June 2013 - galaxy-dev - lists.galaxyproject.org

Tool Shed Request - sanity check uploads?
by Peter Cock 29 Jul '13

29 Jul '13

Hi all, For what is I think the second time (fortunately this was only on the Test Tool Shed), I have managed to upload a tar-ball to the wrong repository: 2:fae4084a0bc0 http://testtoolshed.g2.bx.psu.edu/view/peterjc/fastq_paired_unpaired It could have been a glitch, but more likely is was simply inattention on my part (most likely - multiple tab browsing has its downsides). This leads me to offer some suggestions for how to prevent this kind of user error in future: (1) After the upload, show a preview of the changes for confirmation (the drawback is this could take a long time to process for a large upload, and lead to time outs). (2) After upload, before committing the changes, compare the tool contents - adding or removing some tools is normal, replacing ALL the tools with different tools is probably an error and should be subject to user confirmation. (3) Offer a repository action to revert to a prior commit (current workaround is to re-upload the old good file, which I did as 3:81ac324efa49 in this case). Peter

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GATK
by sridhar srinivasan 29 Jul '13

29 Jul '13

Dear Developers, I am running GATK for first time. In galaxy i use Unified Genotyper. I am getting error as below mentioned. ##### ERROR ------------------------------------------------------------------------------------------ ##### ERROR A USER ERROR has occurred (version 2.5-2-gf57256b): ##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed ##### ERROR Please do not post this error to the GATK forum ##### ERROR ##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments. ##### ERROR Visit our website and forum for extensive documentation and answers to ##### ERROR commonly asked questions http://www.broadinstitute.org/gatk ##### ERROR ##### ERROR MESSAGE: Running with the -et NO_ET or -et STDOUT option requires a GATK Key file. Please see http://gatkforums.broadinstitute.org/discussion/1250/what-is-phone-home-and… for more information and instructions on how to obtain a key. ##### ERROR ------------------------------------------------------------------------------------------ also suggest me about the Rod file for dbSNP. Thanks Sridhar

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DRMAA Runner URL Specify TORQUE host
by Bart Gottschalk 16 Jul '13

16 Jul '13

Is it possible to specify the torque host as part of a DRMAA runner URL? I haven't been able to find a *native_options *parameter to allow for this. I'm using the old style cluster configuration. *drmaa://[native_options]/* * * Also, I haven't been able to find a list of native_options anywhere. Does such a list exist? If so, where?

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Error Uploading Directory of Files
by Nicholas Kline 15 Jul '13

15 Jul '13

Hi, Our lab recently installed a local version of Galaxy on a mid-2012 Mac Pro computer. We can access the Galaxy server and sign in as an administrator. Today we tried creating a Data Library, adding a dataset to it, and uploading a directory of files. We followed the Galaxy documentation at http://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles?act… to setup this feature: - Admin > Data Library > Add datasets > Upload directory of files - file format was set to auto-detect - and we chose the option to link to files instead of copying them Galaxy confirmed that the files were successfully uploaded. However, in the data library, under the Message column, is a message in red saying "Job error (click name for more info)". Clicking on one of the uploaded files displays a page with this information: Date uploaded: 2013-06-28 File size: 7.5 GB Data type: auto Build: sacCer2 Miscellaneous information: Traceback (most recent call last): File "/Users/administrator/galaxy-dist/tools/data_source/upload.py", line 386, in __main__() File "/Users/administrator/galaxy-dist/tools/data_source/upload.py", line 357, in __main__ output_paths = Job Standard Error Traceback (most recent call last): File "/Users/administrator/galaxy-dist/tools/data_source/upload.py", line 386, in __main__() File "/Users/administrator/galaxy-dist/tools/data_source/upload.py", line 357, in __main__ output_paths = parse_outputs( sys.argv[4:] ) File "/Users/administrator/galaxy-dist/tools/data_source/upload.py", line 64, in parse_outputs id, files_path, path = arg.split( ':', 2 ) ValueError: need more than 1 value to unpack error Database/Build: sacCer2 Number of data lines: None Disk file: /Volumes/G-SPEED Q/data/Person 2012 project/DCP2 mef.fastq Questions: 1. Should we be concerned about this error? 2. If so, what is the right way to fix it? 3. If not, how do we remove the red error message next to each file: "Job error (click name for more info)" ? Thank you

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samtools BAM to SAM tmp directory
by Matt Shirley 03 Jul '13

03 Jul '13

Is there a reason that the samtools BAM to SAM does not respect the new_file_path set in the config file? The tmp directory handling by different tool wrappers seems to be an issue right now on systems with small system tmp directories. -- Matt Shirley Ph.D Candidate - BCMB Pevsner Lab <http://pevsnerlab.kennedykrieger.org/> Johns Hopkins Medicine

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nglims/removing multiplexing
by Lee Katz 03 Jul '13

03 Jul '13

Hi, I would like to remove the "multiplexed" menu from the nglims sample information form. How would I do that? In our lab, we don't want submitters making their own libraries since they might accidentally use the same barcodes or somehow mess up others' libraries. We want to remove that option altogether. Actually along the same lines, we would like to remove all "services needed" check boxes too and simply have all of the data entry on one page. Thank you for your help. -- Lee Katz, Ph.D.

