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Update: Cuffdiff question about using an unspecified (?) database/build
by Jennifer Jackson 25 Aug '11

25 Aug '11

cross-post ===> Please use "Reply All" when responding to this email! <=== -------- Original Message -------- Subject: Re: [galaxy-dev] [galaxy-user] Cuffdiff question about using an unspecified (?) database/build Date: Thu, 25 Aug 2011 08:41:21 -0700 From: Jennifer Jackson <jen(a)bx.psu.edu> To: Robert Curtis Hendrickson <curtish(a)uab.edu> CC: 'galaxy-dev(a)lists.bx.psu.edu' <galaxy-dev(a)lists.bx.psu.edu>, David K Crossman <dkcrossm(a)uab.edu> Hi Curtis, Changeset details: http://bitbucket.org/galaxy/galaxy-central/changeset/07de40a5a0b9 We are planning on releasing a distribution within a week, so alternatively you could wait and pull from there, if you normally work from the galaxy-dist repository. And for everyone tracking this fix: the changeset was applied to the public Galaxy main instance yesterday (http://usegalaxy.org) Hope this helps! Jen Galaxy team On 8/25/11 7:55 AM, Robert Curtis Hendrickson wrote: > Jen, > > Can you also please describe the details of the fix? > We need to fix the same issue in our local instance, but don't know if this was a fix to cuffdiff, or to galaxy. Which one should we be updating? > > Regards, > Curtis > > >> -----Original Message----- >> From: galaxy-user-bounces(a)lists.bx.psu.edu [mailto:galaxy-user- >> bounces(a)lists.bx.psu.edu] On Behalf Of David K Crossman >> Sent: Friday, August 19, 2011 11:10 AM >> To: Jennifer Jackson >> Cc: galaxy-user (galaxy-user(a)lists.bx.psu.edu) >> Subject: Re: [galaxy-user] Cuffdiff question about using an unspecified (?) >> database/build >> >> Jen, >> >> Thank you very much for the reply. I'm glad to know it is a known bug >> and not something on my side of things. So, would my analysis be affected if >> I did change the bam file "Database/Build" to the older tree shrew version >> found in the drop down list? What significance does this "Database/Build" box >> have in downstream analysis if you have your own fasta reference genome file >> and gtf annotation file that is being referenced instead of a locally cached >> one? I'm just trying to obtain a better understanding of the "Database/Build" >> box for analyses where I provide the fasta and gtf file. >> >> Thanks, >> David >> >> >> -----Original Message----- >> From: Jennifer Jackson [mailto:jen@bx.psu.edu] >> Sent: Friday, August 19, 2011 9:20 AM >> To: David K Crossman >> Cc: galaxy-user (galaxy-user(a)lists.bx.psu.edu) >> Subject: Re: [galaxy-user] Cuffdiff question about using an unspecified (?) >> database/build >> >> Hello David, >> >> This is a known bug. The correction is planned to be moved out onto the public >> Galaxy instance at the next update (within a week). >> >> Sorry for the current inconvenience, >> >> Best, >> >> Jen >> Galaxy team >> >> On 8/19/11 7:00 AM, David K Crossman wrote: >>> Hello! >>> >>> I have an RNA-Seq project which consists of 5 samples from the species >>> tree shrew. When uploading these fastq files into Galaxy, I chose >>> "unspecified (?)" for the database/build since the latest tree shrew >>> version is not in the drop down list. When using TopHat, >>> Cufflinks/Compare I have selected a reference genome from my history >>> instead of using a built-in index, as well as a gtf annotation file >>> for Cufflinks/Compare and everything has been working fine. Now, I am >>> at the Cuffdiff step and I am running into an error when setting it up >>> to perform replicate analysis. When I select my TopHat accepted hits >>> bam file I see a red X and the error: "Unspecified genome build, click >>> the pencil icon in the history item to set the genome build." Here's a >>> screenshot of what I'm seeing: >>> >>> Since the latest reference genome for tree shrew wasn't listed, that's >>> why I chose "unspecified (?)." Should I go back and edit these >>> accepted hits bam files to say the Database/Build from the drop down >>> list is "Tree shrew Dec. 2006 (Broad/tupBel1) (tupBel1)?" I know that >>> this is simple to change, but will this affect my results in any way? >>> Any help/info would be greatly appreciated. >>> >>> Thanks, >>> >>> David >>> >>> >>> >>> ___________________________________________________________ >>> 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/Support >> >> ___________________________________________________________ >> 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/Support ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/

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output of cuffdiff in galaxy
by chenyao.bioinfor＠gmail.com 25 Aug '11

25 Aug '11

Dear all, I use cuffdiff in galaxy net version. The output are isoform.diff , gene.diff ...etc, but I want to find the differential expressed non-coding RNAs. How can I get these information? Thank you Chen Yao

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Unspecified genome build
by David Joly 25 Aug '11

