified versions of velveth, velvetg and oases into our Galaxy instance. Of course, the first step was to upload the would-be input files. Since these are stored as .dat files in the database/files/000 folder, I symlinked the uploads to another folder. When I run the commands of the aforementioned steps, they access these symlinked files and perform the needed operations using them. I then just copy the data from the generated files onto the output files that would be visible in Galaxy. Is everything still clear? I hope so. Moving on... Now, they have asked me to integrate another script, and this time it is running rsem. It requires corrected left and right reads, and OASES' transcript output. But when I ran the rsem, I got an error concerning the input transcript file. I found two probable reasons why I was getting an error. One was that the transcript file might be empty. I've already checked this, and the file was not empty. Another reason was that the transcript FASTA file might not be following the required format. And so we arrive at my question: Do input and output files go through some minor format modifications when used in Galaxy? I have already manually ran the above commands, and everything works well. But when I downloaded the transcript file from Galaxy to use it via the konsole, I got the same error. Thank you in advance for any help, CL

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using velvet assembler on Galaxy/JGI
by Pitts, Ronald J 20 Jun '12

20 Jun '12

Dear Galaxy Administrator, I would like to attempt to assemble some Illumina RNA-seq reads using velvet on the Galaxy/JGI server, but I am unable to create a user account. Am I allowed to sign up and access the tools as a public user? Thank you, _______________________________________________________________________________________________________________________________ R. Jason Pitts, Ph.D. Dept. of Biological Sciences Vanderbilt University 465 21st Ave. S. Nashville, TN 37232 615-343-3718 *This e-mail, including any attachments, is intended solely for the addressee(s) and may contain legally privileged and/or confidential information.

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Set job_working_directory to a cluster compute node /tmp
by Derrick Lin 20 Jun '12

20 Jun '12

Hi guys, I have deploy a galaxy on a cluster (so I installed it on a NFS share that it's accessible by all cluster compute nodes). Everything is running fine. Now I am looking for a way such that every job dispatched to a compute node uses that node's local /tmp as working directory. I know galaxy config provides job_working_directory for the similar purpose. My question really is, while all my compute nodes can access the NFS share where galaxy installed, but the galaxy host cannot access each compute node's /tmp. Is there a way that for the galaxy to collect job results back to the data directory? Regards, Derrick

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Re: [galaxy-dev] samtools view region
by Jim Johnson 20 Jun '12

20 Jun '12

Jaap, I put a tool: "samtools_filter" into the galaxy toolshed http://toolshed.g2.bx.psu.edu/ that uses samtools view to filter regions. It creates symbolic links as Peter suggests. (The symbolic links are created in the job_working directory which is automatically deleted when the job is finished.) JJ > Hi Peter, Thanks for you quick answer! But I am very new to Galaxy. Could you explain something about those symlinks? > Regards, Jaap > On Wed, Jun 20, 2012 at 2:59 PM, <J.W.F.van_der_Heijden(a)lumc.nl> wrote: >>> Hi all, >>> >>> I was working on the integration of the "samtools view" to work with Galaxy. >>> The idea is to filter an indexed bam file on a chromosome with "samtools >>> view -bh in.bam.bai chr1". >>> After some research I noted that samtools will only execute this command >>> when it can find the corresponding sorted bam file, so the "in.bam". >>> >>> The problem is that Galaxy renames all the files. So "in.bam" will be for >>> instance dataset_1.dat. When I index the bam file I will get an indexed bam >>> file named dataset_2.dat. Samtools can't detect then that dataset_1.dat is >>> the sorted bam file and dataset_2.dat is the bai file. >>> >>> Now I was wondering if it is possible to rename files in the >>> ~/galaxy-dist/database/files/000 with a command line. So that dataset_2.dat >>> will be moved to dataset_1.dat.bai. >>> >>> Does anyone know how to do that? >>> >>> Kind Regards, >>> Jaap >> The simple answer is a wrapper script which makes symlinks for >> the BAM file and its BAI file using the normal naming conventions. >> >> Peter

