June 2010 - galaxy-user - lists.galaxyproject.org

Python error when running Bowtie for Illumina
by Weng Khong Lim 01 Feb '11

01 Feb '11

Hi all, I'm new to next-gen sequencing, so please be gentle. I've just received a pair of Illumina FASTQ files from the sequencing facility and intend to map them to the hg19 reference genome. I first used the FASTQ Groomer utility to convert the reads into Sanger reads. However, when running Bowtie for Illumina on the resulting dataset under default settings, I received the following error: An error occurred running this job: *Error aligning sequence. requested number of bytes is more than a Python string can hold* * * Can someone help point out my mistake? My history is accessible at http://main.g2.bx.psu.edu/u/wengkhong_lim/h/chip-seq-pilot-batch Appreciate the help! Weng Khong, LIM Department of Genetics University of Cambridge E-mail: wkl24(a)cam.ac.uk Tel: +447503225832

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search in libraries
by Davide Cittaro 18 Aug '10

18 Aug '10

Hi all, how does the library search tool work? I'm trying on the public galaxy but I can't get any result... d /* Davide Cittaro Cogentech - Consortium for Genomic Technologies via adamello, 16 20139 Milano Italy tel.: +39(02)574303007 e-mail: davide.cittaro(a)ifom-ieo-campus.it */

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Rhesus Macaque genome in lastz
by Lakshmanan Iyer 20 Jul '10

20 Jul '10

Hi In the NGS mapping option with "lastz" I cannot find the Rhesus Macaque genome. The web site says: "If your genome of interest is not listed, contact the Galaxy team" Could you please make this reference genome available? Rhesus Jan. 2006 (MGSC Merged 1.0/rheMac2) assembly -best -Lax

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New 5' start site, 3' end site and long internal coding exons
by Yanwei Tan 29 Jun '10

29 Jun '10

Deal all, I was wondering if anyone know Galaxy can analyze the New 5' start site, 3' end site and long internal coding exons. Because I just try to run Scripture (http://www.broadinstitute.org/software/scripture/Graph%20building) and got the bed file. Can someone give me some hint? Many thanks in advance! Wei

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hesus RheMac2 genome
by Lakshmanan Iyer 28 Jun '10

28 Jun '10

Hi In the NGS mapping option with "lastz" I cannot find the Rhesus Macaque genome. The web site says: "If your genome of interest is not listed, contact the Galaxy team" Could you please make this reference genome available? Rhesus Jan. 2006 (MGSC Merged 1.0/rheMac2) assembly -best -Lax

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Running workflows from the command line
by Erick Antezana 28 Jun '10

28 Jun '10

Hi, I was wondering about the status of the implementation that could support/enable running wokflows (build using the Galaxy interface) from the command line. cheers, Erick

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Is it possible to upload different files to different directories by Galaxy upload.py script?
by amenda lee 24 Jun '10

24 Jun '10

Hi; Is it poosible to upload files to local different directories by Galaxy upload.py script? It seems to upload all files to the same directory based on the file path in universe_wsgi.ini file. if yes, what part of upload.py needs to be edited? also is it possible to keep name of uploaded file unchanged? Thanks in advance. Amenda Lee

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parallelizing an NGS mapping workflow
by Chris Berthiaume 22 Jun '10

22 Jun '10

Hello, I'd like to use Galaxy on our local beowulf cluster for NGS workflows. One typical use case we'd be replacing with Galaxy is a parallel BWA alignment of large fastq files. To distribute this across the cluster we split the fastq file into many parts, run each separately against the same reference, and then use samtools to merge the SAM output. It's not uncommon to end up with hundreds of parts after splitting. How does Galaxy handle the parallelization of large NGS mappings? I've found the tools for fastq QC, mapping, and SAM merging, but couldn't find any set of tools that would control the parallelization. This trouble ticket (http://bitbucket.org/galaxy/galaxy-central/issue/197/starting-workflows-wit…) would suggest this functionality hasn't been implemented yet, but it seems necessary for many (most?) Illumina or SOLiD runs to get a reasonable mapping turnaround time. If this is already a feature it would be great if I could be pointed to the relevant docs and maybe it could be given a more prominent place in the wiki/interface. If it's not yet a feature, is there a timeline for when it will be added? Thanks, Chris -- Chris Berthiaume Center for Environmental Genomics University of Washington

