Re: [galaxy-user] RSEM on Galaxy

Hi there Alicia! To find the tool in the Galaxy tool search, first you have to put your tool files in tools with .xml files then you have to edit tool_conf.xml file. Here's the step by step tutorial: http://wiki.g2.bx.psu.edu/Admin/Tools/Add%20Tool%20Tutorial Regards, Sachit On Fri, Oct 5, 2012 a

[galaxy-user] Galaxy October 5, 2012 Distribution & News Brief

*Galaxy October 5, 2012 Distribution & News Brief* /http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_10_05/ /* Highlights:* http://wiki.g2.bx.psu.edu/News / ** * *BWA * tool wrappers /migrated

Re: [galaxy-user] RSEM on Galaxy

Hi Alicia, At the moment you have to install the wrapper manually. That is, the current version of the RSEM won't automatically install the rsem binaries for you. We are working on updating the tool from the tool shed. The readme file within the tarball provides instructions on what version of

Re: [galaxy-user] RSEM on Galaxy

Alicia, Some relevant details usually make it easier for list members to help you - please see http://wiki.g2.bx.psu.edu/Support#Public_mailing_list_Q_.26_A_discussions Did you load the offending tool from a toolshed or is it a tool wrapper you wrote yourself? If the latter, I have two suggestion

[galaxy-user] RSEM on Galaxy

Hi all, Recently i installed RSEM into Galaxy. The problem is that now i cannot find the tool when i open "my" galaxy in my computer. I checked and rsem folder is inside the tool folder. Any suggestions? Thanks, Alicia. -- Alicia R. Pérez-Porro PhD student Giribet lab Department of Organism

[galaxy-user] data expiration policy

Good Morning Galaxy Universe: What is the data expiration policy at Galaxy for user created big* files that are then subsequently used in custom tracks at UCSC ? We are noticing users with bigDataUrl paths of: https://main.g2.bx.psu.edu/display_application/.../somefile.bigwig which appear to

[galaxy-user] RNA-seq analysis withtout reference genome

Hi all, I'm about to start doing gene expression analysis but i don't have a reference genome. I got my sequences from Illumina and i did my assemblies with CLC bio. I was planning to use DESeq for the analysis but for that i need my gene expression count values. There is any tool in Galaxy that i