April 2011 - galaxy-user - lists.galaxyproject.org

runtime warning with pysam egg
by Shantanu Pavgi 02 May '11

02 May '11

Hi, I am getting following warning when I start the galaxy server. I am using latest revision (50e249442c5a) of galaxy-dist. Am I missing anything in the configuration here? {{{ $ ./run.sh /home/galaxy/.python-eggs/pysam-0.4.1_kanwei_ae2bd50d9945-py2.6-linux-x86_64-ucs2.egg-tmp/csamtools.so:6: RuntimeWarning: __builtin__.file size changed, may indicate binary incompatibility ###t#|}#######b###############S#5#####D###i)#######[####x,m ###<#=####L########B###########q##.:######$2###rDM###E3A#########j### python path is: /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/numpy-1.3.0-py2.6-linux-x86_64-ucs2.egg, /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/pysam-0.4.1_kanwei_ae2bd50d9945-py2.6-linux-x86_64-ucs2.egg, /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/Whoosh-0.3.18-py2.6.egg, /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/pycrypto-2.0.1-py2.6-linux-x86_64-ucs2.egg, /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/python_lzo-1.08_2.03_static-py2.6-linux-x86_64-ucs2.egg, /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/bx_python-0.7.0_14b6a6c95da6-py2.6-linux-x86_64-ucs2.egg, /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/amqplib-0.6.1-py2.6.egg, /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/pexpect-2.4-py2.6.egg, /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg,/share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/Babel-0.9.4-py2.6.egg, /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/Beaker-1.4-py2.6.egg, /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/Mako-0.2.5-py2.6.egg, /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/WebHelpers-0.2-py2.6.egg, /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs2.egg, /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/wchartype-0.1-py2.6.egg, /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/elementtree-1.2.6_20050316-py2.6.egg, /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/docutils-0.7-py2.6.egg, /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/WebOb-0.8.5-py2.6.egg, /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/Routes-1.12.3-py2.6.egg, /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs2.egg, /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/PasteDeploy-1.3.3-py2.6.egg, /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/PasteScript-1.7.3-py2.6.egg, /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/Paste-1.6-py2.6.egg, /share/apps/galaxy/galaxy-dist-50e249442c5a/lib, /share/apps/galaxy/python/2.6.6/lib/python26.zip, /share/apps/galaxy/python/2.6.6/lib/python2.6, /share/apps/galaxy/python/2.6.6/lib/python2.6/plat-linux2, /share/apps/galaxy/python/2.6.6/lib/python2.6/lib-tk, /share/apps/galaxy/python/2.6.6/lib/python2.6/lib-old, /share/apps/galaxy/python/2.6.6/lib/python2.6/lib-dynload, /share/apps/galaxy/python/2.6.6/lib/python2.6/site-packages galaxy.datatypes.registry DEBUG 2011-04-25 12:37:54,637 Loading datatypes from datatypes_conf.xml galaxy.datatypes.registry DEBUG 2011-04-25 12:37:54,650 Loaded display application 'ucsc_bam' for datatype 'bam', inherit=False ... ... ... }}} -- Thanks, Shantanu.

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Removing deleted datasets
by Simon Lank 02 May '11

02 May '11

Hi. Our current galaxy database is ~ 600 gb, most of which are user deleted datasets. I followed the instructions here: https://bitbucket.org/galaxy/galaxy-central/wiki/Config/PurgeHistoriesAndDa… and ran the shell scripts in recommended order. One of them in particular (I think it was purge_histories.sh) took amost 24 hours to complete. However, it doesn't appear any / most of the files were actually deleted, since we still have ~ 600 gb of dataset files. Is there something obvious I can try to get the files purged correctly? Thanks. Simon Simon Lank Research Specialist O'Connor Lab, WNPRC 555 Science Dr. Madison WI (608) 265-3389

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Move data between histories?
by Sam White 28 Apr '11

28 Apr '11

Hi, I was wondering if there was a way to easily use (or move) data between different histories. I have a large fasta file that I'd like to use in a work flow, but this fasta file only shows up when I have the original history open. Is there a way to select data files that exist in different histories or do I have to download the file and re-up it to any new histories that I'd like to use it in? Thanks in advance for any help. Sam White

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mapping with tophat vs. bwa
by Austin Paul 28 Apr '11

28 Apr '11

Hello, I am getting what seems to me to be strange results using two different mapping tools in Galaxy. I am mapping illumina RNA-seq data and with tophat, while setting # alignments to 1, I get around 15-20% reads mapping. And when I use bwa, I am getting around 75% reads mapping. My reference is a collection of ESTs so the strength of tophat being a spliced read mapper is probably not being utilized, but I am surprised by the difference in the number of reads mapping between the two. Any thoughts? Austin

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getting started with galaxy
by Joanna Rampersad-ammons 28 Apr '11

