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

Re: [galaxy-user] Uploading Genome from Ensembl
by Jennifer Jackson 06 Dec '11

06 Dec '11

Hello Sheena, It is odd that this particular genome exists in two versions, with different content, for the same release number/date. Ensemble will update annotation with new releases, but not the reference genome itself unless they also increment the genome build number. The Zebrafish project page at Ensembl states that UCSC has the latest release, meaning that the genome labeled as "Zebrafish Jul. 2010 (Zv9/danRer7) (danRer7)" in Galaxy is expected to be the same as one would create after combining the files in their download area: http://uswest.ensembl.org/Danio_rerio/Info/Index But, if there are known differences (perhaps you want different masking or haplotypes/chrY PAR inclusion/exclusion), then combining the data can occur prior to upload into Galaxy or after (both invoke a similar tool): -- If prior, using unix and the shell "cat" command is one option. -- If after, then load all chromosomes into your history and use the tool "Text Manipulation -> Concatenate datasets tail-to-head". Best regards, Jen Galaxy team On 12/6/11 2:31 PM, Scroggins, Sheena wrote: > Thanks for responding. I would like to upload the genome to Galaxy, but I'm not sure how to combine all the fa files into one file. The Zebrafish genome from Ensembl comes in 27 separate .fa files. How do I combine these so that when I upload them to Galaxy, I can use the whole genome as my reference genome? > > Thanks, > Sheena > > -----Original Message----- > From: Jennifer Jackson [mailto:jen@bx.psu.edu] > Sent: Tuesday, November 08, 2011 6:58 AM > To: Scroggins, Sheena > Cc: galaxy-user(a)bx.psu.edu > Subject: Re: [galaxy-user] Uploading Genome from Ensembl > > Hello Sheena, > > If you concern with using the UCSC version of the database has to do with the chromosome naming and downstream Cufflinks analysis using Ensembl's reference GTF files, please see #5 on our FAQ, which demonstrates how to modify an Ensembl GTF file to be compatible with the UCSC chromosome naming (slight changes may be needed for each particular > genome): > http://main.g2.bx.psu.edu/u/jeremy/p/transcriptome-analysis-faq > > If there is another reason, please know that custom reference genomes (in fasta format) can be uploaded using FTP following this method: > http://wiki.g2.bx.psu.edu/Learn/Upload%20via%20FTP > > Hopefully this helps, > > Best, > > Jen > Galaxy team > > On 11/4/11 2:50 PM, Scroggins, Sheena wrote: >> How do I upload the Zebrafish genome from Ensembl to my user history >> in Galaxy? I'm trying to map my RNA-Seq data using TopHat and need to >> map it to the Ensembl version of ZFv9, but Galaxy only has the UCSC >> version built in. The Ensembl version is slightly different. >> Thanks, >> Sheena >> >> >> ___________________________________________________________ >> 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/wiki/Support > -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support

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bed file to gene list
by Dr Chris Futtner, Ph.D. 06 Dec '11

06 Dec '11

Can anyone point me to a good workflow to convert my ChIP-seq data intervals to gene names. My peaks fall both within genes and within intergenic areas. Thanks, Chris Christopher Futtner, Ph.D. Dept. of Surgery Duke University Durham, NC 27710 email: christopher.futtner(a)duke.edu phone: 919-684-1183

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How to select line with chr1?
by Di Nguyen 06 Dec '11

06 Dec '11

Hi all, I have a a bed file that I would like sort for chromosome 1 ONLY? Would you tell me the syntax to "select" lines that are chromosome 1 only instead of 1 or 10,11-19? Thank you very much, Di Nguyen U of Washington

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Re: [galaxy-user] [galaxy-dev] Urgent help needed
by Toqa Manasrah 06 Dec '11

