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.laza...@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.boss...@wur.nl<mailto:alex.boss...@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;
___________________________________________________________
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