For the record - mixed tabs/spaces as delimiters in .loc files seem to
have been the problem (again) - maybe we should log errors when ragged
tab delimited loc tables are provided?
---------- Forwarded message ----------
From: Sandrine Imbeaud <sandrine.imbe...@inserm.fr>
Date: Tue, Sep 18, 2012 at 5:54 PM
Subject: Re: [galaxy-dev] none availability genome.fa files through
mapping modules on local server
To: Ross <ross.laza...@gmail.com>
We have checked again the tab delimiters and it works.. Many thanks.
Le 9/14/2012 10:18 AM, Ross a écrit :
> make absolutely sure there are only tab delimiters between loc file
> fields - otherwise they fail.
> On Fri, Sep 14, 2012 at 5:58 PM, Sandrine Imbeaud
> <sandrine.imbe...@inserm.fr> wrote:
>> I apologize for this probably very simple application.
>> We have installed our own Galaxy server and started using in-house the NGS
>> modules. However, during the mapping procedure using either BWA for illumina
>> or BFAST tools, no reference genome index is available.
>> To solve the problem, we have followed the tutorials and have uploaded the
>> hg19.fa file and put it locally in the Galaxy-dist/database folder. We also
>> have modified the *_index.loc files indicating the path to the file. We
>> restarted the Galaxy server. However, still no reference is available
>> through the NGS mapping modules.
>> Is there anyone that may help use solving this probably simple problem?
>> Kind regards
>> / Sandrine
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INSERM, UMR U-674, IUH
Université Paris Descartes
Génomique Fonctionnelle des tumeurs solides
27 rue Juliette Dodu
F75010 Paris, France
TEL: +33 (0)1 53 72 51 98
FAX: +33 (0)1 53 72 51 92
MOBILE: +33 (0)6 12 69 80 29
Ross Lazarus MBBS MPH;
Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444
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