March 2013 - galaxy-user - lists.galaxyproject.org

Why don't we get FPKMs from this gene?
by Dikla Aharonovich 08 Mar '13

08 Mar '13

Hello, We are using BAM to map Illumina reads to a bacterial genome, followed by Cufflinks o get the FPKMs. We have come across many genes for which we get FPKM=0 (using both gene and transcript expression) even though there are reads mapping to these gene IDs (e.g. the region between the dashed lines in the attached screenshot). Can anyone suggest a reason/fix for this? Thanks Dikla

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wrong disk usage figure reported on galaxy main
by pbourbon＠agilent.com 08 Mar '13

08 Mar '13

Hi, I noticed since yesterday that my "disk usage" % (top-right) has jumped from ~20% to ~ 80 % for no apparent reason. The added size of all my current histories is now only 29 Gb, which should be ~11%, and I looked in my deleted histories but all of them are 0 bytes in size and with status "deleted permanently", there are no histories currently shared with me by other users. Is there something else I can check or look into in order to get my disk usage back to where it should be ? Many thanks in advance for your help ! Pierre

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Galaxy Main & Test Server downtime for hardware relocation Thursday, March 14, 2013
by Jennifer Jackson 08 Mar '13

08 Mar '13

Notice Date: Thursday, March 7, 2013 Greetings Galaxy *Main* & *Test* Users, The *Galaxy* *Public* *Main Galaxy Server <http://wiki.galaxyproject.org/Main>* at *http://main.g2.bx.psu.edu* (/usegalaxy.org/) and *Test Galaxy Server <http://wiki.galaxyproject.org/Test>* at *http://test.g2.bx.psu.edu* will be *down on Thursday, March 14, while the team _/relocates core hardware /to a new server room_*. Please note that _/ALL jobs running at the time of the shutdown will be terminated/_. Once the move is complete, any terminated jobs can be easily restarted using the "re-run" function. dataset re-run The /yellow banner on //*Main*//and //*Test*//will provide updates/ (when the servers are up) as well our *@galaxyproject Twitter* posts. Don't use Twitter? See our *Twitter Wiki <http://wiki.galaxyproject.org/Galaxy%20on%20Twitter>*. *Galaxy's **Tool Shed <http://toolshed.g2.bx.psu.edu>**, **GalaxyProject.org <http://wiki.galaxyproject.org>**Wiki, and **Mailing list <http://wiki.galaxyproject.org/MailingLists>**services* will be /*unaffected*/ during this time. /Thanks for using Galaxy!!/ Galaxy team

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Local galaxy install vs cloudman
by James Vincent 06 Mar '13

06 Mar '13

Hello, The cloud version of Galaxy is quite easy to fire up and is very complete with all tools and genomes preinstalled. Local installation on the other hand is painful, contrary to the nice descriptions among the wiki pages. For exmples, see this: http://vallandingham.me/installing_galaxy_tools.html The initial install of galaxy is easy enough, but making a complete setup is quite painful without dedicated IT people. Setting up ftp server access for uploading and installing tool dependencies in particular are not pleasant. Since the cloud version comes with everything including the kitchen sink, would it be possible to create a more compete local install bundle that also includes everything, without resorting to running a VM locally? Have I missed some other really easy process? Thanks, Jim

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What is the quality score type for the Solid datasets downloaded from SRA of NCBI?
by Gene Genome 06 Mar '13

06 Mar '13

Hi all, Please help with the quality score type for the downloaded Solid datasets. I downloaded RNA-seq datasets, which were generated by AB Solid system, as base space and at FastQ format from SRA of NCBI. I uploaded the datasets onto the online sever Galaxy and change the datatype directly into "fastqsanger" and then test the quality by running FastQC. The output "per base quality" of solid dataset (please take look at the attached figure "per_base_quality-Solid") is quite different from the output "per base quality" of Illumina dataset (please compare with the attached figure "per base quality-Illumina"). The top score for Solid dataset is about 31, however the top score for Illumina dataset is 38. What is the quality score type for the downloaded Solid datasets when downloaded as base space and at FastQ format from SRA of NCBI? Please help me solve this problem. Thanks. Best regards. Jianguang Du

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Count reads mapping to introns, extragenic regions
by Alex Koeppel 05 Mar '13

