JBrowse Troubleshooting

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This page collects solutions to problems that people sometimes encounter when installing JBrowse.

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.