galaxy-user August 2011

galaxy-user@lists.galaxyproject.org

61 participants
67 discussions

suggestion for multithreading
by Louise-Amélie Schmitt 09 Aug '11

09 Aug '11

Hello everyone, I'm using TORQUE with Galaxy, and we noticed that if a tool is multithreaded, the number of needed cores is not communicated to pbs, leading to job crashes if the required resources are not available when the job is submitted. Therefore I modified a little the code as follows in lib/galaxy/jobs/runners/pbs.py 256 # define PBS job options 257 attrs.append( dict( name = pbs.ATTR_N, value = str( "%s_%s_% s" % ( job_wrapper.job_id, job_wrapper.tool.id, job_wrapper.user ) ) ) ) 258 mt_file = open('tool-data/multithreading.csv', 'r') 259 for l in mt_file: 260 l = string.split(l) 261 if ( l[0] == job_wrapper.tool.id ): 262 attrs.append( dict( name = pbs.ATTR_l, resource = 'nodes', value = '1:ppn='+str(l[1]) ) ) 263 attrs.append( dict( name = pbs.ATTR_l, resource = 'mem', value = str(l[2]) ) ) 264 break 265 mt_file.close() 266 job_attrs = pbs.new_attropl( len( attrs ) + len( pbs_options ) ) (sorry it didn't come out very well due to line breaking) The csv file contains a list of the multithreaded tools, each line containing: <tool id>\t<number of threads>\t<memory needed>\n And it works fine, the jobs wait for their turn properly, but information is duplicated. Perhaps there would be a way to include something similar in galaxy's original code (if it is not already the case, I may not be up-to-date) without duplicating data. I hope that helps :) Best regards, L-A

7 15

Mosaik with Paired Reads
by John David Osborne 09 Aug '11

09 Aug '11

Hello, I'm trying to run Mosaik on our galaxy instance on Ilumina paired reads. However when I selected "paired reads" and Ilumina as an input option, I can still only select one of the two fastq files as input. No 2nd file selector appears like with bwa, bowtie, etc... Can anybody tell me what is going on - is this a known issue? -John

2 1

keeping aditional data in the aaChanges tool
by Ximena Bonilla 09 Aug '11

09 Aug '11

Dear Galaxy staff, I have recently started using your tool and it has been really helpful, thank you! When using Human Genome Variation, aaChanges, I would like to keep some extra lines in the output file from either of the input files. In the tool description it says I should be able to keep them: "...chromosome, start, and end position as well as the SNP. The SNP can be given using ambiguous-nucleotide symbols or a list of two to four alleles separated by '/'. *Any other columns in the first input file will not be used but will be kept for the output*. The second input file contains..." However, I haven't found a way of actually have them in the output file. What am I missing/doing incorrectly? What I've been trying to keep by the way is rs IDs or Ensembl gene IDs. Thank you in advance for your answer. Kind regards, Ximena

2 2

configuring apache proxy server issue
by Sridhar A Malkaram 08 Aug '11

08 Aug '11

Hi, I have been using galaxy succesfully for my work using its internal web-server. Recently I wanted to use it over the internet and so, I configured it with apache at /galaxy of apache's root. I followed all the instructions in setting up the proxy redirection. But I think the re-direction is not happening. I highly appreciate any suggestions to correct the issue. I checked for the mod_proxy, mod_proxy_http etc modules and they are present and switched on. Apache gives the following error in its error_log file: [Thu Aug 04 14:15:56 2011] [error] [client 127.0.0.1] File does not exist: /usr/local/apache/htdocs/galaxy Galaxy was set up in the directory /home/galaxy/galaxy-dist The lines specific for proxy setting in universe_wsgi.ini are as follows: use = egg:Paste#http port = 8080 host = localhost [filter:proxy-prefix] use = egg:PasteDeploy#prefix prefix = /galaxy [app:main] filter-with = proxy-prefix cookie_path = /galaxy use_remote_user = True remote_user_maildomain = unl.edu httpd.conf settings: RewriteEngine on <Proxy http://localhost:8080> Order deny,allow Allow from all </Proxy> <Location "/galaxy"> Order deny,allow Allow from all # Take the $REMOTE_USER environment variable and set it as a header in the proxy request. RewriteCond %{IS_SUBREQ} ^false$ RewriteCond %{LA-U:REMOTE_USER} (.+) RewriteRule . - [E=RU:%1] RequestHeader set REMOTE_USER %{RU}e RequestHeader set X-URL-SCHEME https RewriteRule ^/galaxy$ /galaxy/ [R] RewriteRule ^/galaxy/(.*) http://localhost:8080/$1 [P] # Compress all uncompressed content. SetOutputFilter DEFLATE SetEnvIfNoCase Request_URI \.(?:gif|jpe?g|png)$ no-gzip dont-vary SetEnvIfNoCase Request_URI \.(?:t?gz|zip|bz2)$ no-gzip dont-vary </Location> Thanks,

3 2

Join on genomic interval
by Seth Kasowitz 08 Aug '11

08 Aug '11

Hello, I am hoping for some clarification on how Join on Genomic Intervals functions. I have two lists of intervals: mapped reads and a list of exons. If I join the two (INNER JOIN), I expect multiple reads to join with the same exon, and see this in the output. What is confusing me is that some output has more joined intervals returned than were present in the input reads. For example: I join 17,000,000 mapped reads with a list of 300,000 exons and retrieve 21,000,000 joined intervals I must be misunderstanding what the function does, and am hoping someone can explain how the output can have more lines than the reads submitted. Thank you, Seth -- Seth Kasowitz University of Connecticut Department of Molecular and Cellular Biology seth.kasowitz(a)uconn.edu Beach Hall Room 335 (6-3580)

