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

Fwd: To get the gene name from BED file
by Anton Nekrutenko 24 May '10

24 May '10

Begin forwarded message: > From: Shibu John <shibujohn82(a)gmail.com> > Date: May 24, 2010 8:25:35 AM EDT > To: Anton Nekrutenko <anton(a)bx.psu.edu> > Subject: To get the gene name from BED file > > Hi, > How can I get the gene names for the whole exome locations ( hg18).. > > ******************** > chr1 58932 59892 > chr1 357510 358470 > chr1 610947 611907 > chr1 851160 851280 > chr1 855395 855608 > chr1 856246 856366 > chr1 860956 861196 > ******************** > > I used the "Profile Annotations for a set of genomic intervals".. > But I am not getting proper output... > > I just want the at least gene name in the fourth column for each > location..like this > ************************** > chr1 58932 59892 OR4F5:ccds|CCDS30547.1 > chr1 357510 358470 OR4F16:ccds|CCDS41220.1 > chr1 610947 611907 OR4F16:ccds|CCDS41221.1 > chr1 851160 851280 SAMD11:ccds|CCDS2.2 > chr1 855395 855608 SAMD11:ccds|CCDS2.2 > chr1 856246 856366 SAMD11:ccds|CCDS2.2 > chr1 860956 861196 SAMD11:ccds|CCDS2.2 > ****************** > > Can you help me to get this information from galaxy? > > Thanks, > Shibu > > On Thu, May 20, 2010 at 2:52 PM, Anton Nekrutenko <anton(a)bx.psu.edu> > wrote: > Shibu: > > We experienced disk problems overnight. Galaxy is back to normal. > > Tx, > > anton > galaxy team > > Anton Nekrutenko http://nekrut.bx.psu.edu http://usegalaxy.org

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To get the gene name from BED file
by Shibu John 24 May '10

24 May '10

Hi, How can I get the gene names for the whole exome locations ( hg18).. ******************** chr1 58932 59892 chr1 357510 358470 chr1 610947 611907 chr1 851160 851280 chr1 855395 855608 chr1 856246 856366 chr1 860956 861196 ******************** I used the "Profile Annotations<http://main.g2.bx.psu.edu/tool_runner?tool_id=Annotation_Profiler_0>for a set of genomic intervals".. But I am not getting proper output... I just want the at least gene name in the fourth column for each location..like this ************************** chr1 58932 59892 OR4F5:ccds|CCDS30547.1 chr1 357510 358470 OR4F16:ccds|CCDS41220.1 chr1 610947 611907 OR4F16:ccds|CCDS41221.1 chr1 851160 851280 SAMD11:ccds|CCDS2.2 chr1 855395 855608 SAMD11:ccds|CCDS2.2 chr1 856246 856366 SAMD11:ccds|CCDS2.2 chr1 860956 861196 SAMD11:ccds|CCDS2.2 ****************** Can you help me to get this information from galaxy? Thanks, Shibu On Thu, May 20, 2010 at 2:52 PM, Anton Nekrutenko <anton(a)bx.psu.edu> wrote: > Shibu: > > We experienced disk problems overnight. Galaxy is back to normal. > > Tx, > > anton > galaxy team > > >

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Problems installing Galaxy
by Rodolfo Aramayo 21 May '10

21 May '10

People, Apologies for the disturbance. On a fresh MacOSX I installed Python, Numpy and Scipy using MacPorts I tested both Numpy and Scipy as follows: == python >>> import numpy >>> numpy.test('1','10') >>> import scipy >>> scipy.test('1','10') == The computer does understand them and processes them as expected. The tests seem to work? However, when I attempt a fresh installation of Galaxy I get the following error: > hg clone http://www.bx.psu.edu/hg/galaxy galaxy_dist requesting all changes adding changesets adding manifests adding file changes added 3787 changesets with 17203 changes to 4176 files updating to branch default 2691 files updated, 0 files merged, 0 files removed, 0 files unresolved >sh setup.sh Copying datatypes_conf.xml.sample to datatypes_conf.xml Copying reports_wsgi.ini.sample to reports_wsgi.ini Copying tool_conf.xml.sample to tool_conf.xml Copying universe_wsgi.ini.sample to universe_wsgi.ini Copying tool-data/alignseq.loc.sample to tool-data/alignseq.loc Copying tool-data/annotation_profiler_options.xml.sample to tool-data/annotation_profiler_options.xml Copying tool-data/annotation_profiler_valid_builds.txt.sample to tool-data/annotation_profiler_valid_builds.txt Copying tool-data/binned_scores.loc.sample to tool-data/binned_scores.loc Copying tool-data/blastdb.loc.sample to tool-data/blastdb.loc Copying tool-data/bowtie_indices.loc.sample to tool-data/bowtie_indices.loc Copying tool-data/encode_datasets.loc.sample to tool-data/encode_datasets.loc Copying tool-data/liftOver.loc.sample to tool-data/liftOver.loc Copying tool-data/maf_index.loc.sample to tool-data/maf_index.loc Copying tool-data/maf_pairwise.loc.sample to tool-data/maf_pairwise.loc Copying tool-data/microbial_data.loc.sample to tool-data/microbial_data.loc Copying tool-data/phastOdds.loc.sample to tool-data/phastOdds.loc Copying tool-data/quality_scores.loc.sample to tool-data/quality_scores.loc Copying tool-data/regions.loc.sample to tool-data/regions.loc Copying tool-data/sam_fa_indices.loc.sample to tool-data/sam_fa_indices.loc Copying tool-data/sequence_index_base.loc.sample to tool-data/sequence_index_base.loc Copying tool-data/sequence_index_color.loc.sample to tool-data/sequence_index_color.loc Copying tool-data/twobit.loc.sample to tool-data/twobit.loc Copying tool-data/shared/ucsc/builds.txt.sample to tool-data/shared/ucsc/builds.txt Creating database/files Creating database/community_files Creating database/tmp Creating database/compiled_templates Creating database/job_working_directory Creating database/pbs Creating static/genetrack/plots Fetched http://eggs.g2.bx.psu.edu/new/Mako/Mako-0.2.5-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/new/Babel/Babel-0.9.4-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/new/Tempita/Tempita-0.1-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/new/lrucache/lrucache-0.2-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/new/boto/boto-1.8d-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/new/NoseHTML/NoseHTML-0.3.1-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/new/pexpect/pexpect-2.4-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/new/PasteDeploy/PasteDeploy-1.3.3-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/new/WebHelpers/WebHelpers-0.2-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/new/docutils/docutils-0.4-py2.6.egg Traceback (most recent call last): File "./scripts/fetch_eggs.py", line 31, in <module> c.resolve() # Only fetch eggs required by the config File "/Library/WebServer/Documents/galaxy_dist/lib/galaxy/eggs/__init__.py", line 284, in resolve egg.resolve() File "/Library/WebServer/Documents/galaxy_dist/lib/galaxy/eggs/__init__.py", line 172, in resolve r = pkg_resources.working_set.resolve( ( self.distribution.as_requirement(), ), env, self.fetch ) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/pkg_resources.py", line 551, in resolve raise DistributionNotFound(req) pkg_resources.DistributionNotFound: numpy==1.3.0 > Any Ideas?

