Re: [galaxy-dev] Configuration of a local install - mi-deploy ?

2011-11-11 Thread Enis Afgan
Hi Clare, As a technical add-on - you didn't mention what type OS you're looking to install this on so I just wanted to mention that mi-deployment scripts are tested primarily on Ubuntu 10.04 LTS and thus most likely to work properly there. If you're also looking to setup the data, unfortunately

[galaxy-dev] Local galaxy Cufflinks problem

2011-11-11 Thread Bidwell, Christopher A.
Colleagues, We have set up a local Galaxy but I am having trouble running Cufflinks with the annotation gtf file. We have the iGenomes btau4.2 genome in the database and use the iGenomes btau4.2 gtf file in the history. However the –G isn’t showing up in the command line (below) and the

[galaxy-dev] Velvetoptimizer won't read in my paired, illumina file

2011-11-11 Thread Lucinda Lawson
Hi. I have an illumina 1.9 file that I renamed, groomed, and interlaced to get to its current state (see first 2 sets of paired sequences below) @1 TTATCTGCATATACGAAATATACATTGAAAGTTGAAATAAATGATAAATTAAACCAATTA +1

[galaxy-dev] barcode splitter made 96 files. Is there a tool to map all of these files to the reference genome?

2011-11-11 Thread Lucinda Lawson
Hi, I have Rad tag data that I'm trying to map to our reference genome in Galaxy on our local instance. After barcode splitter, I have 96 files (one each of all of the sequences for that individual). It seems like the current tools (e.g. bowtie) can only map a single file to the reference. I think

[galaxy-dev] Galaxy Development Workshop: 23 January 2012, Český Krumlov, Czech Republic

2011-11-11 Thread Dave Clements
Hello all, A one day Galaxy Developer Workshophttp://evomics.org/workshops/galaxy-developer-workshop/has been scheduled for 23 January in Český Krumlov http://www.ckrumlov.info/php/, Czech Republic, immediately following the Workshop on