- galaxy-user - lists.galaxyproject.org

promoter question
by Rami Al-Ouran 25 Jul '11

25 Jul '11

Hello, Is there a way in galaxy to retrieve the promoter sequences for a list of genes. I tried using UCSC genome browser, but in many cases it keeps giving more than one promoter sequence per gene. Thank you, Rami

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Fwd: Workflows with conditional statements
by Florent Angly 25 Jul '11

25 Jul '11

I filed an enhancement report since if the workflow conditional facility does not appear to exist in Galaxy: https://bitbucket.org/galaxy/galaxy-central/issue/547/conditional-workflow-… Best, Florent -------- Original Message -------- Subject: Workflows with conditional statements Date: Wed, 18 May 2011 10:31:21 +1000 From: Florent Angly <florent.angly(a)gmail.com> To: galaxy-user(a)lists.bx.psu.edu <galaxy-user(a)lists.bx.psu.edu> Hi all, I was wondering if there is a way to put conditional statements in a Galaxy workflow. This would be useful, for example, in the case of a workflow that has an optional advanced option that the user can click. This advanced option would add some extra steps to the data processing. Another example of how this could be useful is if inside a workflow, the data needs to be processed differently based on the results of previous workflow steps. Say, you have a worflow that takes some sequences, and calculate their average length. Using a conditional statement, the workflow would put the data through DeBruijn assembler if the reads are small, but through a traditional Overlap-Layout-Consensus assembler if the reads are long. Are conditional statements possible in Galaxy workflows and I just don't know how to use them? Best, Florent

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CloudMan automates cluster customization
by Enis Afgan 24 Jul '11

24 Jul '11

Hello all, A new version of CloudMan has just been released. The two most prominent changes in this release include: 1. Support for automated persistance of modifications to the underlying file systems 2. Support for CloudBioLinux clusters on Ubuntu 11.04 --------------------- 1. CloudMan has supported customization of individual instances from its initial release but the most recent changes automates the process. This advance continues to promote use of CloudMan as a platform; you can use CloudMan with all of the infrastructure management capabilities as well as installed and configured Galaxy to customize your own instance by adding your own tools or tools that are not part of the default configuration. Complete instructions on how to use this feature are now available on Galaxy's wiki: http://wiki.g2.bx.psu.edu/Admin/Cloud/Customize%20Galaxy%20Cloud 2. CloudBioLinux offers an AMI on AWS with a pre-configured BioLinux and now CloudMan as well. In the past, CloudMan's AMI has been built on top of the CloudBioLinux and thus offered all of the features of CloudBioLinux. As of recently though, CloudBioLinux AMI build process itself includes CloudMan. As a result, there is now an AMI (ami-dfc502b6) with CloudBiolinux, CloudMan, and Galaxy available on Ubuntu 11.04. Details about CloudBioLinux are available at http://cloudbiolinux.org/.

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batch processing of many input files and then combining the results
by Andrew Straw 24 Jul '11

24 Jul '11

Hi, (Warning: Galaxy newbie here.) I'd like to run a series of galaxy tools repeatedly on multiple input files. In other words, I have input data files [data1, data2, ..., dataN] and I want to apply [step1, step2] to each of these files to produce [output1, output2, ..., outputN]. I know that I can automate the application of the multiple steps to a single input file as a workflow, but is there any way to automate running a workflow multiple times on multiple inputs through the Galaxy web interface? (I see the scripts in scripts/api, but I'm looking for something entirely driven by the web user interface.) For a second question, is there a recommended way of combining then merging the results (e.g. from multiple workflows) into a single file? The use case for this is that we're doing experiments on lots of individual flies from several genotypes and we want to analyze data from our individual fly experiments but then pool results across flies from the same genotype and compare with other genotypes. I imagine this is pretty similar to what a lot of people are doing, but somehow I'm not getting how this might be done with Galaxy. Thanks, Andrew -- Andrew D. Straw, Ph.D. Research Institute of Molecular Pathology Vienna, Austria http://www.imp.ac.at/research/andrew-straw/

