October 2012 - galaxy-user - lists.galaxyproject.org

Batch jobs...
by Neil.Burdett＠csiro.au 30 Oct '12

30 Oct '12

Hi, I've created a workflow that works well. The workflow accepts 2 input files. After uploading all my input files (there is a lot). How can I batch the process, because I don't want to select files manually and run each job manually. Is there a way to batch this action? Thanks Neil

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Re: [galaxy-user] Latest supported Cufflinks?
by hogandj＠gmail.com 29 Oct '12

29 Oct '12

lets.see the.data, i would be surprised if there was much cross hyb T-Mobile. America’s First Nationwide 4G Network ----- Reply message ----- From: "Jennifer Jackson" <jen(a)bx.psu.edu> To: "Bidwell, Christopher A." <cbidwell(a)purdue.edu> Cc: "galaxy-user(a)bx.psu.edu" <galaxy-user(a)bx.psu.edu> Subject: [galaxy-user] Latest supported Cufflinks? Date: Mon, Oct 29, 2012 1:31 pm Hello Chris, Cufflinks 1.3 is currently supported. However, this may be unrelated, or rather you may need so solve another problem first. The error seems to be related to how you have the reference data set up and some of the tool options you are using (bias correction = Y ?). Difficult to tell the root cause with the given data, but here is the information for both so that you can troubleshoot. The goal would be to make sure that the reference genome is in place with indexes, it is in the builds.txt list and configured correctly, and that the same genome is used for all steps in the analysis. Data setup: http://wiki.g2.bx.psu.edu/Admin/Data%20Integration http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup Tool dependencies: http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies More about distributions: http://bitbucket.org/galaxy/galaxy-dist (source) http://wiki.g2.bx.psu.edu/News (has RSS feed, all news) http://wiki.g2.bx.psu.edu/DevNewsBriefs (only releases) http://wiki.g2.bx.psu.edu/Galaxy%20on%20Twitter http://wiki.g2.bx.psu.edu/MailingLists You can follow us on Twitter, watch the wiki/RSS feed or join the galaxy-dev/user/annouce mailing lists to get notice when a new distribution is released along with a News Brief describing key updates and changes, including wrapper updates. Next time, posting to the galaxy-dev(a)bx.psu.edu mailing list would be best for questions about local instances. Thanks! Jen Galaxy team On 10/29/12 12:42 PM, Bidwell, Christopher A. wrote: I am interested in using Cufflinks 2.0 on our local instance of Galaxy but I am not sure if it is supported yet. We did Galaxy update in early October and we tried to install cufflinks V2.0 and it seems to run. I get the output files and they have the genes listed but 0.000 for all results (using files that worked on previous version). The output file summaries contain the following: Info: ERROR: Unable to read builds file: [Errno 2] No such file or directory: '/opt/galaxy/galaxy-dist/lib/galaxy/util/../../../tool-data/shared/ucsc/publicbuilds.txt' ERROR: Unable to read builds file: [Errno 2] No such file or directory: '/opt/galaxy/galaxy-d Is there a fix for this error or do we need to go back to the latest supported version of Cufflinks and if so which version? Thanks Chris Bidwell ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://galaxyproject.org

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MACS failed because of lambdaset options
by Philipe Moncuquet 29 Oct '12

29 Oct '12

Hi, I am trying to use MACS and I get the following error when the job fails : Usage: macs <-t tfile> [-n name] [-g genomesize] [options] Example: macs -t ChIP.bam -c Control.bam -f BAM -g h -n test -w --call-subpeaks macs: error: no such option: --lambdaset I am not really familiar to MACS so I checked the documentation and it seems Galaxy is rigth to complain because there is no such option as --lambdaset (http://liulab.dfci.harvard.edu/MACS/README.html) I went back to the xml wrapper and there is this ( <param name="lambdaset" type="text" ....) parameters that corresponds to the text box 3 levels of regions around the peak region to calculate the maximum lambda as local lambda: Does anyone face the same problem ? Any clue on what I should try, should I modify the wrapper ? Cheers, Philippe

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Import files from filesystem path : No redundance?
by julie dubois 26 Oct '12