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Generating Excel files..
by Khan, Sohail 20 May '10

20 May '10

Hi, I am generating an excel file, I would like it to appear in data history. I followed the direction in your FAQs regarding a similar problem: Added the following to universe_wsgi.ini [galaxy:datatypes] xls = galaxy.datatypes.data:Data,application/vnd.ms-excel restarted galaxy... I get no errors and an empty file in the history pane. My script works fine in the console, outputs a binary .xls file. How can I tell if the above changes to universe_wsgi.ini were "accepted" updated? Thanks. -Sohail

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galaxy server error
by John, Shibu 20 May '10

20 May '10

Hi, I am not able to connect the Galaxy server "main.g2.bx.psu.edu/". Its showing internal error.. can you please help me on the same? Thanks, Shibu John MRC Clinical Sciences Centre Imperial College London Hammersmith Hospital Campus Du Cane Road London, W12 0NN

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Re: [galaxy-user] user reference vs. built-in index
by Viren Patel 20 May '10

20 May '10

Hi Kelly. I just wanted to follow-up on this issue. I did some more tests and it seems that the problem may be because the fragement headers in my custom reference multi-fasta contain the coordinates of the fragment in the form chr:start-stop. Upon mapping with bowtie, the resultant SAM file contains the headers (as expected). But the BAM-to-pileup tool does not play well with such headers. It seems the BAM-to-pileup tool expects headers in only chr format. Since there does not appear to be a tool on galaxy to convert chr:start-stop to chr format in a SAM file (note: this also requires modification of the next column in the SAM file), the solution at this point is to download the SAM file, locally apply the fix, re-upload the SAM file and run the BAM-to-pileup tool with a built-in index (mm9 in my case). Even at this step, I still can't use my custom reference for the pileup because it contains headers in chr:start-stop format. Thoughts?

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galaxy server error
by Shibu John 20 May '10

20 May '10

Hi, I am not able to connect the Galaxy server.. http://main.g2.bx.psu.edu/ It's showing Internal Server Error Can you please have a look into the same? Thanks, Shibu

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Galaxy Sample Tracking System help
by David Sidote 19 May '10

19 May '10

Hi, I'm trying to get the Sample Tracking system installed and I can't seem to figure out how to get started. Can anyone point me in the right direction? Thanks, Dave ____________________________________________________ David Sidote, PhD | Director, Waksman Genomics Core Facility Waksman Institute | Rutgers University 190 Frelinghuysen Road | Piscataway, NJ 08854 dsidote(a)waksman.rutgers.edu | 732.445.4737

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information
by Lovorka Stojic 19 May '10

19 May '10

Dear Sir/Madam, I would like to download the chip seq data from the web links. it comes as aligned.gz file. i can not download it on the galaxy. how do I convert this file in order to be taken buy galaxy? then i would like to overlap this chip seq data with chip seq data from another protein in order to see what are the common targets. what is best way to do it? thank you in advance. best, Lovorka

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defining regions
by research pal 19 May '10

19 May '10

Dear Galaxy, First of all let me thank you people for the effort that you are involved in to help the bench scientists world over. I have the ChIP data from ENCODE and I want to see from which part i.e. Exon,Intron or intergenic regions of the human genome they are derived from.In this case can the tools available at galaxy or genome browser help me to reduce my manual efforts ? warm regards, Amit.

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