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

Sort sam or bam
by Clare Sloggett 23 Jan '12

23 Jan '12

Hi galaxy users, Am I right in thinking there is no tool for sorting a sam/bam file in Galaxy? I think this has probably been discussed before, sorry. I just want to check I haven't missed anything, since sibling tools from e.g. the samtools and picard suites are wrapped. Thanks, Clare -- E: sloc(a)unimelb.edu.au P: 03 903 53357 M: 0414 854 759

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Problem uploading files gt 1 Mbyte to Galaxy Cloud
by Greg Edwards 23 Jan '12

23 Jan '12

Hi, I'm building a Galaxy Cloud implementation, and running into a problem uploading data files > 1 Mbyte, or 1,048,576 bytes. I've started Galaxy Cloudman and a single server, all according to to the Wiki. I can upload fasta format files < 1048756 bytes, and general CSV format peptide files, and indeed junk data files built with variants of " jot -r -c 1030000 a z | rs -g 0 100 >junk ". If I upload files (via the built-in Get Data / Upload Files From Your Computer) that are > than approx 2^20 bytes, the upload just hangs in the History and never completes. These files upload fine to a local Galaxy server, and to Galaxy Main. On the Galaxy local server, they run fine with my custom proteomics code. Ditto on the Cloud galaxy server when the (smaller than 1 Mbtye) files successfully upoad. I can't see anthing useful in the logs, but I'm not sure which logs I should be looking at. I'm just looking at tyhe logs presented on the Cloudman admin page. [image: logs.png] My environment is Mac, OS X 10.6.8. My data files are terminated with /n, but the problem manifests the same with Windows style /r/n files. I'll leave it at that in the hope this is a ridiculously simple probelm and needs no more description ! If not, please let me know the logs I should look at and whatever else I should check. Many thanks, Greg E -- Greg Edwards, Port Jackson Bioinformatics gedwards2(a)gmail.com

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Looking for an easy "load test" for Galaxy Cloudman
by Greg Edwards 22 Jan '12

22 Jan '12

Hi, I'm experimenting with Galaxy Cloudman, and could use a simple workflow to a) test that Galaxy is working ok b) put some significant load on a Galaxy server so that it shows in the load diagram, ie. as below [image: load.png] Suggestions appreciated. Thanks, -- Greg Edwards gedwards2(a)gmail.com

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Could you please add Vibrio cholerae O1 biovar eltor str. N16961 to the reference genome？
by Tao Dong 20 Jan '12

20 Jan '12

Browser Chrom/Plasmid NameLength (bp)GC Content (%)Gene CountNCBI RefSeq AccessionchrI<http://microbes.ucsc.edu/cgi-bin/hgTracks?db=vibrChol1&position=chrI:1-2961…> 296114947.692888NC_002505<http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=NC_002505> chrII<http://microbes.ucsc.edu/cgi-bin/hgTracks?db=vibrChol1&position=chrII:1-107…> 107231546.911119NC_002506<http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=NC_002506>

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Trackster errors
by Erin Shanle 20 Jan '12