25 Aug '11

I'm trying to use the "Extract Genomic DNA" feature from "Fetch Sequences" on Cufflinks-assembled transcripts, using a custom genome. However, when I specify "History" as the "Source for Genomic Data" and a fasta file as the reference file, I still get the "Unspecified genome build" error. I read somewhere that this bug has been solved, but this does not seem to be the case!? I am using the Galaxy webserver. http://main.g2.bx.psu.edu/u/idjoly/h/unnamed-history Any clue? David

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Galaxy public instances: data and job quotas
by Jennifer Jackson 25 Aug '11

25 Aug '11

Galaxy public instances: data and job quotas User data and job quota limits are now implemented at the public Galaxy Test instance http://test.g2.bx.psu.edu: http://galaxyproject.org/Test#Quotas While no quotas are currently implemented at the public Galaxy Main instance http://usegalaxy.org, we do ask that users stay within certain usage limits: http://galaxyproject.org/Main#Quotas If you find that you require additional resources, please consider the alternative Galaxy options explained at: http://galaxyproject.org/Big%20Picture/Choices Thanks for using Galaxy!

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NGS: Indel Analysis tool order
by David K Crossman 24 Aug '11

24 Aug '11

Hello! I have a question about the NGS: Indel Analysis toolset in Galaxy. I have aligned my samples from Illumina's HiSeq2000 to the reference genome using BWA. I've called SNPs using SAMTools and now need to call indels. Under the NGS: Indel Analysis toolset, I see two options: "Filter Indels for SAM" and "Extract indels from SAM." Since the descriptions are a little vague, I would presume that I start with the "Filter Indels for SAM" first on the BWA SAM file and then run "Extract indels from SAM" on the "Filter" output SAM file (i.e. BWA SAM -> Filter Indels for SAM -> Extract indels from SAM). Is this the correct order? Or would I skip the "Filter Indels for SAM" step (since the BWA SAM file technically already contains indels so there would be no need to filter) and just go straight to "Extract indels from SAM" (i.e. BWA SAM -> Extract indels from SAM)? I've tried both ways and get different results. For example: 1. BWA SAM -> Filter Indels for SAM -> Extract indels from SAM -> gives me 26,417 regions of interest 2. BWA SAM -> Extract indels from SAM -> gives me 93,974 regions of interest Which way is correct? Any help/info would be greatly appreciated! Thanks, David

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Re: [galaxy-user] Text Manipulation > Compute > c1[1:c1.find("(")] fails
by Russell Bell 23 Aug '11

23 Aug '11

Hi Curtis, To accomplish things like your "split" command I have had success with Compute using c1.split('(').pop(0) HTH - Russell >Message: 1 >Date: Mon, 22 Aug 2011 09:24:36 -0700 >From: Jennifer Jackson <jen(a)bx.psu.edu> >To: Robert Curtis Hendrickson <curtish(a)uab.edu> >Cc: "galaxy-user(a)lists.bx.psu.edu" <galaxy-user(a)lists.bx.psu.edu> >Subject: Re: [galaxy-user] Text Manipulation > Compute > > c1[1:c1.find("(")] fails >Message-ID: <4E5282C4.3090703(a)bx.psu.edu> >Content-Type: text/plain; charset=windows-1252; format=flowed > >Hello Curtis, > >There is some more feedback from our developers. In your own instance, >this is the recommended change: > >Edit -> > > tools/stats/column_maker.py > >To add -> > > __ob__ and __cb__ to the mapped_str dict. > > >Perhaps this will help if you still needed work-around (or others >reading this thread). > >Best! > >Jen >Galaxy team > >> On 7/20/11 1:13 PM, Robert Curtis Hendrickson wrote: >>> Folks, >>> >>> I have a column c1 that has entries like ?GXP_297346(PVALB/human)?. >>> >>> I?m trying to use Text Manipulation > Compute to strip off the ?(?)? >>> portion, leaving only the accession (which can vary in length). >>> >>> I have tried a variety of things that work in my python command line, >>> but fail here, for example: >>> >>> c1[1:c1.find("(")] >>> >>> or >>> >>> c1.split('(')[0] >>> >>> This gets mangled: >>> >>> An error occurred running this job: Expression >>> "c1__ob__1:c1.find("(")__cb__" likely invalid. >>> >>> Or >>> >>> An error occurred running this job: Expression >>> "c1.split("(")__ob__0__cb__" likely invalid. >>> >>> Please help. This is driving me crazy. >>> >>> Searching the list, I find only >>> >>> >>>http://gmod.827538.n3.nabble.com/inputs-sanitization-tt2664336.html#a266 >>>4911 >>> >>> ?Inputs sanitization? which seems to indicate this is a global mapper >>> that can only be disabled with dire security consequences. >>> >>> And >>> >>> >>>http://gmod.827538.n3.nabble.com/substring-sequence-on-coordinate-in-col >>>umns-tt3026255.html#a3048100 >>> >>> ?substring sequence on coordinate in columns? which doesn?t ever answer >>> the question about how to get compute to work. >>> >>> Thanks, >>> >>> Curtis >>> >>> >>> >>> ___________________________________________________________ >>> 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/Support

