I' am trying to add built-in reference genomes for my local galaxy
installation. I know this topic has been covered multiple times: I have
looked through the discussion threads and the wiki (e.g. NGS Local Setup),
but I' am still unsuccessful. Previously I have just loaded a reference
genome through the history, but in the interest of saving time and space
while I experiment with Galaxy I wish to use the built-in feature.
Here is what I have tried:
1. Indexed ecoli.fa using bwa and put all files (fasta and index files)
The directory looks like:
-rwxrwxrwx@ 1 charlesmurphy staff 4706043 Mar 5 14:54 ecoli.fa
-rwxrwxrwx 1 charlesmurphy staff 12 Mar 5 16:38 ecoli.fa.amb
-rwxrwxrwx 1 charlesmurphy staff 111 Mar 5 16:38 ecoli.fa.ann
-rwxrwxrwx 1 charlesmurphy staff 4639752 Mar 5 16:38 ecoli.fa.bwt
-rwxrwxrwx 1 charlesmurphy staff 1159920 Mar 5 16:38 ecoli.fa.pac
-rwxrwxrwx 1 charlesmurphy staff 2319888 Mar 5 16:38 ecoli.fa.sa
2. Downloaded and installed the bwa wrapper files from the Galaxy main
toolshed, and put bwa in $PATH.
3. Added the following line to the bwa_index.loc (using tabs as the
ecoli ecoli ecoli
4. Added the following line to builds.txt (using tabs as the delimiter):
5. Restarted Galaxy.
The ecoli genome does not show up as a reference genome for BWA (Map with
BWA for Illumina). Any help would be appreciated.
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