def install_proteomics_tools(env):
_prep_galaxy(env)
tools_conf_path = env.get("galaxyp_tools_conf",
os.path.join(env.config_dir, os.pardir,
"contrib", "flavor", "proteomics", "galaxyp", "galaxyp_tools.yaml"))
galaxyp_tools_conf = yaml.load(open(tools_conf_path, "r"))
_install_tools(env, galaxyp_tools_conf)
def install_protkgem(env):
"""This method installs Ira Cooke's ProtK framework for the galaxy user.
By default this will install ProtK from rubygems server, but if
env.protk_version is set to <version>@<url> (e.g.
1.1.5@https://bitbucket.org/iracooke/protk-working) the
gem will be cloned with hg and installed from source.
"""
_prep_galaxy(env)
default_version = "1.2.0"
version_and_revision = env.get("protk_version", default_version)
install_from_source = version_and_revision.find("@") > 0
# e.g. protk_version = 1.1.5@https://bitbucket.org/iracooke/protk-working
if install_from_source:
(version, revision) = version_and_revision.split("@")
url = _get_bitbucket_download_url(revision, "https://bitbucket.org/iracooke/protk")
else:
version = version_and_revision
ruby_version = "1.9.3"
force_rvm_install = False
with prefix("HOME=~%s" % env.galaxy_user):
def rvm_exec(env, cmd="", rvm_cmd="use"):
prefix = ". $HOME/.rvm/scripts/rvm; rvm %s %s; " % (rvm_cmd, ruby_version)
env.safe_sudo("%s %s" % (prefix, cmd), user=env.galaxy_user)
if not exists("$HOME/.rvm") or force_rvm_install:
env.safe_sudo("curl -L get.rvm.io | bash -s stable; source ~%s/.rvm/scripts/rvm" % (env.galaxy_user), user=env.galaxy_user)
rvm_exec(env, rvm_cmd="install")
if not install_from_source:
# Typical rubygem install
rvm_exec(env, "gem install --no-ri --no-rdoc protk -v %s" % version)
else:
with cd("~%s" % env.galaxy_user):
env.safe_sudo("rm -rf protk_source; hg clone '%s' protk_source" % url, user=env.galaxy_user)
rvm_exec(env, "cd protk_source; gem build protk.gemspec; gem install protk")
protk_properties = {}
## ProtK can set these up itself, should make that an option.
protk_properties["tpp_root"] = os.path.join(env.galaxy_tools_dir, "transproteomic_pipeline", "default")
protk_properties['openms_root'] = "/usr" # os.path.join(env.galaxy_tools_dir, "openms", "default", "bin")
### Assumes omssa, blast, and transproteomic_pipeline CBL galaxy installs.
protk_properties['omssa_root'] = os.path.join(env.galaxy_tools_dir, "omssa", "default", "bin")
protk_properties['blast_root'] = os.path.join(env.galaxy_tools_dir, "blast+", "default")
protk_properties['pwiz_root'] = os.path.join(env.galaxy_tools_dir, "transproteomic_pipeline", "default", "bin")
# Other properties: log_file, blast_root
env.safe_sudo("mkdir -p \"$HOME/.protk\"", user=env.galaxy_user)
env.safe_sudo("mkdir -p \"$HOME/.protk/Databases\"", user=env.galaxy_user)
_write_to_file(yaml.dump(protk_properties), "/home/%s/.protk/config.yml" % env.galaxy_user, 0755)
rvm_exec(env, "protk_setup.rb galaxyenv")
install_dir = os.path.join(env.galaxy_tools_dir, "protkgem", version)
env.safe_sudo("mkdir -p '%s'" % install_dir)
_chown_galaxy(env, install_dir)
env.safe_sudo('ln -s -f "$HOME/.protk/galaxy/env.sh" "%s/env.sh"' % install_dir, user=env.galaxy_user)
with cd(install_dir):
with cd(".."):
env.safe_sudo("ln -s -f '%s' default" % version)
def install_protkgem(env):
"""This method installs Ira Cooke's ProtK framework for the galaxy user.
By default this will install ProtK from rubygems server, but if
env.protk_version is set to <version>@<url> (e.g.
1.1.5@https://bitbucket.org/iracooke/protk-working) the
gem will be cloned with hg and installed from source.
"""
_prep_galaxy(env)
default_version = "1.2.0"
version_and_revision = env.get("protk_version", default_version)
install_from_source = version_and_revision.find("@") > 0
# e.g. protk_version = 1.1.5@https://bitbucket.org/iracooke/protk-working
if install_from_source:
(version, revision) = version_and_revision.split("@")
url = _get_bitbucket_download_url(revision, "https://bitbucket.org/iracooke/protk")
else:
version = version_and_revision
ruby_version = "1.9.3"
force_rvm_install = False
with prefix("HOME=~%s" % env.galaxy_user):
def rvm_exec(env, cmd="", rvm_cmd="use"):
prefix = ". $HOME/.rvm/scripts/rvm; rvm %s %s; " % (rvm_cmd, ruby_version)
env.safe_sudo("%s %s" % (prefix, cmd), user=env.galaxy_user)
if not exists("$HOME/.rvm") or force_rvm_install:
env.safe_sudo("curl -L get.rvm.io | bash -s stable; source ~%s/.rvm/scripts/rvm" % (env.galaxy_user), user=env.galaxy_user)
rvm_exec(env, rvm_cmd="install")
if not install_from_source:
# Typical rubygem install
rvm_exec(env, "gem install --no-ri --no-rdoc protk -v %s" % version)
else:
with cd("~%s" % env.galaxy_user):
env.safe_sudo("rm -rf protk_source; hg clone '%s' protk_source" % url, user=env.galaxy_user)
rvm_exec(env, "cd protk_source; gem build protk.gemspec; gem install protk")