05 Mar '13

Hello everyone, I have some SAM/BAM files containing the alignments of some RNA-seq reads to hg19. I'm interested in calculating some mapping statistics, specifically, the percentage of reads mapping to exons, introns, and extragenic regions. I gather that this can be done with bedtools, but I'm finding myself a little bit stuck just figuring out what files I need to get this information. I gather that I need a GTF (or possibly GFF) file, and I downloaded one from the UCSC browser using the settings in the attached image. The first couple lines of the resulting file are pasted below. I see that the file has exon start and end sites. Is there a way to get what I need with this file, or do I need something else? Any assistance would be much appreciated, Thanks Alex cat gencode.gtf | head -3 #bin name chrom strand txStart txEnd cdsStart cdsEnd exonCount exonStarts exonEnds score name2 cdsStartStat cdsEndStat exonFrames 0 ENST00000237247.6 chr1 + 66999065 67210057 67000041 67208778 27 66999065,66999928,67091529,67098752,67099762,67105459,67108492,67109226,67126195,67133212,67136677,67137626,67138963,67142686,67145360,67147551,67149789,67154830,67155872,67161116,67184976,67194946,67199430,67205017,67206340,67206954,67208755, 66999090,67000051,67091593,67098777,67099846,67105516,67108547,67109402,67126207,67133224,67136702,67137678,67139049,67142779,67145435,67148052,67149870,67154958,67155999,67161176,67185088,67195102,67199563,67205220,67206405,67207119,67210057, 0 SGIP1 cmpl cmpl -1,0,1,2,0,0,0,1,0,0,0,1,2,1,1,1,1,1,0,1,1,2,2,0,2,1,1, 0 ENST00000371039.1 chr1 + 66999274 67210768 67000041 67208778 22 66999274,66999928,67091529,67098752,67105459,67108492,67109226,67136677,67137626,67138963,67142686,67145360,67154830,67155872,67160121,67184976,67194946,67199430,67205017,67206340,67206954,67208755, 66999355,67000051,67091593,67098777,67105516,67108547,67109402,67136702,67137678,67139049,67142779,67145435,67154958,67155999,67160187,67185088,67195102,67199563,67205220,67206405,67207119,67210768, 0 SGIP1 cmpl cmpl -1,0,1,2,0,0,1,0,1,2,1,1,1,0,1,1,2,2,0,2,1,1,

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Filter Pileup in SAM tools
by Andrew South 05 Mar '13

05 Mar '13

NGS: SAM Tools I have generated a simple 6 column pileup from my BAM file but when I try to use the Filter Pileup tool it doesn't recognise my pileup file, I receive the message "History does not include a dataset of the required format / build". Build is hg19. Curiously in the same history I have ran the tool through a workflow without a hitch. Any advice to successfully filter my pileup would be gratefully received. Many thanks, Andy The University of Dundee is a registered Scottish Charity, No: SC015096

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Error / Nebula and RepeatMasker
by Sarah Maman 05 Mar '13

05 Mar '13

Hello, I've installed NEBULA tools and "RepeatMasker" tool on our local Galaxy instance. For some tools (others work), I get the following errors: * - *Here is the error I get when running the tool *FilterControl * *** glibc detected *** java: double free or corruption (!prev): 0x00007fe56800ecd0 *** *** glibc detected *** java: double free or corruption (!prev): 0x00007fe56800ecd0 *** *** glibc detected *** java: double free or corruption (!prev): 0x00007fe56800ecd0 *** *** glibc detected *** java: double free or corruption (!prev): 0x00007fe56800ecd0 *** /usr/local/bioinfo/src/galaxy/galaxy-dist/tools/Nebula/FilterControlPeaks/FilterControlPeaks.sh: line 80: 61310 Abandon java -classpath $LOCAL_PATH/ -Xmx6g FilterPeaks -f $inputfile -c $controlfile -t $minHeight -v $minRatio -o $output > /dev/null *** glibc detected *** java: double free or corruption (!prev): 0x00007f1f5800ecd0 *** /usr/local/bioinfo/src/galaxy/galaxy-dist/tools/Nebula/FilterControlPeaks/FilterControlPeaks.sh: line 81: 61351 Abandon - Here is the error I get when running the tool *IntersectBed *//work/galaxy/database/pbs/galaxy_4129.sh: line 13: Erreur de syntaxe près du symbole inattendu « ;; » /work/galaxy/database/pbs/galaxy_4129.sh: line 13: `bedtools intersect -f 0.05/ - Here is the error I get when running the tool *ChIPmunk (thanks Alban for you help (*ChIPMunk v2 is used and all librairies are found) *but here is a new error, maybe a problem of "dirname" ?) */mv: impossible d'évaluer « /work/galaxy/database/job_working_directory/004/4132/galaxy_dataset_5992.dat_0.xml.png »: Aucun fichier ou dossier de ce type mv: impossible d'évaluer « /work/gala /- Here is the error I get when running the tool *PeaksToBed * readline() on closed filehandle FILE at /usr/local/bioinfo/src/galaxy/galaxy-dist/tools/Nebula/Peak2Bed/peak2bed.pl line 124 (#1) (W closed) The filehandle you're reading from got itself closed sometime before now. Check your control flow. Use of uninitialized value $fields[1] in concatenation (.) or string at /usr/local/bioinfo/src/galaxy/galaxy-dist/tools/Nebula/Peak2Bed/peak2bed.pl line 154, <FILE> line 1 (#2) (W uninitialized) An undefined value was used as if it were already defined. It was interpreted as a "" or a 0, but maybe it was a mistake. To suppress this warning assign a defined value to your variables. To help you figure out what was undefined, perl will try to tell you the name of the variable (if any) that was undefined. In some cases it cannot do this, so it also tells you what operation you used the undefined value in. Note, however, that perl optimizes your program and the operation displayed in the warning may not necessarily appear literally in your program. For example, "that $foo" is usually optimized into "that " . $foo, and the warning will refer to the concatenation (.) operator, even though there is no . in your program. Use of uninitialized value in concatenation (.) or string at /usr/local/bioinfo/src/galaxy/galaxy-dist/tools/Nebula/Peak2Bed/peak2bed.pl line 154, <FILE> line 1 (#2) Use of uninitialized value in numeric ge (>=) at /usr/local/bioinfo/src/galaxy/galaxy-dist/tools/Nebula/Peak2Bed/peak2bed.pl line 156, <FILE> line 1 (#2) ...... /usr/local/bioinfo/src/galaxy/galaxy-dist/tools/Nebula/Peak2Bed/peak2bed.pl line 156, <FILE> line 63 (#2) Use of uninitialized value $fields[1] in conc ** I dowloaded tool "RepeatMasker" from Galaxy Tool Shed,and RepeatMasker is installed on our cluster. Here is the error I get when running the tool RepeatMasker: An error occurred running this job: /Epilog : job finished at jeu. janv. 31 14:39:16 CET 2013 /work/galaxy/database/pbs/galaxy_4134.sh: line 13: Erreur de syntaxe près du symbole inattendu « ;; » /work/galaxy/database/pbs/galaxy_4134.sh: line 13: `RepeatMasker -parallel 8 -speci/ Do you have any ideas ? Thank you in advance for your help, Sarah Maman -- --*-- Sarah Maman INRA - LGC - SIGENAE http://www.sigenae.org/ Chemin de Borde-Rouge - Auzeville - BP 52627 31326 Castanet-Tolosan cedex - FRANCE Tel: +33(0)5.61.28.57.08 Fax: +33(0)5.61.28.57.53 --*--

