JBrowse Troubleshooting
This page collects solutions to problems that people sometimes encounter when installing JBrowse.
Contents
Installing prerequisites
JBrowse requires a few fundamental prerequisites that it cannot install itself: these are libpng, zlib, libgd, make, a C compiler, and a C++ compiler.
Linux - Ubuntu / Debian
These commands, or similar, should install what you need:
sudo apt-get install build-essential libpng-dev zlib1g-dev libgd2-xpm-dev
Linux - Red Hat / Fedora / CentOS
These commands, or similar, should install what you need:
sudo yum groupinstall "Development Tools" sudo yum install libpng-devel gd-devel zlib-devel perl-ExtUtils-MakeMaker
Mac OS X
Use MacPorts, Fink, Homebrew, or another package manager to install a C++ compiler, libpng development headers, GD development headers, and Zlib development headers.
Failures of setup.sh
BAM format support (Bio::DB::Sam) fails
Many users will be able to solve this problem by just running the following commands in the jbrowse/
directory:
perl -i -pE 's/^CFLAGS=\s*/CFLAGS=-fPIC / unless /\b-fPIC\b/' samtools/Makefile; make -C samtools clean; ./setup.sh;
These commands add -fPIC
to the samtools Makefile flags and rerun the samtools build. The details of this problem are discussed here.
If this does not solve the problem for you, see #Other Problems below.
Other Problems
setup.sh
creates a log file of debugging information associated with your installation. Email this entire file (as an attachment please, not in the email body) to gmod-ajax@lists.sourceforge.net with a request for support.
As more users try setup.sh
and report problems to the mailing list, this wiki will be updated with fixes for common problems they encounter.