protk_properties = {}
## ProtK can set these up itself, should make that an option.
protk_properties["tpp_root"] = os.path.join(env.galaxy_tools_dir, "transproteomic_pipeline", "default")
protk_properties['openms_root'] = "/usr" # os.path.join(env.galaxy_tools_dir, "openms", "default", "bin")
### Assumes omssa, blast, and transproteomic_pipeline CBL galaxy installs.
protk_properties['omssa_root'] = os.path.join(env.galaxy_tools_dir, "omssa", "default", "bin")
protk_properties['blast_root'] = os.path.join(env.galaxy_tools_dir, "blast", "default")
protk_properties['pwiz_root'] = os.path.join(env.galaxy_tools_dir, "transproteomic_pipeline", "default", "bin")
# Other properties: log_file, blast_root
env.safe_sudo("mkdir -p \"$HOME/.protk\"", user=env.galaxy_user)
env.safe_sudo("mkdir -p \"$HOME/.protk/Databases\"", user=env.galaxy_user)
_write_to_file(yaml.dump(protk_properties), "/home/%s/.protk/config.yml" % env.galaxy_user, 0755)
rvm_exec(env, "protk_setup.rb galaxyenv")
install_dir = os.path.join(env.galaxy_tools_dir, "protkgem", version)
env.safe_sudo("mkdir -p '%s'" % install_dir)
_chown_galaxy(env, install_dir)
env.safe_sudo('ln -s -f "$HOME/.protk/galaxy/env.sh" "%s/env.sh"' % install_dir, user=env.galaxy_user)
with cd(install_dir):
with cd(".."):
env.safe_sudo("ln -s -f '%s' default" % version)
def install_proteomics_tools(env):
_prep_galaxy(env)
tools_conf_path = env.get(
"galaxyp_tools_conf",
os.path.join(env.config_dir, os.pardir, "contrib", "flavor",
"proteomics", "galaxyp", "galaxyp_tools.yaml"))
galaxyp_tools_conf = yaml.load(open(tools_conf_path, "r"))
_install_tools(env, galaxyp_tools_conf)
def install_protk(env):
"""Installs Ira Cooke's ProtK framework for the
galaxy user"""
_prep_galaxy(env)
default_version = "0.95@e81050c1c658"
version_and_revision = env.get("protk_version", default_version)
(version, revision) = version_and_revision.split("@")
url = _get_bitbucket_download_url(revision, "https://bitbucket.org/iracooke/protk")
with prefix("HOME=~%s" % env.galaxy_user):
if not exists("$HOME/.rvm"):
env.safe_sudo("curl -L get.rvm.io | bash -s stable; source ~%s/.rvm/scripts/rvm" % (env.galaxy_user), user=env.galaxy_user)
env.safe_sudo(". $HOME/.rvm/scripts/rvm; rvm install 1.8.7 | cat", user=env.galaxy_user)
env.safe_sudo(". $HOME/.rvm/scripts/rvm; rvm 1.8.7 do gem install rake --no-rdoc --no-ri", user=env.galaxy_user)
install_dir = os.path.join(env.galaxy_tools_dir, "protk", version)
def _make(env):
env.safe_sudo("PROTK_DIR=%s; rm -rf $PROTK_DIR; mkdir -p $PROTK_DIR; mv * $PROTK_DIR" % (install_dir))
_get_install(url, env, _make)
_chown_galaxy(env, install_dir)
with prefix("HOME=~%s" % env.galaxy_user):
import StringIO
output = StringIO.StringIO()
get("%s/config.yml.sample" % install_dir, output)
sample_config = yaml.load(output.getvalue())
sample_config['test']['tpp_bin'] = os.path.join(env.galaxy_tools_dir, "transproteomic_pipeline", "default", "bin")
sample_config['test']['omssa_bin'] = os.path.join(env.galaxy_tools_dir, "omssa", "default", "bin")
sample_config['test']['ncbi_tools_bin'] = os.path.join(env.galaxy_tools_dir, "blast", "default", "bin")
sample_config['test']['openms_bin'] = os.path.join(env.galaxy_tools_dir, "openms", "default", "bin")
#sample_config['test']['galaxy_root']=env.galaxy_home
_write_to_file(yaml.dump(sample_config), "%s/config.yml" % install_dir, 0755)
with cd(install_dir):
#env.safe_sudo("mv /tmp/config.yaml .")
env.safe_sudo(". $HOME/.rvm/scripts/rvm; echo No | ./setup.sh", user=env.galaxy_user)
env.safe_sudo("gcc -o make_random make_random.c -lm; ln -s ../make_random bin", user=env.galaxy_user)
with cd("%s/.." % install_dir):
env.safe_sudo("ln -s -f %s default" % version)
def install_proteomics_tools(env):
_prep_galaxy(env)
galaxyp_tools_conf = yaml.load(open("contrib/flavor/cloudman/galaxyp_tools.yaml", "r"))
_install_tools(env, galaxyp_tools_conf)
def install_cbl_galaxy_tools(env):
_prep_galaxy(env)
_install_tools(env)
def install_proteomics_tools(env):
_prep_galaxy(env)
galaxyp_tools_conf = yaml.load(
open("contrib/flavor/cloudman/galaxyp_tools.yaml", "r"))
_install_tools(env, galaxyp_tools_conf)
