[galaxy-user] Galaxy Has a New Wiki

Hello all, It is my pleasure to announce that Galaxy has a new wiki: http://galaxyproject.org/wiki. This wiki contains all the content from the old bitbucket wiki, plus a bunch of new content (most of which is still work in progress). The new wiki is based on MoinMoin and includes several new or

[galaxy-user] Passing/Referencing arguments from XML to R script while using XML conditional tag

Hi, This may appear as a very basic question. I: I have in the past used "name" as the object that allows the argument reference to passed from XML to Rscript running in the background. However I am currently using a conditional tag that makes this slightly incomprehensible. My command line argu

Re: [galaxy-user] fastx toolkit on solid qual file

Hello Zheng, In the Galaxy UI, the tool "NGS: QC and manipulation -> Convert SOLiD output to fastq" is to be used before running "Compute quality statistics for SOLiD data". You could also run this conversion tool command line, if that is how you are running fastx_quality_stats. Hopefully th

[galaxy-user] fastx toolkit on solid qual file

Hi all, I noticed Galaxy could parse qual file and output kinds of stats, which is said to be based on fastx toolkit. Yet fastx_quality_stats in fastx toolkit doesn't work on qual file of solid. Anyone has idea about the trick? Thanks. Xin Zheng

Re: [galaxy-user] samtools output

As an alternative, you can easily install Galaxy on your own computer to negate the upload time.. it's very easy if you have a *nix system: https://bitbucket.org/galaxy/galaxy-central/wiki/GetGalaxy -K On Thu, Jul 7, 2011 at 11:12 PM, Alison Gardner wrote: > Hello, > > I am having trouble replic

[galaxy-user] samtools output

Hello, I am having trouble replicating the great output you get after running samtools "Filter pileup on coverage & snps with ten columns (with consensus)" when I try to run samtools locally on my computer. Unfortunately we are unable to use Galaxy with our new data as our files are too large to