def _install_brew_baseline(env, brew_cmd, ipkgs, packages):
"""Install baseline brew components not handled by dependency system.
- Installation of required Perl libraries.
- Ensures installed samtools does not overlap with bcftools
- Upgrades any package dependencies
"""
for dep in ["expat", "cmake", "pkg-config"]:
_install_pkg(env, dep, brew_cmd, ipkgs)
for dep in ["sambamba"]: # Avoid conflict with homebrew-science sambamba
env.safe_run("{brew_cmd} remove --force {dep}".format(**locals()))
# if installing samtools, avoid bcftools conflicts
if len([x for x in packages if x.find("samtools") >= 0]):
with settings(warn_only=True):
def _has_prog(prog):
try:
return int(
env.safe_run_output(
"{brew_cmd} list samtools | grep -c {prog} | cat".
format(brew_cmd=brew_cmd, prog=prog)))
except ValueError:
return 0
if any(_has_prog(p) for p in ["bctools", "vcfutils.pl"]):
env.safe_run("{brew_cmd} uninstall {pkg}".format(
brew_cmd=brew_cmd, pkg="samtools"))
ipkgs["current"].pop("samtools", None)
_install_pkg_latest(env, "samtools", ["--without-curses"], brew_cmd,
ipkgs)
for dependency in ["htslib"]:
if dependency in packages:
if (dependency in ipkgs["outdated"]
or "chapmanb/cbl/%s" % dependency in ipkgs["outdated"]
or dependency not in ipkgs["current"]):
_install_pkg_latest(env, dependency, [], brew_cmd, ipkgs)
if "cpanminus" in packages:
_install_pkg_latest(env, "cpanminus", [], brew_cmd, ipkgs)
_install_pkg_latest(env, "samtools-library-0.1", [], brew_cmd, ipkgs)
cpan.install_packages(env)
# Ensure paths we may have missed on install are accessible to regular user
if env.use_sudo:
paths = ["share", "share/java"]
for path in paths:
with quiet():
test_access = env.safe_run(
"test -d %s/%s && test -O %s/%s" %
(env.system_install, path, env.system_install, path))
if test_access.failed and env.safe_exists(
"%s/%s" % (env.system_install, path)):
env.safe_sudo("chown %s %s/%s" %
(env.user, env.system_install, path))
def _install_brew_baseline(env, brew_cmd, ipkgs, packages):
"""Install baseline brew components not handled by dependency system.
- Installation of required Perl libraries.
- Ensures installed samtools does not overlap with bcftools
- Upgrades any package dependencies
"""
for dep in ["openssl"]:
_safe_link_pkg(env, dep, brew_cmd)
for dep in ["expat", "pkg-config", "xz"]:
_install_pkg(env, dep, brew_cmd, ipkgs)
# check if we have an older git and need to install it from brew
git_version = None
with quiet():
with settings(warn_only=True):
git_version = env.safe_run_output("git --version").strip().split()[-1]
if git_version and LooseVersion(git_version) < LooseVersion("1.7"):
_install_pkg(env, "git", brew_cmd, ipkgs)
for dep in ["sambamba"]: # Avoid conflict with homebrew-science sambamba
env.safe_run("{brew_cmd} remove --force {dep}".format(**locals()))
# if installing samtools, avoid bcftools conflicts
if len([x for x in packages if x.find("samtools") >= 0]):
with settings(warn_only=True):
def _has_prog(prog):
try:
return int(env.safe_run_output("{brew_cmd} list samtools | grep -c {prog} | cat".format(
brew_cmd=brew_cmd, prog=prog)))
except ValueError:
return 0
if any(_has_prog(p) for p in ["bctools", "vcfutils.pl"]):
env.safe_run("{brew_cmd} uninstall {pkg}".format(brew_cmd=brew_cmd, pkg="samtools"))
ipkgs["current"].pop("samtools", None)
_install_pkg_latest(env, "samtools", ["--without-curses"], brew_cmd, ipkgs)
for dependency in ["htslib"]:
if dependency in packages:
if (dependency in ipkgs["outdated"] or "chapmanb/cbl/%s" % dependency in ipkgs["outdated"]
or dependency not in ipkgs["current"]):
_install_pkg_latest(env, dependency, [], brew_cmd, ipkgs)
if "cpanminus" in packages:
_install_pkg_latest(env, "cpanminus", [], brew_cmd, ipkgs)
_install_pkg_latest(env, "samtools-library-0.1", [], brew_cmd, ipkgs)
cpan.install_packages(env)
# Ensure paths we may have missed on install are accessible to regular user
if env.use_sudo:
paths = ["share", "share/java"]
for path in paths:
with quiet():
test_access = env.safe_run("test -d %s/%s && test -O %s/%s" % (env.system_install, path,
env.system_install, path))
if test_access.failed and env.safe_exists("%s/%s" % (env.system_install, path)):
env.safe_sudo("chown %s %s/%s" % (env.user, env.system_install, path))
def _install_brew_baseline(env, brew_cmd, ipkgs, packages):
"""Install baseline brew components not handled by dependency system.