28 Apr '11

Hi I am very new to galaxy. I have registered as a user. Is there a set of simple instructions or URL that I can follow that will help me to get my data into a library for analysis? Jo

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Bowtie
by Sher, Falak 27 Apr '11

27 Apr '11

Hi Experts, I have single end Illumina reads from ChIP-Seq experiment. The files have encoding Illumina 1.5, and the sequence length is 76bp. After basic FastQc I want to map the sequences using Bowtie. My question is: do I need to split my reads (farward and backward) before running mapping tool? In one of Galaxy screen shorts reads are spitted while not in the other. Thank you in advance, F

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Re: [galaxy-user] Problems using aaChanges tool
by Evan Schwab 27 Apr '11

27 Apr '11

Hi Jen, I am still having troubles with the aaChanges tool because it doesn't support the Zebrafish Zv9 build. But then as a test I annotated my data as Zv8 as well as the mm9 genome builds and the same error occurred. Is it a problem with the tool itself then and not my specific build? Thanks Evan On Mon, Apr 4, 2011 at 4:58 PM, Jennifer Jackson <jen(a)bx.psu.edu> wrote: > Hi Evan, > I am checking for you, will email back with an update. > Thank you again, > Jen > > On Apr 4, 2011, at 11:57 AM, Evan Schwab <Evan_Schwab(a)hms.harvard.edu> > wrote: > > Hi Jen, > > The aaChanges tool is still not working on the Zebrafish Zv9 build on > Galaxy main. I am wondering if I it is a local problem or if the tool has > not yet been fixed. > > Thanks > > Evan > > On Mon, Mar 28, 2011 at 11:27 AM, Jennifer Jackson < <jen(a)bx.psu.edu> > jen(a)bx.psu.edu> wrote: > >> Hi Evan, >> >> The update to include zebrafish (and a few other genomes) should roll >> out to Galaxy main in the next few days, if not sooner. Feel free to >> check back Friday for an update if you do not see it there by then. >> >> Thank you for your patience! >> >> Best, >> >> Jen >> Galaxy team >> >> On 3/28/11 8:01 AM, Evan Schwab wrote: >> > Hi Jen, >> > >> > The aaChanges tool is still not supporting the zebrafish Zv9 build. Can >> > you please fix this so that I am able to use the aaChanges tool. It's >> > very important. >> > >> > Thanks >> > >> > Evan >> > >> >> -- >> Jennifer Jackson >> <http://usegalaxy.org>http://usegalaxy.org >> <http://galaxyproject.org>http://galaxyproject.org >> > > > > -- > Evan Schwab > Research Associate > Megason Lab > Department of Systems Biology > Harvard Medical School > 200 Longwood Ave > Boston, MA 02115 > 908-938-3779 > > -- Evan Schwab Research Associate Megason Lab Department of Systems Biology Harvard Medical School 200 Longwood Ave Boston, MA 02115 908-938-3779

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Galaxy Community Conference Early Registration Deadline extended to May 1
by Dave Clements 26 Apr '11

26 Apr '11

Hello all, The early registration deadline for the 2011 Galaxy Community Conference has been extended by a week, from April 24 to May 1. The conference is being held in Lunteren, the Netherlands, 25-26 May, with a special "Introduction to Galaxy" session on the evening of May 24. That's the good news. The bad news is that online registration has been taken offline, starting today, until April 26 or 27. We took this step because of unexpectedly high demand for conference centre hotel rooms on May 24 and 26. We still have ample rooms for the night of May 25,* but we are now sold out on the other nights*. We are working with the conference centre to increase our room allotment on May 24 and 26. We are optimistic of getting more rooms on May 26, but we are not as hopeful about getting additional rooms for May 24. We will reopen registration next Tuesday or Wednesday and post an update on the room situation, including alternatives, at that time. As always, please let me know if you have any questions. Thanks for your patience, Dave C. -- http://galaxy.psu.edu/gcc2011/ http://getgalaxy.org http://usegalaxy.org/

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importing histories from main
by Russell Bell 25 Apr '11

25 Apr '11

Hi - There are features in the public test Galaxy that I would like to test using data from a saved history I have in the main public Galaxy. I have exported the history from main but I can't seem to get it to import (using History, Options, Import from file) in test. Is that functionality viable in test? Russell

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Mapping to only 3 genes / targeted resequencing / SOLiD4 / short reads
by Jochen Seggewiß 25 Apr '11

25 Apr '11

Hi! Following situation: 10 barcoded "samples". Each sample consists of a mix of the sequences 3 independent genes (á 2 alleles). I would like to map the SOLiD4 reads only to the sequences of those 3 genes, patient by patient. First, the 10 barcoded samples have to be separated from each other. Then, the short reads have to be mapped to the sequences of the 3 genes, which are available in FASTA-format (single) or multi-FASTA-format (all sequences in one file). Is this possible using the available GALAXY tools? How? Thank you in advance. Jose

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