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mdozmorov / genome_runner

Academic Free License v3.0
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Tabix -B option #82

Closed mdozmorov closed 9 years ago

mdozmorov commented 9 years ago

There are two issues.

First, the newer versions of tabix have removed the -B option (read regions from BED file) which is needed for the script to work. This means you will need this version of tabix: https://github.com/samtools/tabix, rather than the newer version from HTSlib.

Second, annotationAnalysis requires that all inputs be BGZF compressed.

bgzip tmp1.bed bgzip tmp2.bed annotationAnalysis tmp1.bed.gz tmp2.bed.gz

should give correct results.

So, if you want to fix the first problem permanently while simultaneously having HTSlib installed on your system, you will need to do the following

  1. Pick a place where you want to install the old version of tabix. For example, /opt/tabix-0.2.5
  2. Compile old version of tabix:

sudo mkdir /opt/tabix-0.2.5 sudo chmod a+rw /opt/tabix-0.2.5 git clone https://github.com/samtools/tabix /opt/tabix-0.2.5 cd /opt/tabix-0.2.5 make

  1. Then, you need to put somewhere, either in the ~/.bash_profile for your genomerunner user, or in grtk.sh, or whereever, the following line:

export PATH="/opt/tabix-0.2.5:$PATH"

  1. Log out and log-in again
mdozmorov commented 9 years ago

Fixed by installing the "old" tabix version