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Setting up galaxy local server
by Anusha Nagari 04 Mar '13

04 Mar '13

Hi, I am a new user of galaxy and am trying to set up local version of galaxy on my mac. I followed the instructions in this link<http://wiki.galaxyproject.org/Admin/Get%20Galaxy>and successfully installed the local version using the following steps: *mkdir galaxy-python/* *mkdir galaxy-dist/* *ln -s /usr/local/bin/ galaxy-python/python* *export PATH=~/galaxy-python:$PATH* *hg clone https://bitbucket.org/galaxy/galaxy-dist/* *cd galaxy-dist* *sh run.sh* * * I could load galaxy fine for the first time. However after I closed it and tried to run it by sh run.sh, it is giving the following error and am unable to startup galaxy: __import__( "pkg_resources" ).declare_namespace( __name__ ) Traceback (most recent call last): File "./scripts/manage_tools.py", line 12, in <module> from migrate.versioning.shell import main ImportError: No module named migrate.versioning.shell However, I am not able to upload any datasets into galaxy either from UCSC genome browser or from my computer with the following error: An error occurred with this dataset: /Users/anushanagari/Desktop/Softwares/galaxy-dist/lib/galaxy/__init__.py:5: UserWarning: Module site was already imported from /Library/Frameworks/Python.framework/Versions/4.2.30201/lib/python2.5/site.pyc, but /Library/Frameworks/Python.framework/Version Tool execution generated the following error message: /Users/anushanagari/Desktop/Softwares/galaxy-dist/lib/galaxy/__init__.py:5: UserWarning: Module site was already imported from /Library/Frameworks/Python.framework/Versions/4.2.30201/lib/python2.5/site.pyc, but /Library/Frameworks/Python.framework/Versions/4.2.30201/lib/python2.5/site-packages/Enstaller-3.0.9-py2.5.egg is being added to sys.path __import__( "pkg_resources" ).declare_namespace( __name__ ) /Users/anushanagari/Desktop/Softwares/galaxy-dist/lib/galaxy/__init__.py:5: UserWarning: Module pkg_resources was already imported from /Users/anushanagari/Desktop/Softwares/galaxy-dist/lib/pkg_resources.pyc, but /Library/Frameworks/Python.framework/Versions/4.2.30201/lib/python2.5/site-packages/Enstaller-3.0.9-py2.5.egg is being added to sys.path __import__( "pkg_resources" ).declare_namespace( __name__ ) Could you please help me with this and also provide any additional documentation that could help me in getting to know galaxy better? Thanks in advance! Hoping to hear from you soon! Best, Anusha

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March 2013 Galaxy Update
by Dave Clements 01 Mar '13

01 Mar '13

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