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Error running tophat2 in Galaxy
by Sachit Adhikari 02 Jul '13

02 Jul '13

I am getting this error: Error in tophat: [2013-02-13 20:46:41] Beginning TopHat run (v2.0.7) ----------------------------------------------- [2013-02-13 20:46:41] Checking for Bowtie Bowtie version: 2.0.6.0 [2013-02-13 20:46:41] Checking for Samtools Samtools version: 0.1.18.0 [2013-02-13 20:46:41] Checking for Bowtie index files [2013-02-13 20:46:41] Checking for reference FASTA file Warning: Could not find FASTA file /data/rathi/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.fa [2013-02-13 20:46:41] Reconstituting reference FASTA file from Bowtie index Executing: /usr/bin/bowtie2-inspect /data/rathi/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome > ./tophat_out/tmp/genome.fa [2013-02-13 20:48:51] Generating SAM header for /data/rathi/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome format: fastq quality scale: phred33 (default) [2013-02-13 20:49:23] Preparing reads left reads: min. length=34, max. length=34, 2 kept reads (0 discarded) Warning: you have only one segment per read. If the read length is greater than or equal to 45bp, we strongly recommend that you decrease --segment-length to about half the read length because TopHat will work better with multiple segments [2013-02-13 20:49:23] Mapping left_kept_reads to genome genome with Bowtie2 [2013-02-13 20:49:56] Searching for junctions via segment mapping Coverage-search algorithm is turned on, making this step very slow Please try running TopHat again with the option (--no-coverage-search) if this step takes too much time or memory. Warning: junction database is empty! [2013-02-13 20:51:18] Reporting output tracks [FAILED] Error running /usr/local/bin/tophat_reports --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir ./tophat_out/ --max-multihits 20 --max-seg-multihits 40 --segment-length 25 --segment-mismatches 2 --min-closure-exon 100 --min-closure-intron 50 --max-closure-intron 5000 --min-coverage-intron 50 --max-coverage-intron 20000 --min-segment-intron 50 --max-segment-intron 500000 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --max-insertion-length 3 --max-deletion-length 3 -z gzip -p4 --no-closure-search --no-microexon-search --sam-header ./tophat_out/tmp/genome_genome.bwt.samheader.sam --report-discordant-pair-alignments --report-mixed-alignments --samtools=/bin/samtools --bowtie2-max-penalty 6 --bowtie2-min-penalty 2 --bowtie2-penalty-for-N 1 --bowtie2-read-gap-open 5 --bowtie2-read-gap-cont 3 --bowtie2-ref-gap-open 5 --bowtie2-ref-gap-cont 3 ./tophat_out/tmp/genome.fa ./tophat_out/junctions.bed ./tophat_out/insertions.bed ./tophat_out/deletions.bed ./tophat_out/fusions.out ./tophat_out/tmp/accepted_hits ./tophat_out/tmp/left_kept_reads.bam Loading ...done What's wrong?

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Upload files to data library
by Lionel Guy 01 Jul '13

01 Jul '13

Hi! I'm trying to upload multiple files a data library on my local instance of Galaxy. I've looked at the tutorial on the Galaxy wiki (http://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles) where it's said that there are four options to upload files, available by clicking the arrow at the top of the page one gets to when clicking on the add dataset button. However, although the tutorial shows the text "Create new data library datasets" with an arrow next to it, the page I get to when clicking on "Add datasets" shows "Upload files to a data library" with no arrow. I thus cannot add files otherwise than by uploading files one by one. Did I miss something? Am I doing anything wrong? I'm using: $ hg tip changeset: 10003:b4a373d86c51 tag: tip parent: 10001:471484ff8be6 Thanks for your help! Lionel Uppsala University

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Insert link in page editor
by Ted Goldstein 01 Jul '13

01 Jul '13

I want to make the page editor more useful. This may be more a WYM editor question than a Galaxy question. But since Galaxy has its own enhanced WYM editor, I figure I would start here. I was trying to use the galaxy page WYM editor today and I inserted a link (see image below). The behavior seems to put a wym guid as the text. I would have expected the title text prose from the dialogue box. Can anyone comment on this? Why insert a weird non-user friendly WYM stamp guid? Thanks, Ted

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Re: [galaxy-dev] June update breaks saved histories
by Shane Sturrock 30 Jun '13

30 Jun '13

While I never got a reply to this, I did continue trying to figure it out and ended up doing a fresh install on our system and there histories worked. After a bit of back and forth with upgrading the previous install and database the issue appears to be with subtle changes to the universe_wsgi.ini file and starting with a fresh one that came with the new distribution, and then modifying that to suit our environment resulted in an upgrade where histories worked. Shane On 27/06/2013, at 4:00 AM, galaxy-dev(a)lists.bx.psu.edu wrote: > > I've tried updating a couple of times to the latest stable release and each time I find that I can no longer see my saved histories. Roll back my machine to an earlier snapshot and it is fine. The thing that may be different about our system is that we're using Apache authentication rather than using the built in accounts. Nothing about the apache install has changed, just do the update to the June release, start it, run the manage_db.sh upgrade and restart (database is on postgres by the way) and then saved histories is empty and creating new histories never populates the list either. I would like to upgrade since the previous release had issues with sending BAM files to UCSC which this update has fixed. > > Maybe it's related to the upgraded SQLAlchemy? > > Shane -- For urgent cases, contact support(a)biomatters.com Dr Shane Sturrock shane.sturrock(a)biomatters.com Senior Scientist Tel: +64 (0) 9 379 5064 76 Anzac Ave Auckland New Zealand

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