def post_install(self):
env.logger.info("Starting post-install")
env.logger.info("Load Scalability tests")
if exists('Scalability'):
with cd('Scalability'):
run('git pull')
else:
_fetch_and_unpack(
"git clone git://github.com/pjotrp/Scalability.git")
# Now run a post installation routine (for the heck of it)
run('./Scalability/scripts/hello.sh')
env.logger.info("Load Cross-language tests")
if exists('Cross-language-interfacing'):
with cd('Cross-language-interfacing'):
run('git pull')
else:
_fetch_and_unpack(
"git clone git://github.com/pjotrp/Cross-language-interfacing.git"
)
# Special installs for the tests
with cd('Cross-language-interfacing'):
sudo('./scripts/install-packages-root.sh ')
run('./scripts/install-packages.sh')
run('./scripts/create_test_files.rb')
def install_augustus(env):
default_version = "2.7"
version = env.get('tool_version', default_version)
url = "http://bioinf.uni-greifswald.de/augustus/binaries/augustus.%s.tar.gz" % version
install_dir = env.system_install
with _make_tmp_dir() as work_dir:
with cd(work_dir):
_fetch_and_unpack(url, need_dir=False)
env.safe_sudo("mkdir -p '%s'" % install_dir)
env.safe_sudo("mv augustus.%s/* '%s'" % (version, install_dir))
def install_augustus(env):
default_version = "2.7"
version = env.get('tool_version', default_version)
url = "http://bioinf.uni-greifswald.de/augustus/binaries/augustus.%s.tar.gz" % version
install_dir = env.system_install
with _make_tmp_dir() as work_dir:
with cd(work_dir):
_fetch_and_unpack(url, need_dir=False)
env.safe_sudo("mkdir -p '%s'" % install_dir)
env.safe_sudo("mv augustus.%s/* '%s'" % (version, install_dir))
def install_augustus(env):
version = env.tool_version
url = "http://bioinf.uni-greifswald.de/augustus/binaries/augustus.%s.tar.gz" % version
install_dir = env.system_install
with _make_tmp_dir() as work_dir:
with cd(work_dir):
_fetch_and_unpack(url, need_dir=False)
env.safe_sudo("mkdir -p '%s'" % install_dir)
env.safe_sudo("mv * '%s'" % install_dir)
env.safe_sudo("echo 'PATH=%s/bin:%s/scripts:$PATH' > %s/env.sh" % (install_dir, install_dir, install_dir))
env.safe_sudo("echo 'export AUGUSTUS_CONFIG_PATH=%s/config' >> %s/env.sh" % (install_dir, install_dir))
_update_default(env, install_dir)
def _install_from_url(env, cpanm_cmd, package):
"""Check version of a dependency and download and install with cpanm if not up to date.
Packages installed via URL have the package name, target version and URL separated
with '=='. They can also optionally have a build directory or dependency to remove.
"""
parts = package.split("==")
package, target_version, url = parts[:3]
args = {}
if len(parts) > 3:
for key, value in (x.split("=") for x in parts[3:]):
args[key] = value
with settings(warn_only=True):
cur_version = env.safe_run_output("export PERL5LIB=%s/lib/perl5:${PERL5LIB} && " % env.system_install +
"""perl -le 'eval "require $ARGV[0]" and print $ARGV[0]->VERSION' %s"""
% package)
if cur_version != target_version:
with cshared._make_tmp_dir() as work_dir:
with cd(work_dir):
dl_dir = cshared._fetch_and_unpack(url)
if args.get("build"):
dl_dir = os.path.join(dl_dir, args["build"])
with cd(dl_dir):
if args.get("depremove"):
for fname in ["Makefile.PL", "MYMETA.json", "MYMETA.yml"]:
env.safe_run(r"""sed -i.bak -e '/^.*%s.*/s/^/#/' %s""" % (args["depremove"], fname))
env.safe_run("%s -i --notest --local-lib=%s ." % (cpanm_cmd, env.system_install))
def install_jboss(base_dir):
version = "5.1.0"
url = "http://downloads.sourceforge.net/project/jboss/JBoss/JBoss-%s.GA/jboss-%s.GA.zip" % \
(version, version)
java_dir = _java_dir(base_dir)
with cd(java_dir):
jboss_dir = _fetch_and_unpack(url)
return os.path.join(java_dir, jboss_dir)
def _install_galaxy_search(dirs, config):
"""Full text search capability with Lucene.
