Re: [galaxy-user] run tophat in galaxy
I have related question If I have to use Ensembl mouse GTF file (Mus_musculus.NCBIM37.64) Do I have to download and reformat it or Galaxy can take it from the source directly? Thanks On Sun, Aug 28, 2011 at 8:50 AM, Peng, Tao wrote: > ===> Please use "Reply All" when responding to this email! <=== > > > ** > > Hi how can I specify a GTF gene annotation file when running tophat to > guide the alignment to human genome? What is the best way to visualize the > tophat results in the context of annotated human genome, i.e. RefSeq? > > Thanks, > > tao > > > ___ > 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/ > ___ 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/
[galaxy-user] mailing list
Hi, Include me in your mailing list. Mathavan ___ 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/
Re: [galaxy-user] run tophat in galaxy
===> Please use "Reply All" when responding to this email! <=== Hi Tao, I made an error in my prior reply, it is possible to guide assembly in TopHat. To do this, on the TopHat form, change "TopHat settings to use:" from "Use Defaults" to "Full parameter list". In the expanded form: 1 - change "Use Own Junctions:" to be "yes". 2 - change "Use Gene Annotation Model:" to be "yes" 3 - in the new pull-down menu, select the GTF file from your history Great question! Glad that we were able to provide you with the correct instruction, Best, Jen Galaxy team On 9/15/11 1:38 PM, Jennifer Jackson wrote: ===> Please use "Reply All" when responding to this email! <=== Hello Tao, Sorry for the delayed reply, your question did not post to the mailing list since the "to" was not _only_ to galaxy-user. Going forward, please leave off any "to" or "cc" to team members when asking a question. Send all questions directly "to" "galaxy-u...@bx.psu.edu" and do not include any "Re" or "Fwd" text in the subject line. Regarding RNA-seq analysis and reference GTF files, the place to incorporate the GTF file is in the Cufflinks step, the option to select the GTF file from your history is on the tool's form. If you have questions about the tools that are not addressed by these help links: http://usegalaxy.org/u/jeremy/p/transcriptome-analysis-faq http://usegalaxy.org/u/jeremy/p/galaxy-rna-seq-analysis-exercise then contacting the tool authors would be the next step: email tophat.cuffli...@gmail.com To visualize the data, the available options will be links associated with each dataset (expand the dataset box to locate these). The Galaxy Track Browser (GTB) aka "Trackster", UCSC Genome Browser, Ensembl, and GeneTrack are potential options; the datatype will determine which links are provided. Hopefully this helps, Best, Jen Galaxy team Original Message Subject: run tophat in galaxy Date: Sun, 28 Aug 2011 08:50:04 -0700 From: Peng, Tao To: Jennifer Jackson , galaxy-user Hi how can I specify a GTF gene annotation file when running tophat to guide the alignment to human genome? What is the best way to visualize the tophat results in the context of annotated human genome, i.e. RefSeq? Thanks, tao ___ 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/
[galaxy-user] run tophat in galaxy
===> Please use "Reply All" when responding to this email! <=== Hello Tao, Sorry for the delayed reply, your question did not post to the mailing list since the "to" was not _only_ to galaxy-user. Going forward, please leave off any "to" or "cc" to team members when asking a question. Send all questions directly "to" "galaxy-u...@bx.psu.edu" and do not include any "Re" or "Fwd" text in the subject line. Regarding RNA-seq analysis and reference GTF files, the place to incorporate the GTF file is in the Cufflinks step, the option to select the GTF file from your history is on the tool's form. If you have questions about the tools that are not addressed by these help links: http://usegalaxy.org/u/jeremy/p/transcriptome-analysis-faq http://usegalaxy.org/u/jeremy/p/galaxy-rna-seq-analysis-exercise then contacting the tool authors would be the next step: email tophat.cuffli...@gmail.com To visualize the data, the available options will be links associated with each dataset (expand the dataset box to locate these). The Galaxy Track Browser (GTB) aka "Trackster", UCSC Genome Browser, Ensembl, and GeneTrack are potential options; the datatype will determine which links are provided. Hopefully this helps, Best, Jen Galaxy team Original Message Subject:run tophat in galaxy Date: Sun, 28 Aug 2011 08:50:04 -0700 From: Peng, Tao To: Jennifer Jackson , galaxy-user Hi how can I specify a GTF gene annotation file when running tophat to guide the alignment to human genome? What is the best way to visualize the tophat results in the context of annotated human genome, i.e. RefSeq? Thanks, tao ___ 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/
Re: [galaxy-user] Getting (or setting) physical file name
