Re: [galaxy-dev] Installing Prebuilt Indexes for "Tophat for Illumina" - What to do for color space files?

2013-02-20 Thread Jeremy Goecks 
> 
> I see where I would use the *.ebwt files in the bowtie_index.loc file.
> But I'm not sure what to reference in the bowtie_index_color.loc
> file?  (The same *.ebwt files??)

You need to download the colorspace indices separately:

http://bowtie-bio.sourceforge.net/index.shtml

Good luck,
J.___
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[galaxy-dev] Installing Prebuilt Indexes for "Tophat for Illumina" - What to do for color space files?

2013-02-20 Thread greg 
Hi,

I'm trying to install DM3 from this page
(http://tophat.cbcb.umd.edu/igenomes.html) as a pre-built index for
"Tophat for Illumina" in our local galaxy install.

I'm following the instructions on this page:
http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup

I see where I would use the *.ebwt files in the bowtie_index.loc file.
 But I'm not sure what to reference in the bowtie_index_color.loc
file?  (The same *.ebwt files??)

Thanks,

Greg

(I asked this question on the tophat support site too, but on second
look I think it was only for bug reports)

For reference, here's what I downloaded from the DM3 file:

Drosophila_melanogaster
└── UCSC
└── dm3
├── Annotation
│   ├── Archives
│   │   ├── archive-2010-09-27-21-20-17
│   │   │   ├── ChromInfo.txt
│   │   │   ├── cytoBand.txt
│   │   │   ├── DATE.txt
│   │   │   ├── genes.gtf
│   │   │   ├── refFlat.txt
│   │   │   ├── refFlat.txt.gz
│   │   │   ├── refGene.txt
│   │   │   ├── refMrna.fa
│   │   │   ├── refSeqSummary.txt
│   │   │   ├── splice_sites_34
│   │   │   │   ├── exon_coords.txt
│   │   │   │   ├── splice_sites-34.fa
│   │   │   │   ├── splice_sites-34.fa.2bpb
│   │   │   │   ├── splice_sites-34.fa.idx
│   │   │   │   └── splice_sites-34.fa.vld
│   │   │   └── splice_sites_49
│   │   │   ├── exon_coords.txt
│   │   │   ├── splice_sites-49.fa
│   │   │   ├── splice_sites-49.fa.2bpb
│   │   │   ├── splice_sites-49.fa.idx
│   │   │   └── splice_sites-49.fa.vld
│   │   ├── archive-2011-01-27-18-13-06
│   │   │   ├── Genes
│   │   │   │   ├── ChromInfo.txt
│   │   │   │   ├── cytoBand.txt
│   │   │   │   ├── genes.gtf
│   │   │   │   ├── refFlat.txt.gz
│   │   │   │   ├── refGene.txt
│   │   │   │   ├── refMrna.fa
│   │   │   │   └── refSeqSummary.txt
│   │   │   ├── README.txt
│   │   │   ├── SmallRNA
│   │   │   │   ├── hairpin.fa
│   │   │   │   └── mature.fa
│   │   │   └── Variation
│   │   ├── archive-2011-08-30-21-29-02
│   │   │   ├── Genes
│   │   │   │   ├── ChromInfo.txt
│   │   │   │   ├── cytoBand.txt
│   │   │   │   ├── genes.gtf
│   │   │   │   ├── refFlat.txt.gz
│   │   │   │   ├── refGene.txt
│   │   │   │   └── refSeqSummary.txt
│   │   │   ├── README.txt
│   │   │   ├── SmallRNA
│   │   │   │   ├── mature.fa
│   │   │   │   └── precursor.fa
│   │   │   └── Variation
│   │   ├── archive-2012-03-09-03-02-51
│   │   │   ├── Genes
│   │   │   │   ├── ChromInfo.txt
│   │   │   │   ├── cytoBand.txt
│   │   │   │   ├── genes.gtf
│   │   │   │   ├── refFlat.txt.gz
│   │   │   │   ├── refGene.txt
│   │   │   │   └── refSeqSummary.txt
│   │   │   ├── README.txt
│   │   │   ├── SmallRNA
│   │   │   │   ├── mature.fa
│   │   │   │   └── precursor.fa
│   │   │   └── Variation
│   │   └── archive-current -> archive-2012-03-09-03-02-51
│   ├── Genes -> Archives/archive-2012-03-09-03-02-51/Genes
│   ├── README.txt -> Archives/archive-2012-03-09-03-02-51/README.txt
│   ├── SmallRNA -> Archives/archive-2012-03-09-03-02-51/SmallRNA
│   └── Variation -> Archives/archive-2012-03-09-03-02-51/Variation
├── GenomeStudio
│   ├── Archives
│   │   ├── archive-2010-09-27-21-20-17
│   │   │   └── Drosophila_melanogaster
│   │   │   └── UCSC-dm3_BDGP_rel5
│   │   │   ├── ChromInfo.txt ->
../../../../../Annotation/Archives/archive-2010-09-27-21-20-17/ChromInfo.txt
│   │   │   ├── cytoBand.txt ->
../../../../../Annotation/Archives/archive-2010-09-27-21-20-17/cytoBand.txt
│   │   │   ├── DATE.txt ->
../../../../../Annotation/Archives/archive-2010-09-27-21-20-17/DATE.txt
│   │   │   ├── refGene.txt ->
../../../../../Annotation/Archives/archive-2010-09-27-21-20-17/refGene.txt
│   │   │   ├── refMrna.fa ->
../../../../../Annotation/Archives/archive-2010-09-27-21-20-17/refMrna.fa
│   │   │   ├── refSeqSummary.txt ->
../../../../../Annotation/Archives/archive-2010-09-27-21-20-17/refSeqSummary.txt
│   │   │   └── Sequence
│   │   │   ├── chr2L.fa ->
../../../../../../Sequence/Chromosomes/chr2L.fa
│   │   │   ├── chr2LHet.fa ->
../../../../../../Sequence/Chromosomes/chr2LHet.fa
│   │   │   ├── chr2R.fa ->
../../../../../../Sequence/Chromosomes/chr2R.fa
│   │   │   ├── chr2RHet.fa ->
../../../../../../Sequence/Chromosomes/chr2RHet.fa
│   │   │   ├