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
        │   │   │               ├── chr3L.fa ->
../../../../../../Sequence/Chromosomes/chr3L.fa
        │   │   │               ├── chr3LHet.fa ->
../../../../../../Sequence/Chromosomes/chr3LHet.fa
        │   │   │               ├── chr3R.fa ->
../../../../../../Sequence/Chromosomes/chr3R.fa
        │   │   │               ├── chr3RHet.fa ->
../../../../../../Sequence/Chromosomes/chr3RHet.fa
        │   │   │               ├── chr4.fa ->
../../../../../../Sequence/Chromosomes/chr4.fa
        │   │   │               ├── chrM.fa ->
../../../../../../Sequence/Chromosomes/chrM.fa
        │   │   │               ├── chrX.fa ->
../../../../../../Sequence/Chromosomes/chrX.fa
        │   │   │               ├── chrXHet.fa ->
../../../../../../Sequence/Chromosomes/chrXHet.fa
        │   │   │               └── chrYHet.fa ->
../../../../../../Sequence/Chromosomes/chrYHet.fa
        │   │   ├── archive-2011-01-27-18-13-06
        │   │   │   └── Drosophila_melanogaster
        │   │   │       └── UCSC-dm3
        │   │   │           ├── ChromInfo.txt ->
../../../../../Annotation/Archives/archive-2011-01-27-18-13-06/Genes/ChromInfo.txt
        │   │   │           ├── cytoBand.txt ->
../../../../../Annotation/Archives/archive-2011-01-27-18-13-06/Genes/cytoBand.txt
        │   │   │           ├── refGene.txt ->
../../../../../Annotation/Archives/archive-2011-01-27-18-13-06/Genes/refGene.txt
        │   │   │           ├── refMrna.fa ->
../../../../../Annotation/Archives/archive-2011-01-27-18-13-06/Genes/refMrna.fa
        │   │   │           ├── refSeqSummary.txt ->
../../../../../Annotation/Archives/archive-2011-01-27-18-13-06/Genes/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
        │   │   │               ├── chr3L.fa ->
../../../../../../Sequence/Chromosomes/chr3L.fa
        │   │   │               ├── chr3LHet.fa ->
../../../../../../Sequence/Chromosomes/chr3LHet.fa
        │   │   │               ├── chr3R.fa ->
../../../../../../Sequence/Chromosomes/chr3R.fa
        │   │   │               ├── chr3RHet.fa ->
../../../../../../Sequence/Chromosomes/chr3RHet.fa
        │   │   │               ├── chr4.fa ->
../../../../../../Sequence/Chromosomes/chr4.fa
        │   │   │               ├── chrM.fa ->
../../../../../../Sequence/Chromosomes/chrM.fa
        │   │   │               ├── chrX.fa ->
../../../../../../Sequence/Chromosomes/chrX.fa
        │   │   │               ├── chrXHet.fa ->
../../../../../../Sequence/Chromosomes/chrXHet.fa
        │   │   │               └── chrYHet.fa ->
../../../../../../Sequence/Chromosomes/chrYHet.fa
        │   │   ├── archive-2011-08-30-21-29-02
        │   │   │   └── Drosophila_melanogaster
        │   │   │       └── UCSC-dm3
        │   │   │           ├── ChromInfo.txt ->
../../../../../Annotation/Archives/archive-2011-08-30-21-29-02/Genes/ChromInfo.txt
        │   │   │           ├── cytoBand.txt ->
../../../../../Annotation/Archives/archive-2011-08-30-21-29-02/Genes/cytoBand.txt
        │   │   │           ├── refGene.txt ->
../../../../../Annotation/Archives/archive-2011-08-30-21-29-02/Genes/refGene.txt
        │   │   │           ├── refSeqSummary.txt ->
../../../../../Annotation/Archives/archive-2011-08-30-21-29-02/Genes/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
        │   │   │               ├── chr3L.fa ->
../../../../../../Sequence/Chromosomes/chr3L.fa
        │   │   │               ├── chr3LHet.fa ->
../../../../../../Sequence/Chromosomes/chr3LHet.fa
