[galaxy-user] the original subject for the thread
-Original Message- From: galaxy-user-boun...@lists.bx.psu.edu [mailto:galaxy-user-boun...@lists.bx.psu.edu] On Behalf Of galaxy-user-requ...@lists.bx.psu.edu Sent: Tuesday, June 14, 2011 9:00 AM To: galaxy-user@lists.bx.psu.edu Subject: galaxy-user Digest, Vol 60, Issue 14 Send galaxy-user mailing list submissions to galaxy-user@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-requ...@lists.bx.psu.edu You can reach the person managing the list at galaxy-user-ow...@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 al...@mb.au.dk To: galaxy-user@lists.bx.psu.edu Subject: [galaxy-user] SAM to bigbed Message-ID: 20110613184245.14175jqs5ml9m...@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 j...@bx.psu.edu To: Aleks Schein al...@mb.au.dk Cc: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] SAM to bigbed Message-ID: 4df642c8.3070...@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 ozb...@uab.edu To: galaxy-u...@bx.psu.edu galaxy-u...@bx.psu.edu Subject: [galaxy-user] GenBank Submission - How to Generate Fasta (not fastq) files Message-ID: 27f664987feadb4ea29031f58bc42b3e02144...@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
[galaxy-user] can I merge histories?
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 ___ 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] software request
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 ___ 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] software request
Hi Chris You may find DESeq at the Galaxy website http://galaxy.fml.mpg.de/ Le 14/06/2011 19:28, Christopher Balakrishnan a écrit : 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 ___ 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/ -- Best regards/Cordialement __ Philippe Lefebvre, Ph.D. Directeur de Recherche INSERM INSERM UMR 1011-Bâtiment JK Université Lille-Nord de France; Faculté de Médecine de Lille-Pôle Recherche Boulevard du Professeur Leclerc 59045 Lille cedex France Tel +33.3.20974220 Cell. Phone +33.6.87829495 Fax +33.3.20974201 This e-mail, including any attachments, may contain information that is protected by law as privileged and confidential, and is transmitted for the sole use of the intended recipient. If you are not the intended recipient, you are hereby notified that any use, dissemination, copying or retention of this e-mail or the information contained herein is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender by telephone or reply e-mail, and permanently delete this e-mail from your computer system. Thank you ___ 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] working collaboratively in a history: How To?
Hi Curtis, It may be helpful if I first help to clarify how the history/dataset/workflows are organized. 1 - When a dataset is moved (through either method), internal linkage is not preserved. You could resolve this in two ways: a - By annotating where the moved result dataset came from. One suggestion for this would be to add in name of the other history - unique history naming would be advised - and keeping that history around for reference/traceability. b - Putting all of the work in the same history (best solution, especially if you are going to be creating workflows) 2 - When a history is shared, the other user creates a clone of your history as it exists when it is first imported by them. To conserve space, the underlying datasets are kept as a single file on the file system (as long as they are unchanged), but no user accessible linkage exists between the two histories after the clone is created. Changes in one history do not effect the other. If you want to share new results, have your collaborator import the history again. Naming imported histories in some way that will distinguish between revisions would be a good idea (unique names for histories is advised, shared or not). 3 - There are no roles that will allow two users to actively work on the same history. Also, it is not recommended to share the same user/password in an attempt to work in the same space - unexpected results may occur (not bugs, just internal tracking conflicts). Hopefully this helps to address your questions about sharing histories, but please let us know if something was missed or is still unclear. For searching the Galaxy wiki, specificity can be achieved by using a site key plus the search term. This is the Google link with the Galaxy wiki site key included. After clicking into Google with this link, add in your search term(s) after the site key and submit. http://www.google.com/search?q=site%3Ahttp%3A%2F%2Fbitbucket.org%2Fgalaxy%2Fgalaxy-central%2Fwiki This link is also documented at the very bottom of the Galaxy wiki home page: https://bitbucket.org/galaxy/galaxy-central/wiki/Home Thanks for using Galaxy! Jen -- Jennifer Jackson http://usegalaxy.org/ 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 To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] Error running latest Galaxy Distribution: numpy.dtype exception
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 ___ 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/