"""
search_url = "git clone git://github.com/chapmanb/kwd-doc-find.git"
with cd(dirs["base"]):
lucene_dir = _fetch_and_unpack(search_url)
lucene_dir = os.path.join(dirs["base"], lucene_dir)
return ("fulltext_search", lucene_dir, "lein deps && lein run :web 8081",
"run :web 8081", False)
def install_maven(base_dir):
version = "2.2.1"
mirror = "mirror.cc.columbia.edu/pub/software/apache"
java_dir = _java_dir(base_dir)
url = "http://%s/maven/binaries/apache-maven-%s-bin.tar.gz" % ( mirror, version)
with cd(java_dir):
mvn_dir = _fetch_and_unpack(url)
install_mvn = os.path.join(base_dir, "bin", "mvn")
dl_mvn = os.path.join(java_dir, mvn_dir, "bin", "mvn")
sudo("ln -s %s %s" % (dl_mvn, install_mvn))
def post_install(self):
env.logger.info("Starting post-install")
env.logger.info("Load Scalability tests")
if exists('Scalability'):
with cd('Scalability'):
run('git pull')
else:
_fetch_and_unpack("git clone git://github.com/pjotrp/Scalability.git")
# Now run a post installation routine (for the heck of it)
run('./Scalability/scripts/hello.sh')
env.logger.info("Load Cross-language tests")
if exists('Cross-language-interfacing'):
with cd('Cross-language-interfacing'):
run('git pull')
else:
_fetch_and_unpack("git clone git://github.com/pjotrp/Cross-language-interfacing.git")
# Special installs for the tests
with cd('Cross-language-interfacing'):
sudo('./scripts/install-packages-root.sh ')
run('./scripts/install-packages.sh')
run('./scripts/create_test_files.rb')
def _install_bii_tools(config):
bii_git = "git clone git://github.com/ISA-tools/BioInvIndex.git"
mgr_git = "git clone git://github.com/ISA-tools/ISAvalidator-ISAconverter-BIImanager.git"
base_dir = os.path.join(config["base_install"], config["bii_dirname"])
if not exists(base_dir):
sudo("mkdir -p %s" % base_dir)
sudo("chown %s %s" % (env.user, base_dir))
with cd(base_dir):
bii_dir = _fetch_and_unpack(bii_git)
bii_dir = os.path.join(base_dir, bii_dir)
with cd(base_dir):
mgr_base_dir = _fetch_and_unpack(mgr_git)
mgr_build_dir = "val_conv_manager_gui"
with cd(os.path.join(mgr_base_dir, mgr_build_dir)):
target_dir = "target"
if not exists(target_dir):
# need artifacts from BII for tool build
with cd(bii_dir):
run("mvn clean install -Dmaven.test.skip=true")
run("rm -rf ear/target")
# now build BII data manager
run("sh package.sh")
with cd(target_dir):
run("unzip BII-data-mgr-*.zip")
mgr_dir = os.path.join(base_dir, mgr_base_dir, mgr_build_dir, target_dir)
with cd(mgr_dir):
with settings(hide("everything"), warn_only=True):
result = run("ls -1d BII-data-mgr-*")
data_mgr_dir = result.split()[0].strip()
mgr_dir = os.path.join(mgr_dir, data_mgr_dir)
index_dir = os.path.join(base_dir, config["bii_lucene_index"])
if not exists(index_dir):
run("mkdir -p %s" % index_dir)
bii_data_dir = os.path.join(base_dir, config["bii_data_dirname"])
if not exists(bii_data_dir):
run("mkdir -p %s" % bii_data_dir)
return dict(base=base_dir, bii=bii_dir, mgr=mgr_dir, index=index_dir,
bii_data=bii_data_dir)
def _install_galaxy_code(dirs, config):
with cd(dirs["base"]):
code_dir = _fetch_and_unpack("hg clone %s" % config["galaxy_repo"])
code_dir = os.path.join(dirs["base"], code_dir)
library_dir = os.path.join(dirs["base"], config["galaxy_datalib"])
config_file = "universe_wsgi.ini"
remote_config = os.path.join(code_dir, config_file)
if not exists(remote_config):
local_config = os.path.join(config["fab_base_dir"], "install_files",
config_file)
origs = ["DBUSER", "DBPASSWD", "DBNAME", "ADMINUSERS", "LIBRARYDIR"]
vals = [config["db_user"], config["db_pass"], config["galaxy_dbname"],
config["galaxy_adminusers"], library_dir]
put(local_config, remote_config)
for old, new in zip(origs, vals):
sed(remote_config, old, new)
return ("galaxy", code_dir, "sh run.sh",
"paster.py serve universe_wsgi.ini", False)