Homebrew Ensembl

Core formula for creating and installing Ensembl dependencies.

Homebrew/Linuxbrew compatability

These formula have been developed primarily for Linuxbrew. They may work for OSX, they may not. If you are unsure then look at Homebrew Science for more generic solutions.

How Do I Install these Formula

brew install ensembl/ensembl/<formula>

Or brew tap ensembl/ensembl and then brew install <formula>.

Troubleshooting

IMPORTANT First read the Troubleshooting Checklist.).

Use brew gist-logs <formula> to create a Gist and post the link in your issue.

Search open and closed issues. See also Homebrew's Common Issues and FAQ.

Documentation

brew help, man brew or check Homebrew's documentation.

Contributing

There is no guide for this at the moment

Common Errors From Compiled Binaries

libgcc and pthread

libgcc_s.so.1 must be installed for pthread_cancel to work

Solved by https://github.com/Linuxbrew/homebrew-core/pull/2622 where ligcc_s.so.1 is symlinked in to where glibc can find it. If this does appear again though recompiling the affected formula from source (e.g. brew reinstall -s bwa) would work.

examl

unable to open mca_ess_lsf: libbat.so: cannot open shared object file: No such file or directory

Indicates a lack of the LSF libbat.so module on your path. Export LSF's libraries onto your LD_LIBRARY_PATH.

Incompatible GLIBC_VERSION

“version `GLIBC_2.14' not found”

Happens when two binaries have been compiled with different glibc's (more likely different versions of GCC with different versions of glibc). The common error is compiling on a younger version and trying to link back to an older version. Solution is find out where the cross-compile happened and stop it.