def install_cortex_var(env):
    version = "1.0.5.21"
    url = "http://downloads.sourceforge.net/project/cortexassembler/cortex_var/" \
          "latest/CORTEX_release_v{0}.tgz".format(version)
    def _cortex_build(env):
        env.safe_sed("Makefile", "\-L/full/path/\S*",
                     "-L{0}/lib -L/usr/lib -L/usr/local/lib".format(env.system_install))
        env.safe_sed("Makefile", "^IDIR_GSL =.*$",
                     "IDIR_GSL={0}/include -I/usr/include -I/usr/local/include".format(env.system_install))
        env.safe_sed("Makefile", "^IDIR_GSL_ALSO =.*$",
                     "IDIR_GSL_ALSO={0}/include/gsl -I/usr/include/gsl -I/usr/local/include/gsl".format(
                         env.system_install))
        with cd("libs/gsl-1.15"):
            env.safe_run("make clean")
        with cd("libs/htslib"):
            env.safe_run("make clean")
            env.safe_run("make")
        for cols in ["1", "2", "3", "4", "5"]:
            for kmer in ["31", "63", "95"]:
                env.safe_run("make MAXK={0} NUM_COLS={1} cortex_var".format(kmer, cols))
        with cd("scripts/analyse_variants/needleman_wunsch"):
            env.safe_sed("Makefile", "string_buffer.c", "string_buffer.c -lz")
            # Fix incompatibilities with gzfile struct in zlib 1.2.6+
            for fix_gz in ["libs/string_buffer/string_buffer.c", "libs/bioinf/bioinf.c",
                           "libs/string_buffer/string_buffer.h", "libs/bioinf/bioinf.h"]:
                env.safe_sed(fix_gz, "gzFile \*", "gzFile ")
                env.safe_sed(fix_gz, "gzFile\*", "gzFile")
            env.safe_run("make")
    _get_install_local(url, env, _cortex_build)
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