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latest ubuntu version for full unified install
by Joseph Hargitai 22 Jul '11

22 Jul '11

Hi, the cloud version is using Linux ip-10-68-42-15 2.6.32-308-ec2 #16-Ubuntu SMP Thu Sep 16 15:25:39 UTC 2010 x86_64 GNU/Linux what is the latest Ubuntu version we can use for a full unified install using the tool and data scripts to populate both tools and indexes? best, joseph

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Genes from Regions.
by Shawn Anderson 22 Jul '11

22 Jul '11

Hello, I'm not sure if this is the place to ask this, but if so - here goes. If I have a list of genomic regions (from CNV gains and losses) comprised of chromosome, start and stop (ie. chr7 68000000 71000000) for a given genome build (HG 18), and I want to add the genes (ideally HUGO gene Symbols or refseqIDs)that reside within each region per line. So I want to input something like this: Sample Chromosome Region Event Length JC 507 CD19 chr10:11,997,707-12,330,274 CN Gain 332568 JC 507 CD19 chr10:47,563,503-48,085,608 CN Loss 522106 JC 507 CD19 chr10:69,510,584-69,951,738 CN Gain 441155 And get an output similar to this: Sample Chromosome Region Event Length Gene Symbols JC 507 CD19 chr10:11,997,707-12,330,274 CN Gain 332568 CDC123, DHTKD1, NUDT5, SEC61A2, UPF2 JC 507 CD19 chr10:47,563,503-48,085,608 CN Loss 522106 AGAP9, ANXA8, ANXA8L1, CTSL1P2, FAM25B, FAM25C, FAM25G, GDF10, GDF2, LOC642826, RBP3, ZNF488 JC 507 CD19 chr10:69,510,584-69,951,738 CN Gain 441155 ATOH7, DNA2, HNRNPH3, MYPN, PBLD, RUFY2, SLC25A16 Possible ? Shawn Anderson Application Scientist - Laboratory for Advanced Genome Analysis Vancouver Prostate Centre - Vancouver General Hospital 2660 Oak Street Vancouver BC V6H 3Z6 P:604-875-4111 ext. 63436 F:604-875-5654 sanderson(a)prostatecentre.com<mailto:sanderson@prostatecentre.com> www.LAGAPC.ca<http://www.microarray.prostatecentre.com/>

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Re: [galaxy-user] Tophat error: broken pipe
by Jennifer Jackson 21 Jul '11