26 Oct '12

Hi all, I have used the option "Import files from filesystem path" to import a complete arborescence of directories and files in one Data Library of Galaxy. Lot of files and sub-directories wil add to this arborescence. I've hoped import those changes in my data library with the option : add datasets, then indicate the path of this arborescence at the option "import from filesystem path". But when I use this way, Galaxy re-import all arborescence : the new files and sub-directories AND all already imported directories and files! Is there a way to import just the new files without know a priori which are new in my arborescence?* *Thanks. Julie* *

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Manage Jobs...
by Neil.Burdett＠csiro.au 26 Oct '12

26 Oct '12

Hi I have a local install of Galaxy running on my desktop. When I'm running a task I expected to see the process under "Admin->Manage Jobs" but it doesn't appear here. Do I need to set something to see the processes here? Neil

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How to share a dataset without sharing my history ?
by Sarah Maman 26 Oct '12

26 Oct '12

Hello, I would like to know how to share a single dataset without sharing my history through a local instance of Galaxy (with a LDAP identification) ? Thanks in advance, Sarah maman

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Tools Always Failing?
by Yilk, Todd A 25 Oct '12

25 Oct '12

Hello all, I'm using a local install of Galaxy connected to a UGE cluster and Python 2.6.7. Most of my tools are reporting failures in the history with messages like: An error occurred running this job: (34) Job output not returned from cluster; exit status = "0" With the relevant lines from Galaxy's log file looking like: galaxy.jobs.runners.drmaa DEBUG 2012-10-25 10:31:26,586 job 34 working directory is /opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/job_working_directory/000/34 galaxy.jobs.runners.drmaa DEBUG 2012-10-25 10:31:26,636 job 34 input = [["/opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/files/000/dataset_48.dat", "fastq", "5230830"]] galaxy.jobs.runners.drmaa DEBUG 2012-10-25 10:31:26,671 (34) submitting file /opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/uge/galaxy_34.sh galaxy.jobs.runners.drmaa DEBUG 2012-10-25 10:31:26,672 (34) command is: memtimepro -q -o /opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/job_working_directory/000/34/34.drmmt perl /opt/galaxy/dev/Galaxy-JGI_galaxy-dev/tools/lanl/readMapping/fastqSplitter/separate_paired_end_reads.pl -i /opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/files/000/dataset_48.dat -l /opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/files/000/dataset_53.dat -r /opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/files/000/dataset_54.dat ; cd /opt/galaxy/dev/Galaxy-JGI_galaxy-dev; /opt/galaxy/dev/Galaxy-JGI_galaxy-dev/set_metadata.sh ./database/files /opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/job_working_directory/000/34 . /opt/galaxy/dev/Galaxy-JGI_galaxy-dev/universe_wsgi.ini /opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/tmp/tmp831aRx /opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/job_working_directory/000/34/galaxy.json /opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/job_working_directory/000/34/metadata_in_HistoryDatasetAssociation_59_fpBxRp,/opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/job_working_directory/000/34/metadata_kwds_HistoryDatasetAssociation_59_MLg1Aw,/opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/job_working_directory/000/34/metadata_out_HistoryDatasetAssociation_59_ZVYBIT,/opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/job_working_directory/000/34/metadata_results_HistoryDatasetAssociation_59_q4FpIq,,/opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/job_working_directory/000/34/metadata_override_HistoryDatasetAssociation_59_3HXPLq /opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/job_working_directory/000/34/metadata_in_HistoryDatasetAssociation_60_Qw0GpA,/opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/job_working_directory/000/34/metadata_kwds_HistoryDatasetAssociation_60_ZF6Zk_,/opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/job_working_directory/000/34/metadata_out_HistoryDatasetAssociation_60_eEItGr,/opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/job_working_directory/000/34/metadata_results_HistoryDatasetAssociation_60_bMa6HN,,/opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/job_working_directory/000/34/metadata_override_HistoryDatasetAssociation_60_X1El1z galaxy.jobs.runners.drmaa INFO 2012-10-25 10:31:26,720 (34) queued as 553774 galaxy.jobs.runners.drmaa DEBUG 2012-10-25 10:31:28,947 (34/553774) state change: job is running -- snip -- galaxy.jobs.runners.drmaa DEBUG 2012-10-25 10:32:29,411 (34/553774) state change: job finished normally 128.165.72.57 - - [25/Oct/2012:10:32:31 -0600] "POST /root/history_item_updates HTTP/1.0" 200 - "http://galaxy-dev.lanl.gov/history" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.6; rv:15.0) Gecko/20100101 Firefox/15.0.1" galaxy.jobs.runners.drmaa DEBUG 2012-10-25 10:32:31,241 (34) Job output not returned from cluster; exit status = "0 " galaxy.jobs DEBUG 2012-10-25 10:32:31,285 The tool did not define exit code or stdio handling; checking stderr for success galaxy.jobs DEBUG 2012-10-25 10:32:31,427 setting dataset state to ERROR galaxy.jobs DEBUG 2012-10-25 10:32:31,471 setting dataset state to ERROR galaxy.jobs DEBUG 2012-10-25 10:32:31,728 job 34 ended galaxy.datatypes.metadata DEBUG 2012-10-25 10:32:31,729 Cleaning up external metadata files And yet, for this example, the tool did actually run successfully with the expected output files where they should be in the galaxy/database/files directory. Further, the 34.drmec file has just the exit code 0, the 34.drmout file is empty and the 34.drmmt file is: { "program": "perl", "arguments": [ "/opt/galaxy/dev/Galaxy-JGI_galaxy-dev/tools/lanl/readMapping/fastqSplitter/separate_paired_end_reads.pl", "-i", "/opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/files/000/dataset_48.dat", "-l", "/opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/files/000/dataset_53.dat", "-r", "/opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/files/000/dataset_54.dat" ], "exit_status": 0, "start_time": 1351182686, "wall_time": 0.223, "usage": { "utime": 0.04, "stime": 0.08, "max_vmem_kb": 11920, "max_rss_kb": 156, "start_time": 1351182686, "wall_time": 0.223 } } So everything looks good to me but Galaxy is reporting a failed run. What piece am I missing? Thanks!

