Friday, October 23, 2009

Installing Bio::DB::Sam from CPAN

Bio::DB::Sam is Lincoln Stein's BioPerl API to the SamTools package.

Installing via CPAN might skip a necessary question that will cause it to fail.

cpan> install Bio::DB::Sam
...
...
DIED. FAILED tests 1-93
Failed 93/93 tests, 0.00% okay
Failed Test Stat Wstat Total Fail Failed List of Failed
-------------------------------------------------------------------------------
t/01sam.t 2 512 93 186 200.00% 1-93
Failed 1/1 test scripts, 0.00% okay. 93/93 subtests failed, 0.00% okay.
make: *** [test_dynamic] Error 2
/usr/bin/make test -- NOT OK
Running make install
make test had returned bad status, won't install without force


Navigate to where CPAN has downloaded the gz ffile
A closer examination reveals that Build.PL file wants to know where the SamTools header files are located.

Please enter the location of the bam.h and compiled libbam.a files:

I have no idea how to pass these arguments using CPAN. I would just avoid this method of installation. Do the local build instead.

Monday, October 12, 2009

Disable file locking in Eclipse for OS X

Eclipse will refuse to use a workspace on an automounted OS X Server home directory.
Workspace in use or cannot be created

To remedy this problem do the following:
  • Right click the Eclipse application and select "Show Package Contents"
  • Contents->MacOS
  • Edit the eclipse.ini file in a text editor
  • Add -Dosgi.locking=none to the line below -vmargs