21 Jul '11

Hi Song, We have alpha support for Tophat v1.3.0 and it appears to work fine with Galaxy's Tophat wrappers. We'll upgrade and start full testing near term. For now, when running in a local instances, we do encourage users to try it and see if it meets their needs. Perhaps try with an uncompressed version of the same input file and see if that functions as expected or if the same error is given when used with the Galaxy wrappers? If you want to post testing details (Galaxy pull # from bitbucket, gzip, OS version and anything else you feel is relevant) after this sort of testing, the development team will use that information when full integration testing is performed. Perhaps others running local instances will also comment if you post these detailed testing results to the galaxy-dev(a)bx.psu.edu mailing list (will reach the primary external Galaxy development community). Thanks for using Galaxy! Jen Galaxy team On 7/20/11 6:59 AM, Song Li wrote: > > Hi Jen, > > Thank you for the fast reply, however, tophat works fine with this > command when used as stand alone software. I checked the version of gzip > and it's the same on galaxy server and on the machine where I run tophat > alone. > > The broken pipe error is likely due to a file that is not closed by a > previous step. > > Have anyone tested tophat 1.3 on galaxy? > > Thanks, > Song > > On Tue 07/19/11 6:45 PM , Jennifer Jackson <jen(a)bx.psu.edu> wrote: > > Hello Song Li, > > The file extension seems to be a mismatch. > > file.gz <- "gzip" utility > > Exploring the use of gunzip or zcat are options to restore a "file.z". > > Hopefully this helps, > > Jen > Galaxy team > > On 7/19/11 11:52 AM, Song Li wrote: > > Hello everyone, > > > > I was trying to run tophat in a local version of galaxy, but I got the > > following error: > > > > gzip: stdout: Broken pipe > > [Tue Jul 19 14:10:36 2011] Processing bowtie hits > > Error: could not open pipe gzip -cd< > ./tophat_out/tmp/left_kept_reads_missing.fq.z > > > > It seems that when tophat is calling gzip, the pipe can not be open. > > > > Can anyone suggest a fix to this problem? > > > > Thanks, > > Song Li > > -- > > Postdoctoral Associate > > Uwe Ohler Laboratory > > Institute for Genome Sciences and Policy > > 101 Science Drive > > CIEMAS 2171 > > Phone: 919-68-2124 > > Duke University > > > > > > > > ___________________________________________________________ > > 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 <parse.php?redirect=<a > href=>">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/ <parse.php?redirect=<a > href=>">http://lists.bx.psu.edu/ > > -- > Jennifer Jackson > http://usegalaxy.org/ <parse.php?redirect=<a > href=>">http://usegalaxy.org/ > http://galaxyproject.org/ <parse.php?redirect=<a > href=>">http://galaxyproject.org/ > ___________________________________________________________ > 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 <parse.php?redirect=<a > href=>">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/ <parse.php?redirect=<a > href=>">http://lists.bx.psu.edu/ > -- Jennifer Jackson http://usegalaxy.org/ http://galaxyproject.org/

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Cufflinks reporting FPKM values of all zeroes (0)
by David K Crossman 20 Jul '11

20 Jul '11

Hello! I have come across a problem where Cufflinks is reporting all FPKM values as zeroes (0). I have a unique RNA-Seq project from a collaborator where they are studying eyesight by using tree shrews. I found that Ensembl (http://useast.ensembl.org/Tupaia_belangeri/Info/Index) has the FASTA file for the tree shrew genome (only a 2x coverage, so not very good in the first place) and had this file indexed in our local instance of Galaxy. I ran TopHat and it looks as if TopHat ran fine because I'm getting anywhere from 71-80% properly paired when I check the stats using "Flagstat." I then take the accepted hits BAM file from TopHat plus the GTF RefGene file from Ensembl for tree shrew and load that into Cufflinks. It seems as if Cufflinks works okay, but when I inspect Cufflinks three output files, all the FPKM values are 0. I have two other RNA-Seq projects (human and mouse) and both of these projects worked fine through TopHat and Cuff(links/Compare/Diff) and with a RefGene GTF file on our local instance of Galaxy (as well as on the Galaxy instance at Penn State), so it makes me think that both TopHat and Cufflinks are working okay. I'm wondering if it has to do something with the tree shrew reference genome. Has anyone encountered anything like this? If so, how did you solve the problem? If not, do you have any suggestions as to what I can do next? Any help/info would be greatly appreciated. Thanks, David

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Tophat error: broken pipe
by Song Li 20 Jul '11

20 Jul '11

Hello everyone, I was trying to run tophat in a local version of galaxy, but I got the following error: gzip: stdout: Broken pipe [Tue Jul 19 14:10:36 2011] Processing bowtie hits Error: could not open pipe gzip -cd < ./tophat_out/tmp/left_kept_reads_missing.fq.z It seems that when tophat is calling gzip, the pipe can not be open. Can anyone suggest a fix to this problem? Thanks, Song Li -- Postdoctoral Associate Uwe Ohler Laboratory Institute for Genome Sciences and Policy 101 Science Drive CIEMAS 2171 Phone: 919-68-2124 Duke University

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Re: [galaxy-user] using files produced by "Barcode Splitter"
by Jim Johnson 19 Jul '11