06 Dec '11

Thank you so much Dannon. I appreciate your help but I need some more clarification. in the tool I am integrating (which is java classes) if the input parameters are ./main.bash eps0.3_40reads.fa population10_ref.fa 15 6 120 Then teh output is in eps0.3_40reads_I_6_15_CNTGS_DIST0_EM20.txt As u notice the output file name is not specified in teh command line, and actually I dont have the source files to go over this naming restriction. how I can use from_work_dir attribute to tell galaxy this the file to display? note: there are 11 output files and I am interested in this one only ..._CNTGS_DIST0_EM20.txt any other method to overcome such problem I have presentation tomorrwo. hope things will work fine. Thank you, ________________________________________ From: Dannon Baker [dannonbaker(a)me.com] Sent: Monday, December 05, 2011 2:41 PM To: Toqa Manasrah Subject: Re: [galaxy-dev] Urgent help needed Sure. See the link in my previous email (http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax) and look for the <data> section for an explanation of the attributes available to you. For an example of a tool that uses the from_work_dir element, see the cufflinks, cuff compare, top hat, or trinity wrappers in your galaxy install. -Dannon On Dec 5, 2011, at 2:25 PM, Toqa Manasrah wrote: > Thank you Dannon, > I mean the first choice. no way to specify the output name in tool and it has many putputs but I am intereseted in one only. > > Actually I dont know to use this attribute from_work_dir and I cant find help. can u help plz? > > ________________________________________ > From: Dannon Baker [dannonbaker(a)me.com] > Sent: Monday, December 05, 2011 1:54 PM > To: Toqa Manasrah > Cc: galaxy-dev(a)bx.psu.edu dev; Jennifer Jackson; galaxy-user > Subject: Re: [galaxy-dev] Urgent help needed > > Toqa, > > Just to make sure I've understood your question: the problem is that a tool that you're trying to wrap doesn't provide a way to specify a particular output filename? Take a look at the from_work_dir attribute of a <data> element. > > Or are you asking how to define outputs in general? For that, see the wiki at http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Coutputs.3E… > > Lastly, for new questions please start new email threads, instead of replying to old ones. This makes it much easier for us to track our responses and make sure people get appropriate help. > > -Dannon > > > On Dec 5, 2011, at 1:26 PM, Toqa Manasrah wrote: > >> Hi Everybody, >> I am running a tool which is not defining the output file name as parameter. >> the tool is running and I can see the output file in the history directory but not in the history frame. >> >> how could I solve the problem? I should see and download the output file from the history but I see an error message instead. the error message not a real error but rather galaxy cannot figure out which file to display? >> >> your help is appreciated, >> >> >> ________________________________________ >> From: Jennifer Jackson [jen(a)bx.psu.edu] >> Sent: Tuesday, November 08, 2011 8:22 AM >> To: Toqa Manasrah >> Cc: Galaxy Dev >> Subject: Re: [galaxy-dev] Installing Galaxy on local server >> >> Hello Tuqa, >> >> Galaxy will not stop by itself. That said, you will want to monitor the >> instance and any associated cluster, just as you would any other >> important processes. >> >> Please send all follow-up with a cc to the mailing list ("reply-all"). >> The development community is a great resource for administrative advice >> and they may have more to add to this reply, i.e. how stable they have >> found Galaxy to be under various conditions. >> >> Best, >> >> Jen >> Galaxy team >> >> On 11/8/11 4:01 AM, Toqa Manasrah wrote: >>> Thank you so much, >>> >>> I did the installation and I ran it under my server. >>> I have one thing concerning about now. if u can help plz. >>> >>> how to run Galaxy in such way that the html interface will continuously working and available for all users visiting the page? >>> >>> i mean how to guarantee that the "sh run.sh" will keep running without any interrupt? >>> >>> Thank you, >>> Tuqa >>> >>> ________________________________________ >>> From: Jennifer Jackson [jen(a)bx.psu.edu] >>> Sent: Thursday, November 03, 2011 6:47 PM >>> To: Toqa Manasrah >>> Cc: galaxy-dev(a)bx.psu.edu >>> Subject: Re: [galaxy-dev] Installing Galaxy on local server >>> >>> Hello Toqa, >>> >>> From your description, this sounds like a local installation for the >>> Galaxy instance itself. Then you can add on a cluster (local or cloud) >>> as needed. >>> >>> Help is under "Deploy Galaxy" at http://wiki.g2.bx.psu.edu/ >>> Also see the "Tool Shed" at http://wiki.g2.bx.psu.edu/Tool%20Shed >>> >>> Hopefully the documentation is helpful, >>> >>> Best, >>> >>> Jen >>> Galaxy team >>> >>> On 11/3/11 9:40 AM, Toqa Manasrah wrote: >>>> Hello, >>>> >>>> I am a graduate student at GSU. I am looking for installing GALAXY on >>>> our local server http://alla.cs.gsu.edu/~software. as a result I like my >>>> server homepage start with the GALAXY interface, like this one: >>>> http://rna1.engr.uconn.edu:7474/ . after that I wish to integrate some >>>> software tolls that we developed in ourdepartment. my primary question >>>> is which option Ihave to choose: Local or cloud? >>>> >>>> looking forward for your help and directions. >>>> >>>> Thank you. >>>> >>>> Tuqa >>>> >>>> >>>> >>>> ___________________________________________________________ >>>> 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/ >>> >>> -- >>> Jennifer Jackson >>> http://usegalaxy.org >>> http://galaxyproject.org/wiki/Support >>> >> >> -- >> Jennifer Jackson >> http://usegalaxy.org >> http://galaxyproject.org/wiki/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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Re: [galaxy-user] Request to Add Reference Genome
by Jennifer Jackson 06 Dec '11