On Thu, Sep 15, 2011 at 6:11 PM, Paul-Michael Agapow wrote: > So one of my colleagues has a script he wants to turn into a Galaxy tool. > The twist is that script: > > > > 1. Looks for files with a fixed name (e.g. “params.txt”) > > 2. Accepts other file names as commandline arguments, but the actual > names of those files has arguments embedded in it (e.g. > “nuc_100iter_b.fasta” for nucleotide data in fasta format to be run against > model b for 100 iterations.) > > > > I know, awkward and clumsy. But hardly unique for many historical > bioinformatic tools. Anyway, the challenge for me is to pick the easiest > path to port this script to a tool. And it seems to be fairly awkward under > the Galaxy model as I understand it. Possibilities: > > > > 1. Rewrite the script argument parsing and invocation. Obviously, > there will be resistance to this and with some justification (“I thought you > said this could wrap any command line program …”) If this is your own tool, this is the cleanest solution and helps beyond just using it within Galaxy. > 2. Write a script that calls the original script after moving and > renaming files according to desired arguments. Any problems with a > two-script/executable tool like this? That's what I'd go for - a wrapper script which takes command line arguments like a sane command line tool, and uses them to prepare the input files for the weird script. Your tool should automatically be called from a temp working directory so you can probably just make the specially named files right there, and try using links to alias the input files rather than copying them (faster as less IO). > How do I specify the interpreter for both parts of the script? If your script is marked as executable with a suitable hash bang, it doesn't even need the Galaxy interpreter in the XML file. For the internal script it doesn't matter at all - Galaxy doesn't need to know. Peter ___ 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/
Re: [galaxy-user] galaxy test-data organization
To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ You will want to choose one or both of these: http://lists.bx.psu.edu/listinfo/galaxy-user http://lists.bx.psu.edu/listinfo/galaxy-dev -- 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/
[galaxy-user] Getting (or setting) physical file name
So one of my colleagues has a script he wants to turn into a Galaxy
tool. The twist is that script:
1. Looks for files with a fixed name (e.g. "params.txt")
2. Accepts other file names as commandline arguments, but the
actual names of those files has arguments embedded in it (e.g.
"nuc_100iter_b.fasta" for nucleotide data in fasta format to be run
against model b for 100 iterations.)
I know, awkward and clumsy. But hardly unique for many historical
bioinformatic tools. Anyway, the challenge for me is to pick the easiest
path to port this script to a tool. And it seems to be fairly awkward
under the Galaxy model as I understand it. Possibilities:
1. Rewrite the script argument parsing and invocation. Obviously,
there will be resistance to this and with some justification ("I thought
you said this could wrap any command line program ...")
2. Write a script that calls the original script after moving and
renaming files according to desired arguments. Any problems with a
two-script/executable tool like this? How do I specify the interpreter
for both parts of the script?
3. Use config files for the fixed name files. But configuration
files seem to be given a random not fixed name, correct?
4. For the file names with semantic content, extract that from the
dataset metadata. Of course, then it still has to be passed to the
original script somehow.
5. Use
Ideas, suggestions? Obviously a rewrite is the "best" solution, but in
this case we might be looking for the quickest ...
Paul Agapow (paul-michael.aga...@hpa.org.uk)
Bioinformatics, Centre for Infections, Health Protection Agency
-
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Re: [galaxy-user] galaxy test-data organization
Hello Joe, Functional test-data is located here in the source: http://bitbucket.org/galaxy/galaxy-central/src/07c5fbd618f3/test-data/ The name/comments of each is the best way to understand the link between a test and a tool (could be many-to-many). Next time, a question like this about a local instance would be better directed to the galaxy-...@bx.psu.edu mailing list, so I am going to forward this there. There is an active user community, perhaps someone has organized the functional test data in a different other way for their own purposes and would like to share the method. Thanks for using Galaxy! Best, Jen Galaxy team On 8/27/11 7:17 AM, Joseph Hargitai wrote: ===> Please use "Reply All" when responding to this email!<=== Hi, is there by any chance a per application breakdown of the test-data structure? best, joe ___ 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/
Re: [galaxy-user] cufflinks version
Hello Shantanu, A version list for tools is at: http://galaxyproject.org/Admin/Tools/Tool%20Dependencies We are currently working on a global tool versioning strategy. As a result, users will notice more integration with the UI over the upcoming months. Hopefully this helps, Jen Galaxy team On 9/9/11 2:09 PM, Shantanu Pavgi wrote: What version of cufflinks is available on the galaxy site? Is there any page where I can find version of all galaxy tools? Thanks, Shantanu. ___ 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/
Re: [galaxy-user] Merging of illumina paired end files
Hello Arun, In brief, you will want to load your data via FTP, groom the files, and run BWA for Illumina with the paired-end data option (for mapping, not assembly). Help to get started can be found at: http://galaxyproject.org/wiki/Learn An initial input of 30G would likely not be a problem, but it depends on what analysis steps you intend to do after mapping. A Cloudman option may be more suitable, please see: http://galaxyproject.org/wiki/Big%20Picture/Choices Hopefully this helps, Best, Jen Galaxy team On 9/14/11 7:06 PM, Arun Khattri wrote: I have 3 illumina paired end reads of exome capture of the sample. I want to assemble these reads to genome using tools available in Galaxy (BWA etc). My concern is the amount of data that I can analyzed and when these reads should be merged. The total size of data is +30Gb. Thanks, Arun ___ 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/
