def r_library_installer(config):
"""Install R libraries using CRAN and Bioconductor.
"""
if config.get("cran") or config.get("bioc") or config.get("github"):
with shared._make_tmp_dir() as tmp_dir:
with cd(tmp_dir):
# Create an Rscript file with install details.
out_file = os.path.join(tmp_dir, "install_packages.R")
_make_install_script(out_file, config)
# run the script and then get rid of it
# try using either
rlib_installed = False
rscripts = []
conda_bin = shared._conda_cmd(env)
if conda_bin:
rscripts.append(
fabutils.find_cmd(
env,
os.path.join(os.path.dirname(conda_bin),
"Rscript"), "--version"))
rscripts.append(fabutils.find_cmd(env, "Rscript", "--version"))
for rscript in rscripts:
if rscript:
env.safe_run("%s %s" % (rscript, out_file))
rlib_installed = True
break
if not rlib_installed:
env.logger.warn(
"Rscript not found; skipping install of R libraries.")
env.safe_run("rm -f %s" % out_file)
def r_library_installer(config):
"""Install R libraries using CRAN and Bioconductor.
"""
if config.get("cran") or config.get("bioc") or config.get("github"):
with shared._make_tmp_dir() as tmp_dir:
with cd(tmp_dir):
# Create an Rscript file with install details.
out_file = os.path.join(tmp_dir, "install_packages.R")
_make_install_script(out_file, config)
# run the script and then get rid of it
# try using either
rlib_installed = False
rscripts = []
conda_bin = shared._conda_cmd(env)
if conda_bin:
rscripts.append(fabutils.find_cmd(env, os.path.join(os.path.dirname(conda_bin), "Rscript"),
"--version"))
rscripts.append(fabutils.find_cmd(env, "Rscript", "--version"))
for rscript in rscripts:
if rscript:
env.safe_run("%s %s" % (rscript, out_file))
rlib_installed = True
break
if not rlib_installed:
env.logger.warn("Rscript not found; skipping install of R libraries.")
env.safe_run("rm -f %s" % out_file)
def _brew_cmd(env):
"""Retrieve brew command for installing homebrew packages.
"""
cmd = find_cmd(env, "brew", "--version")
if cmd is None:
raise ValueError("Did not find working installation of Linuxbrew/Homebrew")
else:
return cmd
def _brew_cmd(env):
"""Retrieve brew command for installing homebrew packages.
"""
cmd = find_cmd(env, "brew", "--version")
if cmd is None:
raise ValueError(
"Did not find working installation of Linuxbrew/Homebrew")
else:
return cmd
def install_packages(env):
config_file = get_config_file(env, "perl-libs.yaml")
(packages, _) = _yaml_to_packages(config_file.base, subs_yaml_file=config_file.dist, namesort=False)
cpanm_cmd = find_cmd(env, "cpanm", "--version")
for package in packages:
if package.count("==") > 1:
_install_from_url(env, cpanm_cmd, package)
else:
_install_from_cpan(env, cpanm_cmd, package)
def r_library_installer(config):
"""Install R libraries using CRAN and Bioconductor.
"""
# Create an Rscript file with install details.
out_file = "install_packages.R"
if env.safe_exists(out_file):
env.safe_run("rm -f %s" % out_file)
env.safe_run("touch %s" % out_file)
lib_loc = os.path.join(env.system_install, "lib", "R", "site-library")
env.safe_sudo("mkdir -p %s" % lib_loc)
repo_info = """
.libPaths(c("%s"))
library(methods)
cran.repos <- getOption("repos")
cran.repos["CRAN" ] <- "%s"
options(repos=cran.repos)
source("%s")
""" % (lib_loc, config["cranrepo"], config["biocrepo"])
env.safe_append(out_file, repo_info)
install_fn = """
repo.installer <- function(repos, install.fn) {
%s
maybe.install <- function(pname) {
if (!(pname %%in%% installed.packages()))
install.fn(pname)
}
}
"""
if config.get("update_packages", True):
update_str = """
update.packages(lib.loc="%s", repos=repos, ask=FALSE)
""" % lib_loc
else:
update_str = "\n"
env.safe_append(out_file, install_fn % update_str)
std_install = """
std.pkgs <- c(%s)
std.installer = repo.installer(cran.repos, install.packages)
lapply(std.pkgs, std.installer)
""" % (", ".join('"%s"' % p for p in config['cran']))
env.safe_append(out_file, std_install)
if len(config.get("bioc", [])) > 0:
bioc_install = """
bioc.pkgs <- c(%s)
bioc.installer = repo.installer(biocinstallRepos(), biocLite)
lapply(bioc.pkgs, bioc.installer)
""" % (", ".join('"%s"' % p for p in config['bioc']))
env.safe_append(out_file, bioc_install)
# run the script and then get rid of it
rscript = fabutils.find_cmd(env, "Rscript", "--version")
if rscript:
env.safe_sudo("%s %s" % (rscript, out_file))
else:
env.logger.warn("Rscript not found; skipping install of R libraries.")
