Re: [galaxy-user] Most Popular Linux flavour for Galaxy

I have instances running on RHEL 5 and CentOS 5 and never had any OS-specific issues, works great. -Leandro On Tue, Jun 7, 2011 at 4:45 PM, Nate Coraor n...@bx.psu.edu wrote: Matloob Khushi wrote: Hello Galaxy Users We are anticipating setting up a local instance of Galaxy and wondering what

[galaxy-user] Converting transcriptomes to proteomes

Dear Galaxy users, I am trying to modify the human proteome based on my transcriptomeics data. In short I want to use my transcriptomics data to identify snps and from that identify coding changes that result from the snps. Ultimately I'd like to create a customised canonical proteome based on

Re: [galaxy-user] FastQ Groomer and Compute Quality Statistics

Thanks Ross, I don't see it under my local install - are there any pre-written scripts to integrate it with a local galaxy instance? I assume you are talking about this tool here: http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/ -John From: Ross

[galaxy-user] Aligning against Multiple Reference Sequences

Are there any tools in Galaxy to align short reads against multiple reference sequences? I have a dozen microbial genomes sequenced for which there are 2 reference genomes already sequenced. We have tried aligning each of these individually against either of the reference genomes - some align

Re: [galaxy-user] FastQ Groomer and Compute Quality Statistics

On Thu, Jun 9, 2011 at 10:12 AM, John David Osborne ozb...@uab.edu wrote: Thanks Ross, I don't see it under my local install - are there any pre-written scripts to integrate it with a local galaxy instance? I assume you are talking about this tool here:

[galaxy-user] Galaxy tool error report from joh...@ibms.sinica.edu.tw

GALAXY TOOL ERROR REPORT This error report was sent from the Galaxy instance hosted on the server 192.168.0.36:8080 - This is in reference to dataset id 316 from history id 2

Re: [galaxy-user] Cufflinks error in galaxy

John, My best guess is that you are using bias correction but do not have the needed reference genome(s) for the builds that you want to use. See this page for instructions about setting up HTS tools; in particular, you'll need to set up the sam_fa_indices.loc file:

Re: [galaxy-user] Aligning against Multiple Reference Sequences

Hi John, Probably the simplest thing for you to do would be to concatenate the two genomes one after the other using the concatenate tool under text manipulation. This will generate a new organism with apparently two chromosomes one from bacteria A and one from bacteria B. When you run tophat

[galaxy-user] Galaxy tool error report from joh...@ibms.sinica.edu.tw

GALAXY TOOL ERROR REPORT This error report was sent from the Galaxy instance hosted on the server 192.168.0.36:8080 - This is in reference to dataset id 377 from history id 2

Re: [galaxy-user] Galaxy tool error report from joh...@ibms.sinica.edu.tw

Hello, Please don't set your bug report address (error_email_to in universe_wsgi.ini) to the user mailing list. This should be set to a local address at your site. --nate galaxy-user@lists.bx.psu.edu wrote: GALAXY TOOL ERROR REPORT This error report was sent