- galaxy-user - lists.galaxyproject.org

Problem in randomly selecting sequences?
by Daniel Sher 13 Oct '11

13 Oct '11

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Splitting a file
by Daniel Sher 13 Oct '11

13 Oct '11

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using lastz
by N. Walsh 12 Oct '11

12 Oct '11

Hi, I have been using Lastz to perform assemblies of 454 data and I have run into a problem where, after the job has been added to the queue, a message appears saying that: Job is waiting to run. It remains like this indefinitely and when I click the 'edit attributes' button, a message says: 'Required metadata values are missing. Some of these values may not be editable by the user'. I am confused since I was able to previously run Lastz with the same samples and parameters and it worked fine. I have tried changing the parameters around a bit but the job still will not run. I would really appreciate any advice anyone could give on how to resolve this issue. Thanks, Neil

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My tophat jobs are stuck in the queue
by Daniel Lundin 12 Oct '11

12 Oct '11

Hi, I've been running small tophat jobs as part of a student exercise, but since yesterday morning (about 7 am CET, or 24 hours ago) my tophat jobs does not start. Earlier (Monday) jobs started and finished fine. Other jobs like trimming, getting data from the Main table etc. works. /D -- Daniel Lundin, Postdoc SciLifeLab, School of biotechnology, KTH Royal institute of technology, Stockholm, Sweden Postal address: Box 1031 171 21 Solna Sweden Visiting address: Tomtebodavägen 23 A Mobile: +46 (0)708 123 922 Email: daniel.lundin(a)scilifelab.se

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Problem with Cuffcompare
by Chandu Galaxy 12 Oct '11

12 Oct '11

Hello, I'm using Galaxy tool from about two months. I'm very new to this community. I ran into some problems when using the tools for NGS: RNA Analysis. I would like to get from the community. Here is the description of the problem. I've four different datasets (fastqsanger format). I ran the NGS: RNA Analysis tools like "Tophat for Illumina", "Cufflinks", "Cuffcompare". The Tophat and cufflinks tools are working fine but the cuffcompare is giveing out an error message like the below. Dataset generation errors *Dataset 57: Cuffcompare on data 20, data 23, and others: combined transcripts* Tool execution generated the following error message: Error running cuffcompare. Warning: Your version of Cufflinks is not up-to-date. It is recommended that you upgrade to Cufflinks v1.1.0 to benefit from the most recent features and bug fixes (http://cufflinks.cbcb.umd.edu) No fasta index found for ./input1. Rebuilding, please wait.. Error: sequence lines in a FASTA record must have the same length! The tool produced the following additional output: cuffcompare v1.0.3 (2403) cuffcompare -o cc_output -s ./input1 ./input2 ./input3 ./input4 Can anyone help me to figure out what the problem is? Let me know if you need more information. Thank you. -- Chandrasekhar

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Problem starting galaxy on Cygwin
by Oren Livne 12 Oct '11

12 Oct '11

Dear All, There are related posts but it is unclear from them how to resolve the following. I'm trying to start a Galaxy server on Cygwin and it fails when trying to fetch an egg relying on NumPy. Could you kindly advise how to resolve the error? This uses the Cygwin python 2.6.5. I tried to point Cygwin to the Windows python (2.7.2 in my case) but that was even worse, the Mako egg threw a KeyError: 'Mako' exception up front. Thank you so much, Oren -------- $ python --version Python 2.6.5 oren@oren-PC /cygdrive/c/web/galaxy-central $ sh run.sh --reload Some eggs are out of date, attempting to fetch... Fetched http://eggs.g2.bx.psu.edu/Mako/Mako-0.4.1-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/Babel/Babel-0.9.4-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/Whoosh/Whoosh-0.3.18-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/Tempita/Tempita-0.1-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/lrucache/lrucache-0.2-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/NoseHTML/NoseHTML-0.4.1-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/pexpect/pexpect-2.4-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/amqplib/amqplib-0.6.1-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/PasteDeploy/PasteDeploy-1.3.3-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/WebHelpers/WebHelpers-0.2-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/docutils/docutils-0.7-py2.6.egg Traceback (most recent call last): File "./scripts/fetch_eggs.py", line 30, in <module> c.resolve() # Only fetch eggs required by the config File "/cygdrive/c/web/galaxy-central/lib/galaxy/eggs/__init__.py", line 345, i n resolve egg.resolve() File "/cygdrive/c/web/galaxy-central/lib/galaxy/eggs/__init__.py", line 195, i n resolve return self.version_conflict( e.args[0], e.args[1] ) File "/cygdrive/c/web/galaxy-central/lib/galaxy/eggs/__init__.py", line 226, i n version_conflict r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env, egg. fetch ) File "/cygdrive/c/web/galaxy-central/lib/pkg_resources.py", line 565, in resol ve raise DistributionNotFound(req) # XXX put more info here pkg_resources.DistributionNotFound: numpy==1.6.0 Fetch failed.