20 Jan '12

Hello I would like to visualize the tracks of my tophat accepted hits bam file. I ran my first sample that was ~10,000,000 reads and it could be visualized in both Trackster and the UCSC genome browser. When I tried to visualize my other samples (which ranged from 15,000,000 to 35,000,000 reads) it won't show up in trackster because of an indexing error. When I ran Picard statistics on the tophat accepted hits bam output, I see that there was successful alignment of ~90% of the reads. Since I have one sample that works, I am not sure how to address the issue. Here's the error I get from Trackster when I try to visualize the samples: *** glibc detected *** python: double free or corruption (!prev): 0x0000000000ff02b0 *** ======= Backtrace: ========= /lib/libc.so.6(+0x71ad6)[0x7ff6561f7ad6] /lib/libc.so.6(cfree+0x6c)[0x7ff6561fc84c] /lib/libc.so.6(fclose+0x14d)[0x7ff6561e8a1d] /galaxy/home/g2main/galaxy_main/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/csamtools.so(bam_index_load_literal+0x37)[0x7ff655cdbb17] /galaxy/home/g2main/galaxy_main/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/csamtools.so(+0x6e838)[0x7ff655cc7838] python(PyObject_Call+0x47)[0x41ef47] python(PyEval_CallObjectWithKeywords+0x43)[0x4a1a53] /galaxy/home/g2main/galaxy_main/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/csamtools.so(+0x52a44)[0x7ff655caba44] python[0x46f0a3] python(PyObject_Call+0x47)[0x41ef47] python(PyEval_EvalFrameEx+0x4878)[0x4a72b8] python(PyEval_EvalCodeEx+0x911)[0x4a95c1] python(PyEval_EvalFrameEx+0x4d12)[0x4a7752] python(PyEval_EvalCodeEx+0x911)[0x4a95c1] python(PyEval_EvalCode+0x32)[0x4a9692] python(PyRun_FileExFlags+0x13e)[0x4c98be] python(PyRun_SimpleFileExFlags+0xd4)[0x4c9ad4] python(Py_Main+0x9ed)[0x41a6bd] /lib/libc.so.6(__libc_start_main+0xfd)[0x7ff6561a4c4d] python[0x4198d9] ======= Memory map: ======== 00400000-0061d000 r-xp 00000000 fe:00 715090 /usr/bin/python2.6 0081d000-0087f000 rw-p 0021d000 fe:00 715090 /usr/bin/python2.6 0087f000-0088e000 rw-p 00000000 00:00 0 00d1a000-0109a000 rw-p 00000000 00:00 0 [heap] 7ff650000000-7ff650021000 rw-p 00000000 00:00 0 7ff650021000-7ff654000000 ---p 00000000 00:00 0 7ff6556ed000-7ff655702000 r-xp 00000000 fe:00 1512749 /lib/libgcc_s.so.1 7ff655702000-7ff655902000 ---p 00015000 fe:00 1512749 /lib/libgcc_s.so.1 7ff655902000-7ff655903000 rw-p 00015000 fe:00 1512749 /lib/libgcc_s.so.1 7ff655903000-7ff655933000 r-xp 00000000 00:13 1154848 /galaxy/home/g2main/galaxy_main/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/ctabix.so 7ff655933000-7ff655a32000 ---p 00030000 00:13 1154848 /galaxy/home/g2main/galaxy_main/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/ctabix.so 7ff655a32000-7ff655a37000 rw-p 0002f000 00:13 1154848 /galaxy/home/g2main/galaxy_main/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/ctabix.so 7ff655a37000-7ff655a39000 rw-p 00000000 00:00 0 7ff655a39000-7ff655a55000 r-xp 00000000 fe:00 738300 /usr/lib/python2.6/lib-dynload/_ctypes.so 7ff655a55000-7ff655c55000 ---p 0001c000 fe:00 738300 /usr/lib/python2.6/lib-dynload/_ctypes.so 7ff655c55000-7ff655c59000 rw-p 0001c000 fe:00 738300 /usr/lib/python2.6/lib-dynload/_ctypes.so 7ff655c59000-7ff655d29000 r-xp 00000000 00:13 1154847 /galaxy/home/g2main/galaxy_main/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/csamtools.so 7ff655d29000-7ff655e29000 ---p 000d0000 00:13 1154847 /galaxy/home/g2main/galaxy_main/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/csamtools.so 7ff655e29000-7ff655e39000 rw-p 