def create_data_library_for_uploads(options):
with cd(os.path.join(env.galaxy_home, "scripts", "api")):
db_key_arg = get_main_options_string(options, 'db_key')
transfer_history_name = get_main_options_string(options, 'transfer_history_name')
transfer_history_api_key = get_main_options_string(options, 'transfer_history_api_key')
cmd_template = 'python handle_uploads.py --api_key="%s" --db_key="%s" --history="%s" --history_api_key="%s" '
galaxy_data = options["galaxy"]
admin_user_api_key = galaxy_data["users"][0]["api_key"]
cmd = cmd_template % (admin_user_api_key, db_key_arg, transfer_history_name, transfer_history_api_key)
sudo("bash -c 'export PYTHON_EGG_CACHE=eggs; %s'" % cmd, user="******")
def create_data_library_for_uploads(options):
with cd(os.path.join(env.galaxy_home, "scripts", "api")):
db_key_arg = get_main_options_string(options, 'db_key')
transfer_history_name = get_main_options_string(options, 'transfer_history_name')
transfer_history_api_key = get_main_options_string(options, 'transfer_history_api_key')
cmd_template = 'python handle_uploads.py --api_key="%s" --db_key="%s" --history="%s" --history_api_key="%s" '
galaxy_data = options["galaxy"]
admin_user_api_key = galaxy_data["users"][0]["api_key"]
cmd = cmd_template % (admin_user_api_key, db_key_arg, transfer_history_name, transfer_history_api_key)
sudo("bash -c 'export PYTHON_EGG_CACHE=eggs; %s'" % cmd, user="******")
def setup_genomes(options):
install_proc = install_data
sudo("mkdir -p %s" % env.data_files)
sudo("chown -R %s:%s %s" % (env.user, env.user, env.data_files))
put("config/tool_data_table_conf.xml", "%s/tool_data_table_conf.xml" % env.galaxy_home)
indexing_packages = ["bowtie", "bwa", "samtools"]
path_extensions = ":".join(map(lambda package: "/opt/galaxyTools/tools/%s/default" % package, indexing_packages))
with prefix("PATH=$PATH:%s" % path_extensions):
if 'S3' == options['genome_source']:
install_proc = install_data_s3
install_proc(options["genomes"])
if options.get("setup_taxonomy_data", False):
setup_taxonomy_data()
stash_genomes_where = get_main_options_string(options, "stash_genomes")
if stash_genomes_where:
stash_genomes(stash_genomes_where)
def setup_genomes(options):
install_proc = install_data
sudo("mkdir -p %s" % env.data_files)
sudo("chown -R %s:%s %s" % (env.user, env.user, env.data_files))
put("config/tool_data_table_conf.xml", "%s/tool_data_table_conf.xml" % env.galaxy_home)
indexing_packages = ["bowtie", "bwa", "samtools"]
path_extensions = ":".join(map(lambda package: "/opt/galaxyTools/tools/%s/default" % package, indexing_packages))
with prefix("PATH=$PATH:%s" % path_extensions):
if 'S3' == options['genome_source']:
install_proc = install_data_s3
install_proc(options["genomes"])
if options.get("setup_taxonomy_data", False):
setup_taxonomy_data()
stash_genomes_where = get_main_options_string(options, "stash_genomes")
if stash_genomes_where:
stash_genomes(stash_genomes_where)
