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.imbeaud@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.lazarus@gmail.com> We have checked again the tab delimiters and it works.. Many thanks. / Sandrine 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.imbeaud@inserm.fr> wrote:

...

Hello,

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 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:

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-- Sandrine Imbeaud 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 http://www.inserm-u674.net/ -- Ross Lazarus MBBS MPH; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444 http://scholar.google.com/citations?hl=en&user=UCUuEM4AAAAJ