def install(self, local_env={}, force=False):
""" If not already installed, install given tool and all of its dependencies. """
if self.set_env(local_env):
if (not self.is_installed(local_env=local_env) and not self.tool_env['fatal_error']) or force:
if not self.tool_env['dependencies_ok']:
if not self.resolve_dependencies():
print "----- ERROR resolving dependencies -----"
return False
# Maybe the dependencies is all that was missing so check if
# the tool can be considered as installed now
if not self.is_installed(local_env=local_env) or force:
print "Trying to install %s %s as user %s" % (self.tool_env['pkg_name'], self.tool_env['version'], env.user)
# TODO: Get complete file name list
files = ['datagen.py']
install_cmd = sudo if self.tool_env['use_sudo'] else run
if not exists(self.tool_env['install_dir']):
install_cmd("mkdir -p %s" % self.tool_env['install_dir'])
install_cmd("chown %s %s" % (self.tool_env['user'], self.tool_env['install_dir']))
with nested(cd(self.tool_env['install_dir']), settings(hide('stdout'))):
for f in files:
install_cmd("wget --no-check-certificate %s" % (self.tool_env['url']+f))
if self.tool_env.has_key('shogun_env_script') and exists(self.tool_env['shogun_env_script']):
install_cmd("echo '. %s' > %s/env.sh" % (self.tool_env['shogun_env_script'], self.tool_env['install_dir']))
install_cmd("chmod +x %s/env.sh" % self.tool_env['install_dir'])
install_cmd('chown -R %s %s' % (env.user, self.tool_env['install_dir']))
else:
print "ERROR: Required dependency file for not found (for Shogun)."
self.tool_env['fatal_error'] = True
# Make sure the tool installed correctly
if not self.tool_env['fatal_error'] and (self.tool_env['installed'] or self.is_installed()):
return common.compose_successful_return(self.tool_env)
print "----- Problem installing EasySVM -----"
return self.tool_env
def decorator(*args, **kwargs):
with settings(
hide('warnings', 'running', 'stdout', 'stderr'),
warn_only=True):
result = run(pname)
if result.return_code in [0, 1]:
return func(*args, **kwargs)
def install_proftpd(env):
"""Highly configurable GPL-licensed FTP server software.
http://proftpd.org/
"""
version = "1.3.4c"
postgres_ver = "9.1"
url = "ftp://ftp.tpnet.pl/pub/linux/proftpd/distrib/source/proftpd-%s.tar.gz" % version
modules = "mod_sql:mod_sql_postgres:mod_sql_passwd"
extra_modules = env.get("extra_proftp_modules",
"") # Comma separated list of extra modules
if extra_modules:
modules = "%s:%s" % (modules, extra_modules.replace(",", ":"))
install_dir = os.path.join(env.install_dir, 'proftpd')
remote_conf_dir = os.path.join(install_dir, "etc")
# skip install if already present
if exists(remote_conf_dir):
env.logger.debug(
"ProFTPd seems to already be installed in {0}".format(install_dir))
return
with _make_tmp_dir() as work_dir:
with cd(work_dir):
run("wget %s" % url)
with settings(hide('stdout')):
run("tar xvzf %s" % os.path.split(url)[1])
with cd("proftpd-%s" % version):
run("CFLAGS='-I/usr/include/postgresql' ./configure --prefix=%s " \
"--disable-auth-file --disable-ncurses --disable-ident --disable-shadow " \
"--enable-openssl --with-modules=%s " \
"--with-libraries=/usr/lib/postgresql/%s/lib" % (install_dir, modules, postgres_ver))
sudo("make")
sudo("make install")
sudo("make clean")
# Get the init.d startup script
initd_script = 'proftpd.initd'
initd_url = os.path.join(REPO_ROOT_URL, 'conf_files', initd_script)
remote_file = "/etc/init.d/proftpd"
sudo("wget --output-document=%s %s" % (remote_file, initd_url))
sed(remote_file,
'REPLACE_THIS_WITH_CUSTOM_INSTALL_DIR',
install_dir,
use_sudo=True)
sudo("chmod 755 %s" % remote_file)
# Set the configuration file
conf_file = 'proftpd.conf'
conf_url = os.path.join(REPO_ROOT_URL, 'conf_files', conf_file)
remote_file = os.path.join(remote_conf_dir, conf_file)
sudo("wget --output-document=%s %s" % (remote_file, conf_url))
sed(remote_file,
'REPLACE_THIS_WITH_CUSTOM_INSTALL_DIR',
install_dir,