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Xgrid and Galaxy
by Paul Cantalupo 22 Aug '11

22 Aug '11

Hello, I'm trying to determine if Galaxy will work with Xgrid to set up a small cluster of Mac's for next-gen sequencing projects. I saw on http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Production%20Server that Galaxy supports Torque PBS or Sun Grid. I don't think that Sun Grid runs on Snow Leopard and I don't know about Torque. Snow Leopard already comes with Xgrid so I was hoping to use it. Thank you for your help, Paul Cantalupo University of Pittsburgh

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Re: [galaxy-user] New "built in index" for Ler within galaxy
by Jennifer Jackson 22 Aug '11

22 Aug '11

Hello Howard, http://www.arabidopsis.org/browse/Cereon/index.jsp Monsanto SNP and Ler Collections This genome appears to be under specific user conditions. In particular, these would prohibit any data coping into the public Galaxy instance as a native genome, since Galaxy does not have any restrictions on use. However, you may be able to obtain a fasta genome from this source and use it in the public Galaxy instance. Best wishes, Jen Galaxy team On 8/22/11 9:17 AM, Howard M. Goodman wrote: > Hi Jen, > > Thank you. > > I have an index, but not a genomic fasta file. The genomic fasta does not seem to be available as far as I can tell. Is there a way to "unbuild" an index into a fasta file? Or would you reconsider adding this index? > > Note, I am a very novice Galaxy user. > > Thanks again > Howard > > On Aug 19, 2011, at 5:29 PM, Jennifer Jackson wrote: > >> Hello Howard, >> >> To use this alternate as a reference genome: >> >> 1 - load the fasta version of the genome into your history >> 2 - when using tools, select the option "Use reference genome from history" (or similar), then select the fasta file >> >> There is no need to load the index files, only the fasta file and to make certain that Galaxy assigns the file type as "fasta" (using the pencil icon to access the "Edit Attributes" to set the datatype if necessary). >> >> Using FTP to load the data will be necessary. Instructions are on the tool form "Get Data -> Upload" and detailed help is also available at: >> >> http://galaxyproject.org/Learn/Upload%20via%20FTP >> >> http://galaxyproject.org/Learn/Screencasts >> see: Tool tutorials -> Using FTP >> >> Hopefully this helps! >> >> Best, >> >> Jen >> Galaxy team >> >> On 8/19/11 5:14 PM, Howard M. Goodman wrote: >>> I would like to use a "built in" Arabidopsis Landberg erecta (Ler) index instead of TAIR10 for example for all my analysis within Galaxy. I have such an index created by Mathew McCormack and have used it successfully doing a Bowtie test run on my home computer. It has the usual 6 Bowtie index files. Can you add this to the "built in" indexes or is there some way to add it to my history and use it in all the programs? >>> >>> Thank you for you consideration. >>> >>> Howard >>> >>> >>> The information in this e-mail is intended only for the person to whom it is >>> addressed. If you believe this e-mail was sent to you in error and the e-mail >>> contains patient information, please contact the Partners Compliance HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to you in error >>> but does not contain patient information, please contact the sender and properly >>> dispose of the e-mail. >>> >>> >>> ___________________________________________________________ >>> 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/Support > > -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support

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Text Manipulation > Compute > c1[1:c1.find("(")] fails
by Robert Curtis Hendrickson 22 Aug '11

22 Aug '11

Folks, I have a column c1 that has entries like "GXP_297346(PVALB/human)". I'm trying to use Text Manipulation > Compute to strip off the "(...)" portion, leaving only the accession (which can vary in length). I have tried a variety of things that work in my python command line, but fail here, for example: c1[1:c1.find("(")] or c1.split('(')[0] This gets mangled: An error occurred running this job: Expression "c1__ob__1:c1.find("(")__cb__" likely invalid. Or An error occurred running this job: Expression "c1.split("(")__ob__0__cb__" likely invalid. Please help. This is driving me crazy. Searching the list, I find only http://gmod.827538.n3.nabble.com/inputs-sanitization-tt2664336.html#a2664911 "Inputs sanitization" which seems to indicate this is a global mapper that can only be disabled with dire security consequences. And http://gmod.827538.n3.nabble.com/substring-sequence-on-coordinate-in-column… "substring sequence on coordinate in columns" which doesn't ever answer the question about how to get compute to work. Thanks, Curtis

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New "built in index" for Ler within galaxy
by Howard M. Goodman 20 Aug '11

20 Aug '11

I would like to use a "built in" Arabidopsis Landberg erecta (Ler) index instead of TAIR10 for example for all my analysis within Galaxy. I have such an index created by Mathew McCormack and have used it successfully doing a Bowtie test run on my home computer. It has the usual 6 Bowtie index files. Can you add this to the "built in" indexes or is there some way to add it to my history and use it in all the programs? Thank you for you consideration. Howard The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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