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
Hello Sandrine,
It sound like you have a good start at getting this set up and might just need a few more pieces. No mention of the builds list or the indexes for the genome was made, so those would be the places to look into next.
Instructions for full set up, including how to download indexes from our rysnc server should you wish you use our version of them, are here:
http://wiki.g2.bx.psu.edu/Admin/Data%20Integration http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup
Going forward, you will want to direct question about local installs to the galaxy-dev@bx.psu.edu mailing list, for the best feedback (including from other users also running local Galaxy's that can help troubleshoot): http://wiki.g2.bx.psu.edu/Support#Mailing_Lists
Good luck!
Jen Galaxy team
On 9/14/12 12:59 AM, Sandrine Imbeaud 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 ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
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Jennifer Jackson -
Sandrine Imbeaud