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11. Question about formatting mouse (mm9) GTF (shamsher jagat) (galaxy-user Digest, Vol 64, Issue 11)
by Lozach, Jean 12 Oct '11

12 Oct '11

Illumina provides a ftp site where you can download all the files you need to use TopHat and Cufflinks: Bowtie index and gtf files are present for about 20 species. For most species, we do covered different data sources (mainly NCBI, Ensembl and UCSC) as well as different builds. This resource is called iGenomes. You should find in it the Ensembl mm9 GTF file compatible with TopHat You can find all the links here http://cufflinks.cbcb.umd.edu/igenomes.html and more information about iGenomes here ftp://ftp.illumina.com/README.txt The annotations will be updated next week and will also include BWA Index files. Regards Jean Lozach Manager, Bioinformatics Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 ------------------------------ Message: 11 Date: Wed, 12 Oct 2011 04:26:15 -0700 From: shamsher jagat <kanwarjag(a)gmail.com> To: galaxy-user <galaxy-user(a)lists.bx.psu.edu> Subject: [galaxy-user] Question about formattung mouse (mm9) GTF Message-ID: <CAN_Q6i4JS3fJUx__Cbv_H6veScTR0C3k3dLa96LFBRvk3oEcCg(a)mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" I have read in the mailing list that you have a workflow which can modify the human GTF file so that it will be compatible with Top Hat. Will it also work with Ensembl mm9 GTF or there is a different work flow. Thanks

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Question about formattung mouse (mm9) GTF
by shamsher jagat 12 Oct '11

12 Oct '11

I have read in the mailing list that you have a workflow which can modify the human GTF file so that it will be compatible with Top Hat. Will it also work with Ensembl mm9 GTF or there is a different work flow. Thanks

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tophat error
by zohra saci 12 Oct '11

12 Oct '11

Hello, I was trying to run tophat v1.3.2 on SOLID data and I have this error: zohra@bart:~/Bureau/cancer$ tophat -o /tmp/tophat_SRR036752/ -g 1 -p 4 -C /home/zohra/indexes_bowtie/humain_ SRR036752.fastq [Tue Oct 11 13:23:53 2011] Beginning TopHat run (v1.3.2) ----------------------------------------------- [Tue Oct 11 13:23:53 2011] Preparing output location /tmp/tophat_SRR036752// [Tue Oct 11 13:23:53 2011] Checking for Bowtie index files [Tue Oct 11 13:23:53 2011] Checking for reference FASTA file [Tue Oct 11 13:23:53 2011] Checking for Bowtie Bowtie version: 0.12.7.0 [Tue Oct 11 13:23:53 2011] Checking for Samtools Samtools Version: 0.1.18 [Tue Oct 11 13:23:53 2011] Generating SAM header for /home/zohra/indexes_bowtie/humain_ [Tue Oct 11 13:23:55 2011] Preparing reads format: fastq quality scale: phred33 (default) [FAILED] Error running 'prep_reads' Error: qual length (51) differs from seq length (51) for fastq record ! Can you help me. Thanks Zohra Saci

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CompleteGenomics publicly available genomes.
by Melissa A. Wilson Sayres 12 Oct '11

12 Oct '11

Is there a plan to add the 69 publicly available genomes from CompleteGenomics to the SharedData in Galaxy? http://www.completegenomics.com/sequence-data/download-data/ I am planning to do some analysis of a subset of these genomes in Galaxy (and I think many more in the future). I also think many CompleteGenomics users would be more likely to use Galaxy if the masterVar files were already available in Galaxy I just wanted to check if it was already on the list, before I uploaded them myself. Thanks, Melissa -- Melissa A. Wilson Sayres, PhD Miller Fellow University of California, Berkeley

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