        │   │   │               ├── chr3R.fa ->
../../../../../../Sequence/Chromosomes/chr3R.fa
        │   │   │               ├── chr3RHet.fa ->
../../../../../../Sequence/Chromosomes/chr3RHet.fa
        │   │   │               ├── chr4.fa ->
../../../../../../Sequence/Chromosomes/chr4.fa
        │   │   │               ├── chrM.fa ->
../../../../../../Sequence/Chromosomes/chrM.fa
        │   │   │               ├── chrX.fa ->
../../../../../../Sequence/Chromosomes/chrX.fa
        │   │   │               ├── chrXHet.fa ->
../../../../../../Sequence/Chromosomes/chrXHet.fa
        │   │   │               └── chrYHet.fa ->
../../../../../../Sequence/Chromosomes/chrYHet.fa
        │   │   ├── archive-2012-03-09-03-02-51
        │   │   │   └── Drosophila_melanogaster
        │   │   │       └── UCSC-dm3
        │   │   │           ├── ChromInfo.txt ->
../../../../../Annotation/Archives/archive-2012-03-09-03-02-51/Genes/ChromInfo.txt
        │   │   │           ├── cytoBand.txt ->
../../../../../Annotation/Archives/archive-2012-03-09-03-02-51/Genes/cytoBand.txt
        │   │   │           ├── refGene.txt ->
../../../../../Annotation/Archives/archive-2012-03-09-03-02-51/Genes/refGene.txt
        │   │   │           ├── refSeqSummary.txt ->
../../../../../Annotation/Archives/archive-2012-03-09-03-02-51/Genes/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
        │   │   │               ├── chr3L.fa ->
../../../../../../Sequence/Chromosomes/chr3L.fa
        │   │   │               ├── chr3LHet.fa ->
../../../../../../Sequence/Chromosomes/chr3LHet.fa
        │   │   │               ├── chr3R.fa ->
../../../../../../Sequence/Chromosomes/chr3R.fa
        │   │   │               ├── chr3RHet.fa ->
../../../../../../Sequence/Chromosomes/chr3RHet.fa
        │   │   │               ├── chr4.fa ->
../../../../../../Sequence/Chromosomes/chr4.fa
        │   │   │               ├── chrM.fa ->
../../../../../../Sequence/Chromosomes/chrM.fa
        │   │   │               ├── chrX.fa ->
../../../../../../Sequence/Chromosomes/chrX.fa
        │   │   │               ├── chrXHet.fa ->
../../../../../../Sequence/Chromosomes/chrXHet.fa
        │   │   │               └── chrYHet.fa ->
../../../../../../Sequence/Chromosomes/chrYHet.fa
        │   │   └── archive-current -> archive-2012-03-09-03-02-51
        │   ├── Drosophila_melanogaster ->
Archives/archive-2012-03-09-03-02-51/Drosophila_melanogaster
        │   └── README.txt
        └── Sequence
            ├── AbundantSequences
            │   ├── adapter_contam1.fa
            │   ├── adapter_contam1.fa.2bpb
            │   ├── adapter_contam1.fa.vld
            │   ├── chrM.fa
            │   ├── chrM.fa.2bpb
            │   ├── chrM.fa.vld
            │   ├── phix.fa
            │   ├── phix.fa.2bpb
            │   ├── phix.fa.vld
            │   ├── polyA.fa
            │   ├── polyA.fa.2bpb
            │   ├── polyA.fa.vld
            │   ├── polyC.fa
            │   ├── polyC.fa.2bpb
            │   ├── polyC.fa.vld
            │   ├── ribosomal.fa
            │   ├── ribosomal.fa.2bpb
            │   └── ribosomal.fa.vld
            ├── Bowtie2Index
            │   ├── genome.1.bt2
            │   ├── genome.2.bt2
            │   ├── genome.3.bt2
            │   ├── genome.4.bt2
            │   ├── genome.fa -> ../WholeGenomeFasta/genome.fa
            │   ├── genome.rev.1.bt2
            │   └── genome.rev.2.bt2
            ├── BowtieIndex
            │   ├── genome.1.ebwt
            │   ├── genome.2.ebwt
            │   ├── genome.3.ebwt
            │   ├── genome.4.ebwt
