def install_tophat(env): """TopHat is a fast splice junction mapper for RNA-Seq reads http://ccb.jhu.edu/software/tophat/index.shtml """ default_version = "2.0.9" version = env.get("tool_version", default_version) if versioncheck.is_version(env, "tophat", version, args="--version", stdout_flag="TopHat"): env.logger.info("tophat version {0} is up to date; not installing" .format(version)) return platform = "OSX" if env.distribution == "macosx" else "Linux" url = "http://ccb.jhu.edu/software/tophat/downloads/" \ "tophat-%s.%s_x86_64.tar.gz" % (version, platform) _get_install(url, env, _make_copy("find . -perm -100 -type f", do_make=False))
def install_tophat(env): """TopHat is a fast splice junction mapper for RNA-Seq reads http://tophat.cbcb.umd.edu/ """ default_version = "2.0.9" version = env.get("tool_version", default_version) # if versioncheck.up_to_date(env, "tophat", version, stdout_flag="TopHat"): if versioncheck.is_version(env, "tophat", version, args="--version", stdout_flag="TopHat"): env.logger.info("tophat version {0} is up to date; not installing" .format(version)) return url = "http://tophat.cbcb.umd.edu/downloads/" \ "tophat-%s.Linux_x86_64.tar.gz" % version # def premake_cmd(env): # url = "http://dl.dropboxusercontent.com/u/2822886/tophat/tophat_fix.diff" # _apply_patch(env, url) _get_install(url, env, _make_copy("find -perm -100 -type f", do_make=False))
def install_tophat(env): """TopHat is a fast splice junction mapper for RNA-Seq reads http://tophat.cbcb.umd.edu/ """ default_version = "2.0.9" version = env.get("tool_version", default_version) if versioncheck.is_version(env, "tophat", version, args="--version", stdout_flag="TopHat"): env.logger.info( "tophat version {0} is up to date; not installing".format(version)) return platform = "OSX" if env.distribution == "macosx" else "Linux" url = "http://tophat.cbcb.umd.edu/downloads/" \ "tophat-%s.%s_x86_64.tar.gz" % (version, platform) _get_install(url, env, _make_copy("find . -perm -100 -type f", do_make=False))