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Question: None Availability Genome.Fa Files Through Mapping Modules On Local Server
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gravatar for Sandrine Imbeaud
6.2 years ago by
Sandrine Imbeaud • 20
Sandrine Imbeaud • 20 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
bwa alignment • 759 views
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modified 6.2 years ago by Jennifer Hillman Jackson ♦ 25k • written 6.2 years ago by Sandrine Imbeaud • 20
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gravatar for Jennifer Hillman Jackson
6.2 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:
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 -- Jennifer Jackson http://galaxyproject.org
ADD COMMENT • link written 6.2 years ago by Jennifer Hillman Jackson ♦ 25k
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