Setting up JBrowse 1.8.1 on a CentOS 5.8

Some important details to successfully set up JBrowse on a Centos 5.8 machine.

Install and compile samtools from source.  I built it with fPIC flags like this:

make CXXFLAGS=-fPIC CFLAGS=-fPIC CPPFLAGS=-fPIC

Be sure that the file libbam.a that you just created with the fPIC flag is (also) present in the lib directory.  I had to rename the old one and copy the new one there.


# ls -al /usr/local/samtools/lib*
-rw-rw-r-- 1 odsolbe odsolbe 309986 Feb 27 09:51 /usr/local/samtools/libbam.a

/usr/local/samtools/lib:
total 1316
drwxr-xr-x 2 odsolbe odsolbe    4096 Feb 27 09:54 .
drwxr-xr-x 7 odsolbe odsolbe    4096 Feb 27 09:51 ..
-rw-rw-r-- 1 odsolbe odsolbe  309986 Feb 27 09:54 libbam.a
-rw-r--r-- 1 odsolbe odsolbe 1000346 Oct 24  2011 libbam.a_orig

Set two env variables: SAMTOOLS and PARL5LIB (see here)

export PERL5LIB=/path/to/...../jbrowse/extlib/lib/perl5 export SAMTOOLS=/usr/local/samtools

This is what worked for me.  Your milage may vary.