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Managing datasets...
by Neil.Burdett＠csiro.au 24 Oct '12

24 Oct '12

Hi, We have a local instance of Galaxy installed. If a user logs into their account and uploads a file, only they can view the file in the history. Is there any way for an Admin user to also see this history? I've set up a admin account and added it to "admin_users" in universe_wsgi.ini, but they are unable to view other users' history Thanks Neil

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Galaxy October 23, 2012 Distribution & News Brief
by Jennifer Jackson 24 Oct '12

24 Oct '12

*Galaxy Oct 23, 2012 Distribution & News Brief */http://wiki.g2.bx.psu.edu/2012_10_23_DistributionNewsBrief/* * * * *Highlights: * /http://wiki.g2.bx.psu.edu/News/ * *Important Security Fix <http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_10_23#Compute_Tool_Security_Fix>* - upgrade *NOW*. * *New Trello Issue Board <http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_10_23#New_Trello_Issue_Board>* - Learn how to submit, vote, and comment on tickets. * *http://wiki.g2.bx.psu.edu/Tool Shed <http://wiki.g2.bx.psu.edu/Tool%20Shed>* direct updates and changes in Galaxy <http://usegalaxy.org> improve metadata updating, repository management, and more control over tool config. * Updates to the *Visualization <http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_10_23#Visualization_framework>* tool set cover *Trackster*, *Circster*, and new *Scatter Plot* tool. That's an example plot below. scatterplot-partialscreen <http://usegalaxy.org> * New *API <http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_10_23#API>* fixes, tuneups, and brand-new methods to control libraries. * Multiple *Admin <http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_10_23#Source>* changes enable better access to user data to solve problems. *http://getgalaxy.org* *http://bitbucket.org/galaxy/galaxy-dist* new: $ hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist upgrade: $ hg pull -u -r 12fcd068b12e *Thanks for using Galaxy!* Jennifer Jackson <http://wiki.g2.bx.psu.edu/JenniferJackson> & the Galaxy Team <http://wiki.g2.bx.psu.edu/Galaxy%20Team>

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Ion Torrent data analysis
by Xu, Jianpeng 23 Oct '12

23 Oct '12

Hi All, I am trying to use Galaxy to analyze the Ion Torrent data. I have uploaded my data to the galaxy. However, when I try to use FASTQ Quality Trimmer and Trim sequences to trim my fastq files, my file does not show in the FASTQ File menu. Do you know why ? How to fix it? Do these programs work on Ion Torrent data ? Thanks, Jianpeng ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).

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