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

galaxy cluster setup
by Robert Jackson 16 Jun '11

16 Jun '11

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 Fax: 956-665-8777

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New Galaxy User
by gaurav thareja 16 Jun '11

16 Jun '11

Hi All, I am a new user of Galaxy. I am trying to configure galaxy on my local system. I took clone of repository(https://bitbucket.org/galaxy/galaxy-dist). But I have couple of issues while understanding code base: 1. Is there any help file explaining directory structure and what all configuration files used for? 2. I got list of all dependencies from website, Do I have to install all tools in /usr/local/bin/ or can be installed at any custom location? I have already gone through tutorial (http://gmod.org/wiki/Galaxy_Tutorial) which was quite helpful and interesting but doesn't quite talk about my doubts above. Regards Gaurav Thareja -- Regards Gaurav Thareja

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Cufflinks advice
by Michael Gooch 15 Jun '11

15 Jun '11

I attempted to run cufflinks on some RNA sequencing data. It seemed to complete without any errors, but the output files were empty. I am trying to figure out if I did something wrong or whether my data needs some additional processing before cufflinks will be able to use it. (Or whether the data is unsuitable for cufflinks.) The data is paired end reads. M. Gooch

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Error running latest Galaxy Distribution: numpy.dtype exception
by Michael Steder 15 Jun '11

15 Jun '11

I'm just following the documentation here: https://bitbucket.org/galaxy/galaxy-central/wiki/GetGalaxy And I ran into the following error: $ hg clone https://bitbucket.org/galaxy/galaxy-dist $ cd galaxy-dist $ sh run.sh Fetch successful. Traceback (most recent call last): File "/Users/steder/GO/GoGalaxy/galaxy-dist/lib/galaxy/web/buildapp.py", line 81, in app_factory from galaxy.app import UniverseApplication File "/Users/steder/GO/GoGalaxy/galaxy-dist/lib/galaxy/app.py", line 11, in <module> from galaxy.tools.imp_exp import load_history_imp_exp_tools File "/Users/steder/GO/GoGalaxy/galaxy-dist/lib/galaxy/tools/imp_exp/__init__.py", line 6, in <module> from galaxy.web.base.controller import UsesHistory File "/Users/steder/GO/GoGalaxy/galaxy-dist/lib/galaxy/web/base/controller.py", line 12, in <module> from galaxy.visualization.tracks.data_providers import get_data_provider File "/Users/steder/GO/GoGalaxy/galaxy-dist/lib/galaxy/visualization/tracks/data_providers.py", line 16, in <module> from bx.arrays.array_tree import FileArrayTreeDict File "numpy.pxd", line 119, in init bx.arrays.array_tree (lib/bx/arrays/array_tree.c:11323) ValueError: numpy.dtype does not appear to be the correct type object I was able to run the previous stable version of Galaxy. Is there something I can do to get galaxy-dist running? Should I be running galaxy-central instead? ~Mike

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can I merge histories?
by Robert Curtis Hendrickson 14 Jun '11

14 Jun '11

Folks, Is there some way I can merge histories? I ran a workflow on 3 different samples in one history, each time putting them in a different history with the same name. However, Galaxy created 3 new histories, each with the same name! But I need the data in the same history to compare and contrast it. Thanks, Curtis

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MACS
by Sher, Falak 14 Jun '11

14 Jun '11

while using MSCS tool from Galaxy I get following mesg. with BED file: "Treatment tags and Control tags are uneven! FDR may be wrong" Any suggestion to fix it.. I don't understand its implication, my data is form single illumina chIP-Seq experiment. I use Bowtie from Galaxy for mapping. F

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software request
by Christopher Balakrishnan 14 Jun '11

14 Jun '11

Hi there, I noticed on Seqanswers there was a post inquiring about the potential addition of DE-Seq (Anders & Huber) to the growing stack of tools available in galaxy. I for one would love to see this integrated. I typically use it in combination with HT-Seq, a set of python scripts also from Simon Anders. This simply has the functionality of converting a SAM alignment to simple counts of reads per transcript across the genome. Probably there are tools is Galaxy that do a similar thing. In any case I think many people are using TopHat -> HT- Seq -> DE-Seq for analysis of RNAseq data so it would be great if DE- Seq were supported in Galaxy My two cents.. Thanks for all your great work! Chris Christopher Balakrishnan Institute for Genomic Biology University of Illinois 1206 W. Gregory Drive MC-195 Urbana, IL 61801 phone: 617-905-2910 http://myweb.ecu.edu/balakrishnanc

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the original subject for the thread
by David Wang 14 Jun '11