env.safe_run("rm -f %s" % out_file)
def r_library_installer(config):
"""Install R libraries using CRAN and Bioconductor.
"""
# Create an Rscript file with install details.
out_file = "install_packages.R"
if env.safe_exists(out_file):
env.safe_run("rm -f %s" % out_file)
env.safe_run("touch %s" % out_file)
lib_loc = os.path.join(env.system_install, "lib", "R", "site-library")
env.safe_sudo("mkdir -p %s" % lib_loc)
repo_info = """
.libPaths(c("%s"))
library(methods)
cran.repos <- getOption("repos")
cran.repos["CRAN" ] <- "%s"
options(repos=cran.repos)
source("%s")
""" % (lib_loc, config["cranrepo"], config["biocrepo"])
env.safe_append(out_file, repo_info)
install_fn = """
repo.installer <- function(repos, install.fn) {
%s
maybe.install <- function(pname) {
if (!(pname %%in%% installed.packages()))
install.fn(pname)
}
}
"""
if config.get("update_packages", True):
update_str = """
update.packages(lib.loc="%s", repos=repos, ask=FALSE)
""" % lib_loc
else:
update_str = "\n"
env.safe_append(out_file, install_fn % update_str)
std_install = """
std.pkgs <- c(%s)
std.installer = repo.installer(cran.repos, install.packages)
lapply(std.pkgs, std.installer)
""" % (", ".join('"%s"' % p for p in config['cran']))
env.safe_append(out_file, std_install)
if len(config.get("bioc", [])) > 0:
bioc_install = """
bioc.pkgs <- c(%s)
bioc.installer = repo.installer(biocinstallRepos(), biocLite)
lapply(bioc.pkgs, bioc.installer)
""" % (", ".join('"%s"' % p for p in config['bioc']))
env.safe_append(out_file, bioc_install)
# run the script and then get rid of it
rscript = fabutils.find_cmd(env, "Rscript", "--version")
if rscript:
env.safe_sudo("%s %s" % (rscript, out_file))
else:
env.logger.warn("Rscript not found; skipping install of R libraries.")
env.safe_run("rm -f %s" % out_file)
def r_library_installer(config):
"""Install R libraries using CRAN and Bioconductor.
"""
with shared._make_tmp_dir() as tmp_dir:
with cd(tmp_dir):
# Create an Rscript file with install details.
out_file = os.path.join(tmp_dir, "install_packages.R")
_make_install_script(out_file, config)
# run the script and then get rid of it
rscript = fabutils.find_cmd(env, "Rscript", "--version")
if rscript:
env.safe_run("%s %s" % (rscript, out_file))
else:
env.logger.warn("Rscript not found; skipping install of R libraries.")
env.safe_run("rm -f %s" % out_file)
def r_library_installer(config):
"""Install R libraries using CRAN and Bioconductor.
"""
with shared._make_tmp_dir() as tmp_dir:
with cd(tmp_dir):
# Create an Rscript file with install details.
out_file = os.path.join(tmp_dir, "install_packages.R")
_make_install_script(out_file, config)
# run the script and then get rid of it
rscript = fabutils.find_cmd(env, "Rscript", "--version")
if rscript:
env.safe_run("%s %s" % (rscript, out_file))
else:
env.logger.warn(
"Rscript not found; skipping install of R libraries.")
env.safe_run("rm -f %s" % out_file)