000d0000 00:13 1154847 /galaxy/home/g2main/galaxy_main/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/csamtools.so 7ff655e39000-7ff655ec0000 rw-p 00000000 00:00 0 7ff655fc0000-7ff656185000 rw-p 00000000 00:00 0 7ff656186000-7ff6562de000 r-xp 00000000 fe:00 1514734 /lib/libc-2.11.2.so 7ff6562de000-7ff6564dd000 ---p 00158000 fe:00 1514734 /lib/libc-2.11.2.so 7ff6564dd000-7ff6564e1000 r--p 00157000 fe:00 1514734 /lib/libc-2.11.2.so 7ff6564e1000-7ff6564e2000 rw-p 0015b000 fe:00 1514734 /lib/libc-2.11.2.so 7ff6564e2000-7ff6564e7000 rw-p 00000000 00:00 0 7ff6564e7000-7ff656567000 r-xp 00000000 fe:00 1514738 /lib/libm-2.11.2.so 7ff656567000-7ff656767000 ---p 00080000 fe:00 1514738 /lib/libm-2.11.2.so 7ff656767000-7ff656768000 r--p 00080000 fe:00 1514738 /lib/libm-2.11.2.so 7ff656768000-7ff656769000 rw-p 00081000 fe:00 1514738 /lib/libm-2.11.2.so 7ff656769000-7ff656780000 r-xp 00000000 fe:00 713314 /usr/lib/libz.so.1.2.3.4 7ff656780000-7ff65697f000 ---p 00017000 fe:00 713314 /usr/lib/libz.so.1.2.3.4 7ff65697f000-7ff656980000 rw-p 00016000 fe:00 713314 /usr/lib/libz.so.1.2.3.4 7ff656980000-7ff656af5000 r-xp 00000000 fe:00 713850 /usr/lib/libcrypto.so.0.9.8 7ff656af5000-7ff656cf5000 ---p 00175000 fe:00 713850 /usr/lib/libcrypto.so.0.9.8 7ff656cf5000-7ff656d1d000 rw-p 00175000 fe:00 713850 /usr/lib/libcrypto.so.0.9.8 7ff656d1d000-7ff656d21000 rw-p 00000000 00:00 0 7ff656d21000-7ff656d70000 r-xp 00000000 fe:00 713852 /usr/lib/libssl.so.0.9.8 7ff656d70000-7ff656f6f000 ---p 0004f000 fe:00 713852 /usr/lib/libssl.so.0.9.8 7ff656f6f000-7ff656f76000 rw-p 0004e000 fe:00 713852 /usr/lib/libssl.so.0.9.8 7ff656f76000-7ff656f78000 r-xp 00000000 fe:00 1514753 /lib/libutil-2.11.2.so 7ff656f78000-7ff657177000 ---p 00002000 fe:00 1514753 /lib/libutil-2.11.2.so 7ff657177000-7ff657178000 r--p 00001000 fe:00 1514753 /lib/libutil-2.11.2.so 7ff657178000-7ff657179000 rw-p 00002000 fe:00 1514753 /lib/libutil-2.11.2.so 7ff657179000-7ff65717b000 r-xp 00000000 fe:00 1514737 /lib/libdl-2.11.2.so 7ff65717b000-7ff65737b000 ---p 00002000 fe:00 1514737 /lib/libdl-2.11.2.so 7ff65737b000-7ff65737c000 r--p 00002000 fe:00 1514737 /lib/libdl-2.11.2.so 7ff65737c000-7ff65737d000 rw-p 00003000 fe:00 1514737 /lib/libdl-2.11.2.so 7ff65737d000-7ff657394000 r-xp 00000000 fe:00 1514748 /lib/libpthread-2.11.2.so 7ff657394000-7ff657593000 ---p 00017000 fe:00 1514748 /lib/libpthread-2.11.2.so 7ff657593000-7ff657594000 r--p 00016000 fe:00 1514748 /lib/libpthread-2.11.2.so 7ff657594000-7ff657595000 rw-p 00017000 fe:00 1514748 /lib/libpthread-2.11.2.so 7ff657595000-7ff657599000 rw-p 00000000 00:00 0 7ff657599000-7ff6575b7000 r-xp 00000000 fe:00 1514704 /lib/ld-2.11.2.so 7ff6575ec000-7ff65762d000 rw-p 00000000 00:00 0 7ff65762e000-7ff6576f1000 rw-p 00000000 00:00 0 7ff657723000-7ff6577aa000 rw-p 00000000 00:00 0 7ff6577b1000-7ff6577b2000 rw-p 00000000 00:00 0 7ff6577b2000-7ff6577b3000 rwxp 00000000 00:00 0 7ff6577b3000-7ff6577b6000 rw-p 00000000 00:00 0 7ff6577b6000-7ff6577b7000 r--p 0001d000 fe:00 1514704 /lib/ld-2.11.2.so 7ff6577b7000-7ff6577b8000 rw-p 0001e000 fe:00 1514704 /lib/ld-2.11.2.so 7ff6577b8000-7ff6577b9000 rw-p 00000000 00:00 0 7fffc7e81000-7fffc7ea2000 rw-p 00000000 00:00 0 [stack] 7fffc7fff000-7fffc8000000 r-xp 00000000 00:00 0 [vdso] ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall] Aborted -- Erin Shanle Graduate Research Assistant Molecular and Environmental Toxicology 425 McArdle Laboratory for Cancer Research 1400 University Ave Madison, WI 53706 608 262 9834 shanle(a)wisc.edu

