Re: [galaxy-dev] Error moving tool-data dir ... bowite indexes missing - galaxy-dev

22 Jul 2011


      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.nlmailto: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;