Forget #2, I got confused with something else. J

From: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of Chorny, Ilya
Sent: Wednesday, September 28, 2011 4:06 PM
To: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] GTF files in Cufflinks and Tophat

Jeremy,

1.) Would you be interested in a feature in which the gtf files could be “locally cached” instead of only “from history”?

2.) Would you be interested in a feature in which cufflinks choses the genome in a fashion similar to how samtools know which which genome to use? i.e.:

<when value="cached">

        <param name="input1" type="data" format="sam" metadata_name="dbkey" label="SAM File to Convert">

           <validator type="unspecified_build" />

        <validator type="dataset_metadata_in_file" filename="sam_fa_indices.loc" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." line_startswith="index" />

      </param>

    </when>

I am happy on working on these changes if they will be put into galaxy-central.

Best,

Ilya

Ilya Chorny Ph.D.

Bioinformatics Scientist I

Illumina, Inc.

9885 Towne Centre Drive

San Diego, CA 92121

Work: 858.202.4582

Email: ichorny@illumina.com

Website: www.illumina.com