Hi,
I set up a local galaxy in my MacPro on 1/3/2013 using:
hg clone https://bitbucket.org/galaxy/galaxy-dist/
into this directory:
~/ngs/applications/galaxy-dist
Indexed hg19.fa using bwa index to ~/ngs/refgenomes/hg19/bwa_indexed/
-rw-r--r-- 1 JS staff 6597 Jan 2
15:03 hg19.fa.amb
-rw-r--r-- 1 JS staff 6844 Jan 2
15:03 hg19.fa.ann
-rw-r--r-- 1 JS staff 3101804844 Jan 2 15:02
hg19.fa.bwt
-rw-r--r-- 1 JS staff 775451186 Jan 2 15:03
hg19.fa.pac
-rw-r--r-- 1 JS staff 1550902424 Jan 2 15:06
hg19.fa.sa
Added:
hg19 hg19 hg19 ~/ngs/refgenomes/hg19/bwa_indexed/hg19
to this file:
~/ngs/applications/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/ffa8aaa14f7c/bwa_wrappers/tool-data/bwa_index.loc
BWA shows up on the galaxy tools list, but the local reference genome box
remains empty. It runs fine when I use a reference sequence (chr22.fa) from
history.
If I download bwa (or bowtie2) and install according to the steps in
http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup I have the same problem
(empty local reference).
What am I missing?
Jorge Sepulveda, MD, PhD
Associate Director for Laboratory Medicine,
Medical Director of Laboratory Informatics,
Columbia University Medical Center
Associate Professor,
Department of Pathology & Cell Biology
Columbia University College of Physicians and Surgeons
PH1590B
622 W 168 St
New York, NY 10032
Cell: (917) 862-6050
Office: 212-305-6360
E-mail:[email protected]
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