19 Jul '11

Jeremy, Usually, the users saved the files to their local machine by clicking on the links, and then uploaded them again to the galaxy server. It can be possible to copy the link location, and paste it into the upload tools URL textarea. Ideally, it would be nice for the tool developer to be able to include a link in the html that would "promote" the file to a dataset in the current history. JJ On 7/19/11 3:08 PM, Jeremy Coate wrote: > Thanks, Jim! > > I'll see if my limited Galaxy/bioinformatics skills can rise to the challenge of using your wrapper (I've never visited the "tool shed" before). > > Out of curiosity, how did people use the files generated by the barcode splitter without this? I'm assuming there was/is a way, but I'm not figuring it out. > > Jeremy > > > On Tue, Jul 19, 2011 at 11:26 AM, Jim Johnson <johns198(a)umn.edu <mailto:johns198@umn.edu>> wrote: > > I've had users make a similar request for the split files to appear in their history. I made my own wrapper to enable this behavior. It presents a list of barcodes from the barcode file input. Any barcodes the user selects will have the resulting files copied to the users history as new datasets. I uploaded my barcode splitter tool configs to the toolshed: http://toolshed.g2.bx.psu.edu/ as repository: barcode_splitter JJ Date: Mon, 18 Jul 2011 13:33:58 -0700 From: Jeremy Coate <jec73(a)cornell.edu> <mailto:jec73@cornell.edu> To: David K Crossman <dkcrossm(a)uab.edu> <mailto:dkcrossm@uab.edu> Cc: "galaxy-user(a)lists.bx.psu.edu" <mailto:galaxy-user@lists.bx.psu.edu> <galaxy-user(a)lists.bx.psu.edu> <mailto:galaxy-user@lists.bx.psu.edu> Subject: Re: [galaxy-user] using files produced by "Barcode Splitter" Message-ID: <CAA2BWd5uERaqEoUeQ97TfNhkwvHziq89wHVR-Oy04ov-K4ju6Q(a)mail.gmail.com> <mailto:CAA2BWd5uERaqEoUeQ97TfNhkwvHziq89wHVR-Oy04ov-K4ju6Q@mail.gmail.com> Content-Type: > text/plain; charset="iso-8859-1" Thanks David, I had considered this possibility but, curiously, the files don't show up in the FastQ Groomer pull-down menu either. The original (multiplexed) data file that I split using the Barcode Splitter is there (and, incidentally, I ran FastQ Groomer on that before doing the barcode split), but none of the 3 files resulting from the splitter show up. Any other thoughts? It seems like the new files just aren't landing in my history, though I can look at them by clicking their links from the Barcode Splitter output. Jeremy On Mon, Jul 18, 2011 at 12:01 PM, David K Crossman <dkcrossm(a)uab.edu> <mailto:dkcrossm@uab.edu> wrote: > >> Jeremy,**** ** ** The files need to be groomed using the FastQ Groomer so that they will end up in the fastqsanger state. Then your files will show up in the pull-down menus.**** ** ** David**** ** ** ** ** *From:* galaxy-user-bounces(a)lists.bx.psu.edu <mailto:galaxy-user-bounces@lists.bx.psu.edu> [mailto: galaxy-user-bounces(a)lists.bx.psu.edu <mailto:galaxy-user-bounces@lists.bx.psu.edu>] *On Behalf Of *Jeremy Coate *Sent:* Monday, July 18, 2011 1:44 PM *To:* galaxy-user(a)lists.bx.psu.edu <mailto:galaxy-user@lists.bx.psu.edu> >> >> *Subject:* [galaxy-user] using files produced by "Barcode Splitter"**** >> >> ** ** >> >> I used the "Barcode Splitter" tool to split multiplexed RNA-Seq libraries >> into separate files. I would now like to map the reads from each of these >> fastq files to a reference genome. However, the fastq files generated by >> Barcode Splitter don't appear in the "Fastq File" pull-down menus within the >> the BWA or Bowtie launch pages. I'm probably missing something obvious, but >> what is the trick for making these files available for the mapping tools? Do >> I need to import them into my history somehow?**** >> >> ** ** >> >> Thanks! >> Jeremy**** >> > > > > > > ___________________________________________________________ > 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/ > >

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