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Some eggs are out of date (not really)
by Pieter Neerincx 22 Jun '10

22 Jun '10

Hi, I recently installed a new version of Galaxy on a server and now I have the problem that Galaxy keeps complaining some eggs are out of date. However this does not seem to be correct as I already have those eggs. Galaxy will try to fetch them and fails with "Removed conflicting egg...." This happens whenever I start Galaxy and even when the daemon process is not running and I simply check the status. See below for an example. Does anyone on the list know what is causing this and how I can prevent this? Cheers, Pi [root@app-prod-vh02 ~]# /nbic/prog/galaxy/run.sh --status Some eggs are out of date, attempting to fetch... Fetched http://eggs.g2.bx.psu.edu/new/Tempita/Tempita-0.1-py2.4.egg Removed conflicting egg: /nbic/prog/galaxy/eggs/Tempita-0.1-py2.4.egg Fetched http://eggs.g2.bx.psu.edu/new/lrucache/lrucache-0.2-py2.4.egg Removed conflicting egg: /nbic/prog/galaxy/eggs/lrucache-0.2-py2.4.egg Fetched http://eggs.g2.bx.psu.edu/new/NoseHTML/NoseHTML-0.3.1-py2.4.egg Removed conflicting egg: /nbic/prog/galaxy/eggs/NoseHTML-0.3.1-py2.4.egg Fetched http://eggs.g2.bx.psu.edu/new/Beaker/Beaker-1.4-py2.4.egg Removed conflicting egg: /nbic/prog/galaxy/eggs/Beaker-1.4-py2.4.egg Fetched http://eggs.g2.bx.psu.edu/new/WebError/WebError-0.8a-py2.4.egg Removed conflicting egg: /nbic/prog/galaxy/eggs/WebError-0.8a-py2.4.egg Fetched http://eggs.g2.bx.psu.edu/new/twill/twill-0.9-py2.4.egg Removed conflicting egg: /nbic/prog/galaxy/eggs/twill-0.9-py2.4.egg Fetched http://eggs.g2.bx.psu.edu/new/decorator/decorator-3.1.2-py2.4.egg Removed conflicting egg: /nbic/prog/galaxy/eggs/decorator-3.1.2-py2.4.egg Fetched http://eggs.g2.bx.psu.edu/new/wsgiref/wsgiref-0.1.2-py2.4.egg Removed conflicting egg: /nbic/prog/galaxy/eggs/wsgiref-0.1.2-py2.4.egg Fetched http://eggs.g2.bx.psu.edu/new/nose/nose-0.11.1-py2.4.egg Removed conflicting egg: /nbic/prog/galaxy/eggs/nose-0.11.1-py2.4.egg Fetch successful. No PID file paster.pid --------------------------------------------------------------- Biomolecular Mass Spectrometry & Proteomics group Utrecht University Visiting address: H.R. Kruyt building room O607 Padualaan 8 3584 CH Utrecht The Netherlands Mail address: P.O. box 80.082 3508 TB Utrecht The Netherlands phone: +31 6 143 66 783 email: pieter.neerincx(a)gmail.com skype: pieter.online ---------------------------------------------------------------

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June 21, 2010 Galaxy Development News Brief
by Greg Von Kuster 22 Jun '10

22 Jun '10

The latest news brief is available at the following link. You are strongly encouraged to upgrade to the revision detailed in this news brief as it contains important security fixes for data libraries. http://bitbucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBrief/2010_… Greg Von Kuster Galaxy Development Team greg(a)bx.psu.edu

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