06 Dec '11

Hello Matt, I am not sure what you mean by an annotated genome, would you be able to send more details? Meanwhile, I can let you know that the tools that use a reference genome (custom or native) all expect a fasta formatted input and use the data directly or create indexes from the data. Any DNA (and sometime RNA) nucleotide fasta file can be used and whether using something other than a complete genome makes sense scientifically is up to the user to determine. Thanks! Jen Galaxy team On 12/5/11 6:59 PM, Matthew Biggs wrote: > Hello Jennifer, > > Thanks for your prompt reply. I had one other question about using a > custom reference genome. Is it possible to use an annotated genome as > the reference for a Bowtie alignment? Using a genome in fasta format is > only so helpful. > > Thanks, > Matt Biggs > > > > > > On Mon, Dec 5, 2011 at 8:24 AM, Jennifer Jackson <jen(a)bx.psu.edu > <mailto:jen@bx.psu.edu>> wrote: > > Hi Matt, > > The quickest way to use new genomes with most tools, including > Bowtie, is to use them as a custom reference genome. To do this, > load the genome in fasta format into your history. > > Then, on the tool form (for Bowtie, will vary slightly between > tools), set: > > Will you select a reference genome from your history or use a > built-in index?: "Use one from the history" > > The form will refresh, them set: > > Select the reference genome: "dataset_for_your_loaded___genome" > > Best practice: > 1 - double check that the format is strict fasta (all lines > wrapped to same length, no extra lines or hidden characters, > sequence entries are unique within file). > 2 - use the same genome dataset for all steps within an analysis > 3 - load using FTP and make certain load is complete > http://galaxyproject.org/wiki/__Learn/Upload%20via%20FTP > <http://galaxyproject.org/wiki/Learn/Upload%20via%20FTP> > > > Hopefully this helps! > > Best, > > Jen > Galaxy team > > > On 12/3/11 6:37 PM, Matthew Biggs wrote: > > Hello Galaxy Team, > > I am writing to request that the genome of /Sinorhizobium > meliloti /1021 > > be added to the "Map with Bowtie for Illumina" tool. I am using > the main > server http://main.g2.bx.psu.edu/ and my user name is mbiggs. > > Please let me know if this email is received. > > Thanks, > Matt Biggs > > > _____________________________________________________________ > 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 > <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/wiki/__Support > <http://galaxyproject.org/wiki/Support> > > -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support

