Jellyfish 2.1.1

SOAPdenovo2 is a popular genome assembler.

Module file

The module file can be found in this location:

 /cm/shared/modulefiles/SHARED/

#%Module1.0#######################################################################
## Jellyfish 2.1.1 modulefile
##
proc ModulesHelp { } {

        puts stderr "\tAdds Jellyfish 2.1.1 to your environment"
}

module-whatis   "Adds Jellyfish 2.1.1 to your environment"

set             jellyfish_211_bin         /cm/shared/apps/SHARED/jellyfish/jellyfish-2.1.1/bin/bin
set             jellyfish_211_ldpath      /cm/shared/apps/SHARED/jellyfish/jellyfish-2.1.1/bin/lib
set             jellyfish_211_man         /cm/shared/apps/SHARED/jellyfish/jellyfish-2.1.1/bin/share/man
set             jellyfish_211_pkg         /cm/shared/apps/SHARED/jellyfish/jellyfish-2.1.1/bin/lib/pkgconfig

prepend-path     PATH             $jellyfish_211_bin
prepend-path     LD_LIBRARY_PATH  $jellyfish_211_ldpath
prepend-path     MANPATH          $jellyfish_211_man
prepend-path     PKG_CONFIG_PATH  $jellyfish_211_pkg

Installation details

Compiled from source using the stock gcc 4.4 of Scientific Linux on 15-03-2014:

  http://www.genome.umd.edu/jellyfish.html

This included the GapCloser software (v1.12), ErrorCorrection (v0.04), and SOAPec (v2.01, includes Corrector_AR, Corrector_HA, KmerFreq_AR and KmerFreq_HA binaries).

See also

• Globally installed software
• ABGC specific modules

External links

• SOAPdenovo2 home page