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))