            │   ├── genome.fa -> ../WholeGenomeFasta/genome.fa
            │   ├── genome.rev.1.ebwt
            │   └── genome.rev.2.ebwt
            ├── BWAIndex
            │   ├── genome.fa -> version0.6.0/genome.fa
            │   ├── genome.fa.amb -> version0.6.0/genome.fa.amb
            │   ├── genome.fa.ann -> version0.6.0/genome.fa.ann
            │   ├── genome.fa.bwt -> version0.6.0/genome.fa.bwt
            │   ├── genome.fa.pac -> version0.6.0/genome.fa.pac
            │   ├── genome.fa.sa -> version0.6.0/genome.fa.sa
            │   ├── version0.5.x
            │   │   ├── genome.fa -> ../../WholeGenomeFasta/genome.fa
            │   │   ├── genome.fa.amb
            │   │   ├── genome.fa.ann
            │   │   ├── genome.fa.bwt
            │   │   ├── genome.fa.pac
            │   │   ├── genome.fa.rbwt
            │   │   ├── genome.fa.rpac
            │   │   ├── genome.fa.rsa
            │   │   └── genome.fa.sa
            │   └── version0.6.0
            │       ├── genome.fa -> ../../WholeGenomeFasta/genome.fa
            │       ├── genome.fa.amb
            │       ├── genome.fa.ann
            │       ├── genome.fa.bwt
            │       ├── genome.fa.pac
            │       └── genome.fa.sa
            ├── Chromosomes
            │   ├── chr2L.fa
            │   ├── chr2LHet.fa
            │   ├── chr2R.fa
            │   ├── chr2RHet.fa
            │   ├── chr3L.fa
            │   ├── chr3LHet.fa
            │   ├── chr3R.fa
            │   ├── chr3RHet.fa
            │   ├── chr4.fa
            │   ├── chrM.fa
            │   ├── chrX.fa
            │   ├── chrXHet.fa
            │   └── chrYHet.fa
            ├── Squashed-Drosophila_melanogaster-UCSC-dm3
            │   ├── chr2L.fa -> ../Chromosomes/chr2L.fa
            │   ├── chr2L.fa.2bpb
            │   ├── chr2L.fa.vld
            │   ├── chr2LHet.fa -> ../Chromosomes/chr2LHet.fa
            │   ├── chr2LHet.fa.2bpb
            │   ├── chr2LHet.fa.vld
            │   ├── chr2R.fa -> ../Chromosomes/chr2R.fa
            │   ├── chr2R.fa.2bpb
            │   ├── chr2R.fa.vld
            │   ├── chr2RHet.fa -> ../Chromosomes/chr2RHet.fa
            │   ├── chr2RHet.fa.2bpb
            │   ├── chr2RHet.fa.vld
            │   ├── chr3L.fa -> ../Chromosomes/chr3L.fa
            │   ├── chr3L.fa.2bpb
            │   ├── chr3L.fa.vld
            │   ├── chr3LHet.fa -> ../Chromosomes/chr3LHet.fa
            │   ├── chr3LHet.fa.2bpb
            │   ├── chr3LHet.fa.vld
            │   ├── chr3R.fa -> ../Chromosomes/chr3R.fa
            │   ├── chr3R.fa.2bpb
            │   ├── chr3R.fa.vld
            │   ├── chr3RHet.fa -> ../Chromosomes/chr3RHet.fa
            │   ├── chr3RHet.fa.2bpb
            │   ├── chr3RHet.fa.vld
            │   ├── chr4.fa -> ../Chromosomes/chr4.fa
            │   ├── chr4.fa.2bpb
            │   ├── chr4.fa.vld
            │   ├── chrM.fa -> ../Chromosomes/chrM.fa
            │   ├── chrM.fa.2bpb
            │   ├── chrM.fa.vld
            │   ├── chrX.fa -> ../Chromosomes/chrX.fa
            │   ├── chrX.fa.2bpb
            │   ├── chrX.fa.vld
            │   ├── chrXHet.fa -> ../Chromosomes/chrXHet.fa
            │   ├── chrXHet.fa.2bpb
            │   ├── chrXHet.fa.vld
            │   ├── chrYHet.fa -> ../Chromosomes/chrYHet.fa
            │   ├── chrYHet.fa.2bpb
            │   └── chrYHet.fa.vld
            └── WholeGenomeFasta
                ├── genome.dict
                ├── genome.fa
                └── genome.fa.fai

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