I got it! Stupid mistake of relying on the editor to add tabs to the

hg19 hg19 hg19 ~/ngs/refgenomes/hg19/bwa_indexed/hg19 statement, while it was replacing each tab with 4 spaces. Now all is working fine!

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Message: 13 Date: Wed, 9 Jan 2013 14:31:52 -0500 From: Jorge Sepulveda <jls2282@columbia.edu> To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] Blank local reference - even after following NGS installation instructions Message-ID: <8AB4A885-98C8-4D44-B51F-CFCD2BD56662@columbia.edu> Content-Type: text/plain; charset=us-ascii

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:jls2282@columbia.edu