14 Jun '11

-----Original Message----- From: galaxy-user-bounces(a)lists.bx.psu.edu [mailto:galaxy-user-bounces@lists.bx.psu.edu] On Behalf Of galaxy-user-request(a)lists.bx.psu.edu Sent: Tuesday, June 14, 2011 9:00 AM To: galaxy-user(a)lists.bx.psu.edu Subject: galaxy-user Digest, Vol 60, Issue 14 Send galaxy-user mailing list submissions to galaxy-user(a)lists.bx.psu.edu To subscribe or unsubscribe via the World Wide Web, visit http://lists.bx.psu.edu/listinfo/galaxy-user or, via email, send a message with subject or body 'help' to galaxy-user-request(a)lists.bx.psu.edu You can reach the person managing the list at galaxy-user-owner(a)lists.bx.psu.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of galaxy-user digest..." HEY! This is important! If you reply to a thread in a digest, please 1. Change the subject of your response from "Galaxy-user Digest Vol ..." to the original subject for the thread. 2. Strip out everything else in the digest that is not part of the thread you are responding to. Why? 1. This will keep the subject meaningful. People will have some idea from the subject line if they should read it or not. 2. Not doing this greatly increases the number of emails that match search queries, but that aren't actually informative. Today's Topics: 1. SAM to bigbed (Aleks Schein) 2. Re: SAM to bigbed (Jennifer Jackson) 3. GenBank Submission - How to Generate Fasta (not fastq) files (John David Osborne) ---------------------------------------------------------------------- Message: 1 Date: Mon, 13 Jun 2011 18:42:45 +0200 From: Aleks Schein <aleks(a)mb.au.dk> To: galaxy-user(a)lists.bx.psu.edu Subject: [galaxy-user] SAM to bigbed Message-ID: <20110613184245.14175jqs5ml9mqrp(a)webmail.nfit.au.dk> Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Hi, Is it possible to generate a bigbed or bigwig file from SAM (or BAM) file using Galaxy? It looks like there is such option in the full version of SAMTools, but I have no appropriate machine to run SAMTools. Thanks, Aleks ------------------------------ Message: 2 Date: Mon, 13 Jun 2011 10:03:04 -0700 From: Jennifer Jackson <jen(a)bx.psu.edu> To: Aleks Schein <aleks(a)mb.au.dk> Cc: galaxy-user(a)lists.bx.psu.edu Subject: Re: [galaxy-user] SAM to bigbed Message-ID: <4DF642C8.3070000(a)bx.psu.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi Aleks, There is no function in Galaxy for this in one step, but there are other options: 1) only convert to BAM and view at UCSC that way, if visualization is your goal. This preserves the primary sequence information in the file so that it can be viewed/used in downstream analysis. 2) use "Generate Pileup" then "Pileup-to-Interval". Interval can be changed to BED using the pencil icon (you may need to arrange column order first to meet spec, as BED columns must be in a specific order, as defined on any of the tools involving BED files). The resulting BED file can then be condensed by "BED-to-bigBed". This loses the primary sequence information - only coordinates are retained - may or may not be desirable. Hopefully this helps, Jen Galaxy team On 6/13/11 9:42 AM, Aleks Schein wrote: > Hi, > Is it possible to generate a bigbed or bigwig file from SAM (or BAM) > file using Galaxy? It looks like there is such option in the full > version of SAMTools, but I have no appropriate machine to run SAMTools. > > Thanks, > > Aleks > ___________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at 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/ -- Jennifer Jackson http://usegalaxy.org/ http://galaxyproject.org/ ------------------------------ Message: 3 Date: Mon, 13 Jun 2011 13:34:11 -0500 From: John David Osborne <ozborn(a)uab.edu> To: "galaxy-user(a)bx.psu.edu" <galaxy-user(a)bx.psu.edu> Subject: [galaxy-user] GenBank Submission - How to Generate Fasta (not fastq) files Message-ID: <27F664987FEADB4EA29031F58BC42B3E02144922(a)UABEXMBS5.ad.uab.edu> Content-Type: text/plain; charset="iso-8859-1" I still haven't found an easy solution to this problem and I am afraid I'm going to have to write one my own - which makes little sense as I bet this has been solved thousands of times! Can anybody point me to a script/software to convert a samtools pileup file into a fasta consensus file? It would be nice to set coverage thresholds, etc... but I'll take anything I can work with. The best google could do for me was this: http://biostar.stackexchange.com/questions/1389/how-to-generate-a-consen sus-fasta-sequence-from-sam-tools-pileup Not that helpful, -John P.S. If there is a better way of doing this (something other than samtools) I'm all ears.

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SAM to bigbed
by Aleks Schein 13 Jun '11

13 Jun '11

Hi, Is it possible to generate a bigbed or bigwig file from SAM (or BAM) file using Galaxy? It looks like there is such option in the full version of SAMTools, but I have no appropriate machine to run SAMTools. Thanks, Aleks

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uploading files via FTP
by somy ork 13 Jun '11

13 Jun '11

Hi, Am trying to configure galaxy to enable file upload via FTP. My server is configured with SFTP. and not FTP. Will this create a problem in galaxy? coz all my input files are above 2 GB. Should i change any settings in the universe_wsgi.ini file? Please guide me. Regards somy.

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