Hi,

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)
under /Users/charlesmurphy/Desktop/Research/data/genome/ecoli/bwa/

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
delimiter):
ecoli   ecoli   ecoli
/Users/charlesmurphy/Desktop/Research/data/genome/ecoli/bwa/ecoli.fa
4. Added the following line to builds.txt (using tabs as the delimiter):
ecoli ecoli
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.

Thanks,
Charlie
___________________________________________________________
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:

  http://lists.bx.psu.edu/

Reply via email to