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history was empty
by dongdong zhaoweiming 06 Dec '11

06 Dec '11

Hi, I open my galaxy and found the history was empty, I could not found my previous history, so how can I find it? Thanks a lot! Reards weimin zhao

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history was empty
by dongdong zhaoweiming 06 Dec '11

06 Dec '11

Hi, I opened my galaxy and found the history was empty, I could not found my previous history, so how could I find it? Thanks a lot! Reards weimin zhao

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small RNA analysis
by shamsher jagat 05 Dec '11

05 Dec '11

I posted this question previously- IS there any work flow for analysis of microRNA/ small RNA in galaxy, please. I have run microRNA sequencing for control and treated cells. Thanks

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[galaxy-dev] Urgent help needed
by Toqa Manasrah 05 Dec '11

05 Dec '11

Hi Everybody, I am running a tool which is not defining the output file name as parameter. the tool is running and I can see the output file in the history directory but not in the history frame. how could I solve the problem? I should see and download the output file from the history but I see an error message instead. the error message not a real error but rather galaxy cannot figure out which file to display? your help is appreciated, ________________________________________ From: Jennifer Jackson [jen(a)bx.psu.edu] Sent: Tuesday, November 08, 2011 8:22 AM To: Toqa Manasrah Cc: Galaxy Dev Subject: Re: [galaxy-dev] Installing Galaxy on local server Hello Tuqa, Galaxy will not stop by itself. That said, you will want to monitor the instance and any associated cluster, just as you would any other important processes. Please send all follow-up with a cc to the mailing list ("reply-all"). The development community is a great resource for administrative advice and they may have more to add to this reply, i.e. how stable they have found Galaxy to be under various conditions. Best, Jen Galaxy team On 11/8/11 4:01 AM, Toqa Manasrah wrote: > Thank you so much, > > I did the installation and I ran it under my server. > I have one thing concerning about now. if u can help plz. > > how to run Galaxy in such way that the html interface will continuously working and available for all users visiting the page? > > i mean how to guarantee that the "sh run.sh" will keep running without any interrupt? > > Thank you, > Tuqa > > ________________________________________ > From: Jennifer Jackson [jen(a)bx.psu.edu] > Sent: Thursday, November 03, 2011 6:47 PM > To: Toqa Manasrah > Cc: galaxy-dev(a)bx.psu.edu > Subject: Re: [galaxy-dev] Installing Galaxy on local server > > Hello Toqa, > > From your description, this sounds like a local installation for the > Galaxy instance itself. Then you can add on a cluster (local or cloud) > as needed. > > Help is under "Deploy Galaxy" at http://wiki.g2.bx.psu.edu/ > Also see the "Tool Shed" at http://wiki.g2.bx.psu.edu/Tool%20Shed > > Hopefully the documentation is helpful, > > Best, > > Jen > Galaxy team > > On 11/3/11 9:40 AM, Toqa Manasrah wrote: >> Hello, >> >> I am a graduate student at GSU. I am looking for installing GALAXY on >> our local server http://alla.cs.gsu.edu/~software. as a result I like my >> server homepage start with the GALAXY interface, like this one: >> http://rna1.engr.uconn.edu:7474/ . after that I wish to integrate some >> software tolls that we developed in ourdepartment. my primary question >> is which option Ihave to choose: Local or cloud? >> >> looking forward for your help and directions. >> >> Thank you. >> >> Tuqa >> >> >> >> ___________________________________________________________ >> 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/ > > -- > Jennifer Jackson > http://usegalaxy.org > http://galaxyproject.org/wiki/Support > -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support

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bowtie and bwa queue'd up for hours
by Keith Giles 05 Dec '11

05 Dec '11

Does anyone know why these mapping programs are taking so long to start running? Is there a problem with the servers? -- Keith E Giles, PhD Assistant Professor Biochemistry & Molecular Genetics University of Alabama at Birmingham

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