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 _get_isatab_config(dirs, config):
"""Retrieve ISA-tab configuration files.
Need to add SCDE configurations to GitHub repo.
"""
config_git = "git clone git://github.com/ISA-tools/Configuration-Files.git"
with cd(dirs["base"]):
config_dir = _fetch_and_unpack(config_git)
our_config_dir = os.path.join(dirs["base"], config_dir, config["isatab_config"])
assert exists(our_config_dir), our_config_dir
dirs["config"] = our_config_dir
return dirs
def _download_isatab_s3(name, perm_type, bucket, dirs):
"""Download an ISA-tab data file from the S3 bucket.
"""
s3_key = bucket.get_key("%s.tar.gz" % name)
assert s3_key is not None, name
url = s3_key.generate_url(expires_in=60)
out_dir = os.path.join(dirs["isatab"], perm_type)
if not exists(out_dir):
run("mkdir -p %s" % out_dir)
with cd(out_dir):
cur_dir = _fetch_and_unpack(url)
return os.path.join(out_dir, cur_dir)
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)