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using x11 or freenx to connect to ASW cloud instance of CloudMan / Galaxy
by Dellwo, Martin J. [JRDUS] 20 Jun '12

20 Jun '12

Hi there, I am piloting my own instance of CloudMan in Amazon Web Services, using the current public AMI (according to your Wiki), AMI: ami-da58aab3 and Name: 861460482541/galaxy-cloudman-2011-03-22. I'd like to either tunnel X11 through SSH (either PuTTY on Windows, or just at a Linux prompt with "ssh -X"), or use an NX client to connect. I'm very familiar with how to do both, and have tested both locally. I have a local X server (latest XMing) on my Windows box, latest PuTTY, latest nomachine.com NX client. When I first start up CloudMan and login as user 'ubuntu', it asks if I would like to set up NX, and I've added myself as a user there. I can log in as that user via normal SSH connection. I can't seem to either tunnel X11 over SSH or connect w/ NX. NX connects up through the initial stage and asks me for my password, but doesn't start a desktop. Trying to tunnel X11 (xclock command) just sits forever (either via PuTTY or just normal "ssh -X" at a Linux command line). I see that Xvfb is running, and I can use 'xwd' to see an image of what is in the virtual frame buffer, ie the xclock window. It does seem like not all the required packages are installed, or possibly I just need to start a different service. Should I expect that either tunneling or NX works 'out of the box', or are there more packages I need to install and configure? Any tutorials or pointers out on the web? Thanks. I did search mail archives. :) Martin J. Dellwo, Ph.D. Manager, Translational Informatics Janssen Research & Development, LLC Information Technology Welsh & McKean Roads, Spring House, PA 19477 mdellwo(a)its.jnj.com <mailto:mdellwo@its.jnj.com> ************************************************** Confidentiality Notice: This e-mail transmission may contain confidential or legally privileged information that is intended only for the individual or entity named in the e-mail address. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution, or reliance upon the contents of this e-mail is strictly prohibited. If you have received this e-mail transmission in error, please reply to the sender, so that Johnson & Johnson can arrange for proper delivery, and then please delete the message from your inbox. Thank you.

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circular import in tool_shed code gives unit test failure
by Anne Pajon 20 Jun '12

20 Jun '12

Dear, I've been running unit tests on the latest galaxy-central 7294:663e03e40c86 that have me this error: [localhost] out: ====================================================================== [localhost] out: ERROR: Failure: ImportError (cannot import name install_manager) [localhost] out: ---------------------------------------------------------------------- [localhost] out: Traceback (most recent call last): [localhost] out: File "/Users/pajon01/galaxy-test/galaxy-central/eggs/nose-0.11.1-py2.7.egg/nose/loader.py", line 379, in loadTestsFromName [localhost] out: addr.filename, addr.module) [localhost] out: File "/Users/pajon01/galaxy-test/galaxy-central/eggs/nose-0.11.1-py2.7.egg/nose/importer.py", line 39, in importFromPath [localhost] out: return self.importFromDir(dir_path, fqname) [localhost] out: File "/Users/pajon01/galaxy-test/galaxy-central/eggs/nose-0.11.1-py2.7.egg/nose/importer.py", line 86, in importFromDir [localhost] out: mod = load_module(part_fqname, fh, filename, desc) [localhost] out: File "/Users/pajon01/galaxy-test/galaxy-central/lib/galaxy/tool_shed/install_manager.py", line 10, in <module> [localhost] out: from galaxy.tool_shed.migrate.common import * [localhost] out: File "/Users/pajon01/galaxy-test/galaxy-central/lib/galaxy/tool_shed/migrate/common.py", line 9, in <module> [localhost] out: from galaxy.tool_shed import install_manager [localhost] out: ImportError: cannot import name install_manager [localhost] out: ---------------------------------------------------------------------- I fixed it by commenting out the circular import in tool_shed/install_manager.py hg diff diff -r 663e03e40c86 lib/galaxy/tool_shed/install_manager.py --- a/lib/galaxy/tool_shed/install_manager.py Wed Jun 20 03:39:05 2012 -0400 +++ b/lib/galaxy/tool_shed/install_manager.py Wed Jun 20 16:37:06 2012 +0100 @@ -7,7 +7,7 @@ from galaxy.util.json import from_json_string, to_json_string from galaxy.util.shed_util import * from galaxy.util.odict import odict -from galaxy.tool_shed.migrate.common import * +#from galaxy.tool_shed.migrate.common import * Hope it would be useful to someone else. Kind regards, Anne. -- Anne Pajon, Ph.D. Cancer Research UK - Cambridge Research Institute Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE anne.pajon(a)cancer.org.uk | +44 (0)1223 404 334 NOTICE AND DISCLAIMER This e-mail (including any attachments) is intended for the above-named person(s). If you are not the intended recipient, notify the sender immediately, delete this email from your system and do not disclose or use for any purpose. We may monitor all incoming and outgoing emails in line with current legislation. We have taken steps to ensure that this email and attachments are free from any virus, but it remains your responsibility to ensure that viruses do not adversely affect you. Cancer Research UK Registered in England and Wales Company Registered Number: 4325234. Registered Charity Number: 1089464 and Scotland SC041666 Registered Office Address: Angel Building, 407 St John Street, London EC1V 4AD.