- Installation of required Perl libraries.
- Upgrades any package dependencies
"""
for dep in ["openssl"]:
_safe_link_pkg(env, dep, brew_cmd)
for dep in ["expat", "pkg-config", "xz", "unzip"]:
_install_pkg(env, dep, brew_cmd, ipkgs)
# check if we have an older git and need to install it from brew
git_version = None
with quiet():
with settings(warn_only=True):
git_version = env.safe_run_output(
"git --version").strip().split()[-1]
if git_version and LooseVersion(git_version) < LooseVersion("1.7"):
_install_pkg(env, "git", brew_cmd, ipkgs)
for dep in ["sambamba"]: # Avoid conflict with homebrew-science sambamba
env.safe_run("{brew_cmd} remove --force {dep}".format(**locals()))
for dependency in ["htslib"]:
if dependency in packages:
if (dependency in ipkgs["outdated"]
or "chapmanb/cbl/%s" % dependency in ipkgs["outdated"]
or dependency not in ipkgs["current"]):
_install_pkg_latest(env, dependency, [], brew_cmd, ipkgs)
if "cpanminus" in packages:
_install_pkg_latest(env, "cpanminus", [], brew_cmd, ipkgs)
_install_pkg_latest(env, "samtools-library-0.1", [], brew_cmd, ipkgs)
cpan.install_packages(env)
# Ensure paths we may have missed on install are accessible to regular user
if env.use_sudo:
paths = ["share", "share/java"]
for path in paths:
with quiet():
test_access = env.safe_run(
"test -d %s/%s && test -O %s/%s" %
(env.system_install, path, env.system_install, path))
if test_access.failed and env.safe_exists(
"%s/%s" % (env.system_install, path)):
env.safe_sudo("chown %s %s/%s" %
(env.user, env.system_install, path))
def _install_brew_baseline(env, brew_cmd, ipkgs, packages):
"""Install baseline brew components not handled by dependency system.
- Installation of required Perl libraries.
- Upgrades any package dependencies
"""
for dep in ["openssl"]:
_safe_link_pkg(env, dep, brew_cmd)
for dep in ["expat", "pkg-config", "xz", "unzip"]:
_install_pkg(env, dep, brew_cmd, ipkgs)
# check if we have an older git and need to install it from brew
git_version = None
with quiet():
with settings(warn_only=True):
git_version = env.safe_run_output("git --version").strip().split()[-1]
if git_version and LooseVersion(git_version) < LooseVersion("1.7"):
_install_pkg(env, "git", brew_cmd, ipkgs)
for dep in ["sambamba"]: # Avoid conflict with homebrew-science sambamba
env.safe_run("{brew_cmd} remove --force {dep}".format(**locals()))
for dependency in ["htslib"]:
if dependency in packages:
if (dependency in ipkgs["outdated"] or "chapmanb/cbl/%s" % dependency in ipkgs["outdated"]
or dependency not in ipkgs["current"]):
_install_pkg_latest(env, dependency, [], brew_cmd, ipkgs)
if "cpanminus" in packages:
_install_pkg_latest(env, "cpanminus", [], brew_cmd, ipkgs)
_install_pkg_latest(env, "samtools-library-0.1", [], brew_cmd, ipkgs)
cpan.install_packages(env)
# Ensure paths we may have missed on install are accessible to regular user
if env.use_sudo:
paths = ["share", "share/java"]
for path in paths:
with quiet():
test_access = env.safe_run("test -d %s/%s && test -O %s/%s" % (env.system_install, path,
env.system_install, path))
if test_access.failed and env.safe_exists("%s/%s" % (env.system_install, path)):
env.safe_sudo("chown %s %s/%s" % (env.user, env.system_install, path))