Ross, I think I don't understand what you mean. Do you mean the actual reference to the files contained in the loc file? I have all non-relative paths to the bowtie indexes (snippet below). The last column is an additional column for some plotting tools to have a sensible short name and works fine in the original location. Separators are tabs. Alex {still confused} == Part of the bowtie_indices.loc -- Bos_taurus_ensembl Bos_taurus_ensembl Bos taurus ensembl 4.0.61 /share/bowtie/indexes/Bos_taurus_ensembl BosTaurus Homo_sapiens.GRCh37 Homo_sapiens.GRCh37 Homo sapiens ensembl GRch37 /share/bowtie/indexes/Homo_sapiens.GRCh37 Human Macaca_mulatta_NCBIdraft20110405 Macaca_mulatta_NCBIdraft20110405 Macaca mulatta (rhesus monkey draft NCBI) /share/bowtie/indexes/Macaca_mulatta_NCBIdraft20110405 Macaca Mus_musculus.NCBIM37 Mus_musculus.NCBIM37 Mus musculus NCBIM37 /share/bowtie/indexes/Mus_musculus.NCBIM37 Mouse -- -----Oorspronkelijk bericht----- Van: Ross [mailto:ross.lazarus@gmail.com] Verzonden: vrijdag 22 juli 2011 15:15 Aan: Bossers, Alex Onderwerp: Re: [galaxy-dev] Error moving tool-data dir ... bowite indexes missing If those changes invalidate your loc files, you may need to adjust them? On Fri, Jul 22, 2011 at 11:02 PM, Bossers, Alex <Alex.Bossers@wur.nl<mailto:Alex.Bossers@wur.nl>> wrote:

On our up-to-date galaxy_central version I have successfully moved the database/files directory to mounted storage. After adapting the universe_wsgi.ini it works fine after galaxy restart.

Now the tool-data dir becomes bigger and bigger and I wanted to move that to mounted storage as well.

I moved the tool-data dir to the other location, made sure file permissions were ok and adapted the universe_wsgi.ini tool_data_path to match the new tool-data location.

Galaxy restarts and the loc files are read (since blast recognises its databases). However, the bowtie indexes are not read since they do not show up in the NGS bowtie mapper for illumina..... what could be wrong?

When I restore the universe_wsgi.ini it works all fine.

I am puzzled.

Alex

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-- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Director of Bioinformatics, Channing Lab; Tel: +1 617 505 4850; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;