[galaxy-dev] QUAL file format(s)
Hi all, Is there any documentation on what Galaxy means by the different qual formats? In particular why is there a qual454 and not a qualsanger (to match fastq)? Historically QUAL files were used back in Sanger/capillary sequencing by PHRED, and just hold PHRED scores as integers. This was followed by the Roche 454 output. Peter ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] rpy and R
Sarah Diehl wrote: Hi all, I'm currently working on setting up a fresh Galaxy server at our institute. I'm going through the tool dependencies list and install everything on it. I installed the latest R version (2.12.2) and now I'm trying to install rpy. With some workarounds I managed to compile rpy, but when I try to import it in python, I get the following error: import rpy Traceback (most recent call last): File stdin, line 1, in module File rpy.py, line 134, in module % RVERSION) RuntimeError: No module named _rpy2122 RPy module can not be imported. Please check if your rpy installation supports R 2.12.2. If you have multiple R versions installed, you may need to set RHOME before importing rpy. For example: from rpy_options import set_options set_options(RHOME='c:/progra~1/r/rw2011/') from rpy import * It looks like my version of R isn't supported by rpy. Does anybody know which version of R still works with rpy? I couldn't find anything about it. What about rpy2? Is it not supported by Galaxy? Hi Sarah, Although I haven't tested with 2.12.2, I know it works with at least 2.11.0. The error above is indicating that rpy is installed somewhere on python's path but the C-extension module for the version of R found on your $PATH (2.12.2) is not present. Most likely this is because rpy was already installed, and is being found earlier on python's path than the version of rpy that you installed. The older rpy was built against a different version of R. If you find the original installation of rpy you should be able to determine from _rpyversion.so what version of R it was built against, and put that version of R ahead of 2.12.2 in your $PATH. Alternatively, you can find and uninstall the old version of rpy, which should allow your newer version to be found and used. python's path can be determined with: python -c 'import sys; print \n.join( sys.path )' There is some effort underway in the community to rewrite rpy tools to use rpy2, but this work is not yet complete. Hope this helps, --nate Thanks very much in advance for your help! Best regards, Sarah Diehl ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] rpy and R
Hi Nate, thank you very much for your help! I managed to figure out the problem. There seemed to be an old version of R and somehow (I still don't know how) the rpy installation did only find the old one. I hard-coded the directory of the new R in the setup.py (everything else failed) and then it compiled against the new R version. Best regards, Sarah On 03/03/2011 05:11 PM, Nate Coraor wrote: Sarah Diehl wrote: Hi all, I'm currently working on setting up a fresh Galaxy server at our institute. I'm going through the tool dependencies list and install everything on it. I installed the latest R version (2.12.2) and now I'm trying to install rpy. With some workarounds I managed to compile rpy, but when I try to import it in python, I get the following error: import rpy Traceback (most recent call last): File stdin, line 1, inmodule File rpy.py, line 134, inmodule % RVERSION) RuntimeError: No module named _rpy2122 RPy module can not be imported. Please check if your rpy installation supports R 2.12.2. If you have multiple R versions installed, you may need to set RHOME before importing rpy. For example: from rpy_options import set_options set_options(RHOME='c:/progra~1/r/rw2011/') from rpy import * It looks like my version of R isn't supported by rpy. Does anybody know which version of R still works with rpy? I couldn't find anything about it. What about rpy2? Is it not supported by Galaxy? Hi Sarah, Although I haven't tested with 2.12.2, I know it works with at least 2.11.0. The error above is indicating that rpy is installed somewhere on python's path but the C-extension module for the version of R found on your $PATH (2.12.2) is not present. Most likely this is because rpy was already installed, and is being found earlier on python's path than the version of rpy that you installed. The older rpy was built against a different version of R. If you find the original installation of rpy you should be able to determine from _rpyversion.so what version of R it was built against, and put that version of R ahead of 2.12.2 in your $PATH. Alternatively, you can find and uninstall the old version of rpy, which should allow your newer version to be found and used. python's path can be determined with: python -c 'import sys; print \n.join( sys.path )' There is some effort underway in the community to rewrite rpy tools to use rpy2, but this work is not yet complete. Hope this helps, --nate Thanks very much in advance for your help! Best regards, Sarah Diehl ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] Fwd: [Bosc] Bioinformatics Open Source Conference (BOSC 2011)--Call for Abstracts
Hopefully this will be of interest to some of you... -- Forwarded message -- From: Nomi Harris nlhar...@lbl.gov Date: Thu, Mar 3, 2011 at 7:37 PM Subject: [Bosc] Bioinformatics Open Source Conference (BOSC 2011)--Call for Abstracts To: bosc-annou...@lists.open-bio.org, memb...@open-bio.org, GMOD Announcements List gmod-annou...@lists.sourceforge.net, GMOD Developers List gmod-de...@lists.sourceforge.net Cc: Nomi Harris nlhar...@lbl.gov We invite you to submit an abstract to BOSC 2011! Please forward this message as appropriate, and forgive multiple postings. Call for Abstracts for the 12th Annual Bioinformatics Open Source Conference (BOSC 2011) An ISMB 2011 Special Interest Group (SIG) Dates: July 15-16, 2011 Location: Vienna, Austria Web site: http://www.open-bio.org/wiki/BOSC_2011 Email: b...@open-bio.org BOSC announcements mailing list: http://lists.open-bio.org/mailman/listinfo/bosc-announce Important Dates: April 18, 2011: Deadline for submitting abstracts to BOSC 2011 May 9, 2011: Notifications of accepted abstracts emailed to corresponding authors July 13-14, 2011: Codefest 2011 programming session (see http://www.open-bio.org/wiki/Codefest_2011 for details) July 15-16, 2011: BOSC 2011 July 17-19, 2011: ISMB 2011 The Bioinformatics Open Source Conference (BOSC) is sponsored by the Open Bioinformatics Foundation (O|B|F), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development within the biological research community. To be considered for acceptance, software systems representing the central topic in a presentation submitted to BOSC must be licensed with a recognized Open Source License, and be freely available for download in source code form. We invite you to submit abstracts for talks and posters. Sessions include: - Approaches to parallel processing - Cloud-based approaches to improving software and data accessibility - The Semantic Web in open source bioinformatics - Data visualization - Tools for next-generation sequencing - Other Open Source software In addition to the above sessions, there will be a panel discussion about Meeting the challenges of inter-institutional collaboration. We are also working to arrange a joint session with one of the other ISMB SIGs. Thanks to generous sponsorship from Eagle Genomics and an anonymous donor, we are pleased to announce a competition for three Student Travel Awards for BOSC 2011. Each winner will be awarded $250 to defray the costs of travel to BOSC 2011. For instructions on submitting your abstract, please visit http://www.open-bio.org/wiki/BOSC_2011#Abstract_Submission_Information BOSC 2011 Organizing Committee: Nomi Harris and Peter Rice (co-chairs); Brad Chapman, Peter Cock, Erwin Frise, Darin London, Ron Taylor ___ BOSC mailing list b...@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bosc ___ 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/
