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