def install_gemini(env):
"""A lightweight db framework for disease and population genetics.
https://github.com/arq5x/gemini
"""
version = "0.6.4"
if versioncheck.up_to_date(env, "gemini -v", version,
stdout_flag="gemini"):
return
elif not shared._executable_not_on_path("gemini -v"):
env.safe_run("gemini update")
else:
iurl = "https://raw.github.com/arq5x/gemini/master/gemini/scripts/gemini_install.py"
data_dir = os.path.join(
env.system_install,
"local" if env.system_install.find("/local") == -1 else "",
"share", "gemini")
with _make_tmp_dir(ext="-gemini") as work_dir:
with cd(work_dir):
if env.safe_exists(os.path.basename(iurl)):
env.safe_run("rm -f %s" % os.path.basename(iurl))
installer = shared._remote_fetch(env, iurl)
env.safe_run("%s %s %s %s %s" %
(_python_cmd(env), installer, "" if env.use_sudo
else "--nosudo", env.system_install, data_dir))
env.safe_run("rm -f gemini_install.py")
def get_installed_version(env,
cmd,
version,
args=None,
stdout_flag=None,
stdout_index=-1):
"""Check if the given command is up to date with the provided version.
"""
if shared._executable_not_on_path(cmd):
return False
if args:
cmd = cmd + " " + " ".join(args)
with quiet():
path_safe = (
"export PKG_CONFIG_PATH=$PKG_CONFIG_PATH:{s}/lib/pkgconfig && "
"export PATH=$PATH:{s}/bin && "
"export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:{s}/lib && ".format(
s=env.system_install))
out = env.safe_run_output(path_safe + cmd)
if stdout_flag:
iversion = _parse_from_stdoutflag(out, stdout_flag, stdout_index)
else:
iversion = out.strip()
iversion = _clean_version(iversion)
if " not found in the pkg-config search path" in iversion:
return False
return iversion
def _download_executables(env, base_url, tools):
install_dir = shared._get_bin_dir(env)
with _make_tmp_dir() as work_dir:
with cd(work_dir):
for tool in tools:
final_tool = os.path.join(install_dir, tool)
if not env.safe_exists(final_tool) and shared._executable_not_on_path(tool):
shared._remote_fetch(env, "%s%s" % (base_url, tool))
env.safe_sudo("cp -f %s %s" % (tool, install_dir))
def _download_executables(env, base_url, tools):
install_dir = shared._get_bin_dir(env)
with _make_tmp_dir() as work_dir:
with cd(work_dir):
for tool in tools:
final_tool = os.path.join(install_dir, tool)
if not env.safe_exists(final_tool) and shared._executable_not_on_path(tool):
env.safe_run("wget %s%s" % (base_url, tool))
env.safe_sudo("cp -f %s %s" % (tool, install_dir))
def up_to_date(env, cmd, version, args=None, stdout_flag=None):
"""Check if the given command is up to date with the provided version.
"""
if shared._executable_not_on_path(cmd):
return False
if args:
cmd = cmd + " " + " ".join(args)
with quiet():
out = env.safe_run_output(cmd)
if stdout_flag:
iversion = _parse_from_stdoutflag(out, stdout_flag)
else:
iversion = out.strip()
return LooseVersion(iversion) >= LooseVersion(version)
def up_to_date(env, cmd, version, args=None, stdout_flag=None,
stdout_index=-1):
"""Check if the given command is up to date with the provided version.
"""
if shared._executable_not_on_path(cmd):
return False
if args:
cmd = cmd + " " + " ".join(args)
with quiet():
path_safe = "export PATH=$PATH:%s/bin && " % env.system_install
out = env.safe_run_output(path_safe + cmd)
if stdout_flag:
iversion = _parse_from_stdoutflag(out, stdout_flag, stdout_index)
else:
iversion = out.strip()
iversion = _clean_version(iversion)
return LooseVersion(iversion) >= LooseVersion(version)
def get_installed_version(env, cmd, version, args=None, stdout_flag=None,
stdout_index=-1):
"""Check if the given command is up to date with the provided version.
"""
if shared._executable_not_on_path(cmd):
return False
if args:
cmd = cmd + " " + " ".join(args)
with quiet():
path_safe = ("export PKG_CONFIG_PATH=$PKG_CONFIG_PATH:{s}/lib/pkgconfig && "
"export PATH=$PATH:{s}/bin && "
"export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:{s}/lib && ".format(s=env.system_install))
out = env.safe_run_output(path_safe + cmd)
if stdout_flag:
iversion = _parse_from_stdoutflag(out, stdout_flag, stdout_index)
else:
iversion = out.strip()
iversion = _clean_version(iversion)
return iversion
def up_to_date(env,
cmd,
version,
args=None,
stdout_flag=None,
stdout_index=-1):
"""Check if the given command is up to date with the provided version.
"""
if shared._executable_not_on_path(cmd):
return False
if args:
cmd = cmd + " " + " ".join(args)
with quiet():
path_safe = "export PATH=$PATH:%s/bin && "
out = env.safe_run_output(path_safe + cmd)
if stdout_flag:
iversion = _parse_from_stdoutflag(out, stdout_flag, stdout_index)
else:
iversion = out.strip()
iversion = _clean_version(iversion)
return LooseVersion(iversion) >= LooseVersion(version)
def install_gemini(env):
"""A lightweight db framework for disease and population genetics.
https://github.com/arq5x/gemini
"""
version = "0.6.1"
if versioncheck.up_to_date(env, "gemini -v", version, stdout_flag="gemini"):
return
elif not shared._executable_not_on_path("gemini -v"):
env.safe_run("gemini update")
else:
iurl = "https://raw.github.com/arq5x/gemini/master/gemini/scripts/gemini_install.py"
data_dir = os.path.join(env.system_install,
"local" if env.system_install.find("/local") == -1 else "",
"share", "gemini")
with _make_tmp_dir(ext="-gemini") as work_dir:
with cd(work_dir):
if env.safe_exists(os.path.basename(iurl)):
env.safe_run("rm -f %s" % os.path.basename(iurl))
installer = shared._remote_fetch(env, iurl)
env.safe_run("%s %s %s %s %s" %
(_python_cmd(env), installer, "" if env.use_sudo else "--nosudo",
env.system_install, data_dir))
env.safe_run("rm -f gemini_install.py")
def decorator(*args, **kwargs):
if not shared._executable_not_on_path(pname):
return func(*args, **kwargs)
def decorator(*args, **kwargs):
if not shared._executable_not_on_path(pname):
return func(*args, **kwargs)