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Cuffdiff errors
by Erin Shanle 20 Jan '12

20 Jan '12

Hello I am having a problem running Cuffdiff on some RNA-seq data. I want to compare 2 of my conditions. I successfully used Cuffdiff three days ago to compare two sets of data that are processed the exact same way (align with Tophat and use Picard to confirm adequate alignment). I am using Galaxy through MAIN and I tried Cuffdiff with these samples on 1/18 and 1/19. Here's the error: An error occurred running this job: *cuffdiff v1.3.0 (3022) cuffdiff --no-update-check -q -p 8 -c 1000 --FDR 0.050000 -b /galaxy/data/hg19/sam_index/hg19.fa --labels DMSO,E2 /galaxy/main_pool/pool2/files/003/607/dataset_3607369.dat /galaxy/main_pool/pool2/files/003/590/dataset_3590726.dat,/g* Thanks for the help. -- Erin Shanle Graduate Research Assistant Molecular and Environmental Toxicology 425 McArdle Laboratory for Cancer Research 1400 University Ave Madison, WI 53706 608 262 9834 shanle(a)wisc.edu

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January 20, 2012 Galaxy Development News Brief
by Jennifer Jackson 20 Jan '12

20 Jan '12

January 20, 2012 Galaxy Development News Brief Highlights: * New Object Store data integration layer introduced * RNA-seq updates: TopHat to 1.4.0 and Cufflinks, CuffDiff, CuffCompare to 1.3.0. * Tool Shed installation features and community tool additions * Trackster performance upgrades and new drag & drop composite track creation Mercurial pull: hg pull -u -r 63bc46cc73b7 Complete News Brief http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_01_20 Release history http://wiki.g2.bx.psu.edu/DevNewsBriefs/ Install/Administration Help http://getgalaxy.org Support http://galaxyproject.org/wiki/Support Thanks for using Galaxy!

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Recent problematic change in the Galaxy Toolshed
by Florent Angly 19 Jan '12

19 Jan '12

Hi, I just tried to upload a new version of the Grinder Galaxy wrapper to the Galaxy ToolShed and am encountering difficulties that I did have in previous versions. When I upload my .tar.gz file, the upload is aborted and I get the error: > 'GalaxyWebUITransaction' object has no attribute 'tool_data_tables' When I remove my tool_data_table_conf.xml.sample file from the tarball and try re-uploading, I get this warning: > The file 'grinder-galaxy-0.4.3.tar.gz' has been successfully > uncompressed and uploaded to the repository. 1 files were removed from > the repository root. > Metadata cannot be defined for revision 'c9fee6113b0d' so this > revision cannot be automatically installed into a local Galaxy > instance. Correct the following problems and reset metadata. > grinder.xml - This file requires an entry in the > tool_data_table_conf.xml file. Upload a file named > tool_data_table_conf.xml.sample to the repository that includes the > required entry to resolve this issue. These two messages are contradictory. Also, if I am not allowed to define a new datatable with this name, how I am suppose to have a tool use data tables? Thanks, Florent

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tar.gz files
by Jennifer Jackson 18 Jan '12

18 Jan '12

Hi Rich, Sorry for the delayed reply, this message didn't get routed correctly. Next time, please just send directly "to" as "galaxy-user(a)bx.psu.edu". For the tar question, unfortunately this is not supported. Instead use: .gzip, .bz, bzip2, or single-file .zip. http://wiki.g2.bx.psu.edu/Learn/Upload%20via%20FTP Hopefully you have worked this out already, but I wanted to give you confirmation, Take care, Jen Galaxy team On 12/13/11 8:30 AM, Richard Mark White wrote: > Hi, > My seq core returns FASTQ files to me in *.txt.tar.gz format. When I > upload this to galaxy, it unzips, but it is apparently still TAR'd and > cannot be read. > Is it possible to upload this format, or do I need to untar and unzip it > first (which is less than ideal)? > > Rich > -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support

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fetch sequence functionality
by Lawrence Mckechnie 18 Jan '12

18 Jan '12

Hi, I uploaded a tab-delimited file(this was constructed within R using write.table) into Galaxy with chr, start, end, and esembl_TSS_name. Whilst I am able to use fetch sequence function, currently not able to include the Esembl ID in the FASTA output. I am able to include the Ensembl name in the interval format but not in FASTA format. thanks, Lawrence

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