[galaxy-user] Galaxy does not startup on machine with no Internet access

2011-01-12 Thread Sonali Amonkar
Hi, I'm trying to install and run galaxy-dist-8729d2e29b02 on a Linux RHEL 5.5 box. This machine has no direct access to the Internet. I followed the steps listed on the page https://bitbucket.org/galaxy/galaxy-central/wiki/Config/Eggs to download the eggs offline and placed them in the

Re: [galaxy-user] Converting pileup files to wig/bigwig

2011-01-12 Thread Ann Loraine
My apologies. I mis-spoke. (Mis-typed?) The wiggles program is in the TopHat distribution: $ ls AUTHORSfix_map_orderingsam_juncs COPYINGgtf_juncssegment_juncs READMEjuncs_dbsra_to_solid bed_to_juncslibrary_statstophat

Re: [galaxy-user] Converting pileup files to wig/bigwig

2011-01-12 Thread Swathi Ashok Kumar
Can it be integrated into galaxy ? I found another tool that does this at http://galaxy.fml.mpg.de/Under their SAM tools they have a pileup to wiggle conversion tool On Wed, Jan 12, 2011 11:01 AM, Jeremy Goecks jeremy.goe...@emory.edu wrote: I can't find any mention of a program called

Re: [galaxy-user] [Genome] Problems with MAF blocks from Galaxy

2011-01-12 Thread James Taylor
Excerpts from ele.ga...@tiscali.it's message of Wed Jan 12 15:19:36 + 2011: I have a problem with MAF blocks using Galaxy. Hi Elena, I'm copying the galaxy-user list since this is a Galaxy related question. 1) the starting position of the MAF block extracted from Galaxy is shifted of

[galaxy-user] Ordering Workflow Inputs on Run?

2011-01-12 Thread Jesse Erdmann
Hi, I have a workflow that requires a large number of files that happen to come in pair but are processed by different tools. One tool allows the user to specify inputs 1...N and produce a single output. The other tool takes a single input and produces a single output. In the simplest example