2 1

Re: [galaxy-user] galaxy cluster setup
by Bernhard Gschloessl 05 Aug '11

05 Aug '11

Dear all, I wonder if someone of you has already tested Galaxy with the ProActive scheduler (since it is not listed on the page http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster )? If yes, could you give me a feedback? Thanks in advance, Bernhard > > > > From: *Roman Valls* <brainstorm(a)nopcode.org > <mailto:brainstorm@nopcode.org>> > Date: Thu, Jun 16, 2011 at 4:41 PM > Subject: Re: [galaxy-user] galaxy cluster setup > To: galaxy-user(a)lists.bx.psu.edu <mailto:galaxy-user@lists.bx.psu.edu> > > > Hello Robert, > > You may have a look at the official documentation on the wiki: > > https://bitbucket.org/galaxy/galaxy-central/wiki/Config/Cluster > https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer > > You may also have a look at the slides from the past Galaxy Community > conference: > > http://wiki.g2.bx.psu.edu/GCC2011 > > You might be interested on the one Nate Coraor gave: > > "Galaxy Deployment and API" > > Cheers ! > Roman > > On 2011-06-15 23:01, Robert Jackson wrote: > > Does anyone have practical info on galaxy setup on a cluster? > > > > > > > > Robert C. Jackson > > > > Software Systems Specialist III > > > > The University of Texas Pan-American > > > > Computer Support Services > > > > Division of Information Technology > > > > Phone: 956-665-2455 <tel:956-665-2455> > > > > Fax: 956-665-8777 <tel:956-665-8777> > > > > > > > > > > > > ___________________________________________________________ > > The Galaxy User list should be used for the discussion of > > Galaxy analysis and other features on the public server > > at usegalaxy.org <http://usegalaxy.org>. Please keep all replies on > the list by > > using "reply all" in your mail client. For discussion of > > local Galaxy instances and the Galaxy source code, please > > use the Galaxy Development list: > > > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > > > To manage your subscriptions to this and other Galaxy lists, > > please use the interface at: > > > > http://lists.bx.psu.edu/ > ___________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org <http://usegalaxy.org>. Please keep all replies on > the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/ > -- Bernhard GSCHLOESSL, PhD Bioinformatics Research Engineer / IR2 Bioinformatique INRA-CBGP (UMR 1062) The Center for Biology and Management of Populations / Centre de Biologie et de Gestion des Populations Campus International de Baillarguet CS 30016 34988 Montferrier-sur-Lez cedex, FRANCE email: bernhard.gschloessl(a)supagro.inra.fr phone: +33(0)4 30 63 04 19 fax: +33(0)4 99 62 33 45 web: http://www.ensam.inra.fr/cbgp/?q=en

2 1

BedGraph format
by 吳正華 05 Aug '11

05 Aug '11

Dear all: I want to transform a text file to BedGraph format and show it on UCSC genome browser, but it seems that in galaxy I cannot assign a column that has values in configuration screen (BedGraph format). How should I do the above task in galaxy? Thanks John Wu

2 1

Re: [galaxy-user] Question about Cuffdiff
by Jennifer Jackson 04 Aug '11

04 Aug '11

Hello Luciano, This was a bug, fixed in galaxy-central yesterday: changeset 4212f675f95b . You can either pull the changeset into your local instance or wait for it to be incorporated into the next distribution (within the next few weeks). Next time, it would be great if you would send questions like this directly to the mailing lists: - galaxy-user(a)bx.psu.edu for data/tool questions like this one - galaxy-dev(a)bx.psu.edu local install/technical questions Thanks! Jen Galaxy team On 8/3/11 4:16 PM, Luciano Cosme wrote: > Hi Jeni, > I am sorry to bother you again. I am also running galaxy locally and > I solved all the problems so far. Now I am running cuffdiff and when I > select my data input at "SAM or BAM file of aligned RNA-Seq reads:" I > get a red message telling me to choose the genome build for that data > set "Unspecified genome build, click the pencil icon in the history item > to set the genome build". The problem is that used a custom index since > AaegL1 is not available locally. Any thoughts how to go around it. I > will attach a ss. > Thank you . > Luciano > > > -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support

1 0

GATK best practices with local installation of Galaxy
by Camille Stephan 04 Aug '11

04 Aug '11

Hello guys, I'm trying to run a pipeline of the best practices for snp and indel discovery as described by the people at Broad and I'm running into troubles with the GATK tools in a local installation of Galaxy. The main problem I have is that merging bam files with the samtools merge tool doesn't keep read group for each sample, causing "Count Covariates" to crash. The pipeline works fine with a single bam file, but I need to realign at least two files at a time. Is there a way to set the read group of a merged bam inside Galaxy? Are there plans to include the "merge" tool from Picard in Galaxy? Is there an easy way for me to do this locally? (Although I would like to run this in the cloud later on when the workflow is ready). Thanks! Camille -- *** Camille Stephan-Otto Attolini, PhD Senior Research Officer, Bioinformatics and Biostatistics unit IRB Barcelona Tel (+34) 93 402 0553

2 4

(no subject)
by tarek addwebi 03 Aug '11

03 Aug '11

Hi Dear Is there anybody whom I can share my data with? I have an important question that I tried to answer, but I could not. Please see the attachment first, and let us see the first read in the first row. I need to know how many times I have this read in the whole data. Do I have to count all reads manually to know the number of this read? It would take a long time to count 11 million reads. Thank you

2 1

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

galaxy-user August 2011