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samtools view region
by J.W.F.van_der_Heijden＠lumc.nl 20 Jun '12

20 Jun '12

Hi all, I was working on the integration of the "samtools view" to work with Galaxy. The idea is to filter an indexed bam file on a chromosome with "samtools view -bh in.bam.bai chr1". After some research I noted that samtools will only execute this command when it can find the corresponding sorted bam file, so the "in.bam". The problem is that Galaxy renames all the files. So "in.bam" will be for instance dataset_1.dat. When I index the bam file I will get an indexed bam file named dataset_2.dat. Samtools can't detect then that dataset_1.dat is the sorted bam file and dataset_2.dat is the bai file. Now I was wondering if it is possible to rename files in the ~/galaxy-dist/database/files/000 with a command line. So that dataset_2.dat will be moved to dataset_1.dat.bai. Does anyone know how to do that? Kind Regards, Jaap

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No module named galaxy !!
by Chebbi Mohamed Amine 20 Jun '12

20 Jun '12

Hi Galaxy team ! I'am trying to remove userless histories from my galaxy database as mentoned in this link ( by using the command above : python cleanup_datasets.py universe_wsgi.ini -d 60 -1 However I get an error message like this : File "cleanup_datasets.py", line 13, in <module> from galaxy import eggs ImportError: No module named galaxy Although I set cleanup_job = never in my Galaxy config and check the PBS script like mentioned in the mailing list discussions as above , i have always the same problem of galaxy module : GALAXY_LIB="/path/to/galaxy-dist/lib" if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then export PYTHONPATH="$GALAXY_LIB:$PYTHONPATH" else export PYTHONPATH="$GALAXY_LIB" fi fi Could someone help me please ! Thanks Amine

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Tophat and Bowtie2
by Luciano Cosme 19 Jun '12

19 Jun '12

Hi, I installed bowtie2 and when running tophat I get the following error: Error in tophat: [2012-06-19 14:02:39] Beginning TopHat run (v2.0.3) ----------------------------------------------- [2012-06-19 14:02:39] Checking for Bowtie Bowtie version: 2.0.0.6 [2012-06-19 14:02:39] Checking for Samtools Samtools version: 0.1.18.0 [2012-06-19 14:02:39] Checking for Bowtie index files Error: Could not find Bowtie 2 index files (/tmp/tmpojo7bV/AgamP3.14.dna.toplevel.*.bt2) I was wondering if I can create the index files using bowtie2 via command line and then change the universe_wsgi.ini to: # Temporary files are stored in this directory. new_file_path = database/tmp and put the index files there. Anyway, why is it not creating the indexes? I created links to all bowtie2 executable files. If I remove bowtie 0.12.8, then I get a error from tophat (bowtie not installed). Is it creating the index with bowtie 0.12.8? Thank you. Luciano

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