use_sudo=True)
# Get the custom welcome msg file
welcome_msg_file = 'welcome_msg.txt'
welcome_url = os.path.join(REPO_ROOT_URL, 'conf_files', welcome_msg_file)
sudo("wget --output-document=%s %s" %
(os.path.join(remote_conf_dir, welcome_msg_file), welcome_url))
# Stow
sudo("cd %s; stow proftpd" % env.install_dir)
env.logger.debug("----- ProFTPd %s installed to %s -----" %
(version, install_dir))
def install_proftpd(env):
version = "1.3.3d"
postgres_ver = "8.4"
url = "ftp://mirrors.ibiblio.org/proftpd/distrib/source/proftpd-%s.tar.gz" % version
install_dir = os.path.join(env.install_dir, 'proftpd')
remote_conf_dir = os.path.join(install_dir, "etc")
# skip install if already present
if exists(remote_conf_dir):
return
with _make_tmp_dir() as work_dir:
with cd(work_dir):
run("wget %s" % url)
with settings(hide('stdout')):
run("tar xvzf %s" % os.path.split(url)[1])
with cd("proftpd-%s" % version):
run("CFLAGS='-I/usr/include/postgresql' ./configure --prefix=%s --disable-auth-file --disable-ncurses --disable-ident --disable-shadow --enable-openssl --with-modules=mod_sql:mod_sql_postgres:mod_sql_passwd --with-libraries=/usr/lib/postgres/%s/lib" % (install_dir, postgres_ver))
sudo("make")
sudo("make install")
sudo("make clean")
# Get init.d startup script
initd_script = 'proftpd'
initd_url = os.path.join(REPO_ROOT_URL, 'conf_files', initd_script)
sudo("wget --output-document=%s %s" % (os.path.join('/etc/init.d', initd_script), initd_url))
sudo("chmod 755 %s" % os.path.join('/etc/init.d', initd_script))
# Get configuration files
proftpd_conf_file = 'proftpd.conf'
welcome_msg_file = 'welcome_msg.txt'
conf_url = os.path.join(REPO_ROOT_URL, 'conf_files', proftpd_conf_file)
welcome_url = os.path.join(REPO_ROOT_URL, 'conf_files', welcome_msg_file)
sudo("wget --output-document=%s %s" % (os.path.join(remote_conf_dir, proftpd_conf_file), conf_url))
sudo("wget --output-document=%s %s" % (os.path.join(remote_conf_dir, welcome_msg_file), welcome_url))
sudo("cd %s; stow proftpd" % env.install_dir)
def start_services(site_name):
run('sudo service nginx reload')
with settings(
hide('warnings'),
warn_only=True
):
run('sudo start gunicorn-%s' % site_name)
def install(self, local_env={}):
""" If not already installed, install given tool and all of its dependencies. """
if self.set_env(local_env):
if not self.is_installed(local_env=local_env):
print "Trying to install %s %s as user %s" % (self.tool_env['pkg_name'], self.tool_env['version'], env.user)
packages = ['gcc', 'g++', 'octave3.0-headers', 'python-dev', 'python-numpy',
'liblapack-dev', 'libatlas3gf-base', 'python-numpy-ext', 'python-matplotlib',
'swig']
common.install_required_packages(packages)
install_cmd = sudo if self.tool_env['use_sudo'] else run
with common.make_tmp_dir(self.tool_env) as work_dir:
with nested(cd(work_dir), settings(hide('stdout'))):
install_cmd("wget %s" % self.tool_env['url'])
install_cmd("tar xvjf %s" % os.path.split(self.tool_env['url'])[1])
with cd("shogun-%s/src" % self.tool_env['version']):
install_cmd("./configure --prefix=%s --interfaces=libshogun,libshogunui,python,python_modular,octave" % self.tool_env['install_dir'])
print "Making Shogun..."
install_cmd("make")
install_cmd("make install")
install_cmd("echo 'export LD_LIBRARY_PATH=%s/lib:$LD_LIBRARY_PATH' > %s/env.sh" % (self.tool_env['install_dir'], self.tool_env['install_dir']))
install_cmd("cd %s/lib; ln -s python* python" % self.tool_env['install_dir'])
install_cmd("echo 'export PYTHONPATH=%s/lib/python/dist-packages:$PYTHONPATH' >> %s/env.sh" % (self.tool_env['install_dir'], self.tool_env['install_dir']))
install_cmd("chmod +x %s/env.sh" % self.tool_env['install_dir'])
install_dir_root = os.path.join(self.tool_env['install_dir_root'], self.tool_env['pkg_name'])
install_cmd('if [ ! -d %s/default ]; then ln -s %s %s/default; fi' % (install_dir_root, self.tool_env['install_dir'], install_dir_root))
install_cmd('chown -R %s:%s %s' % (env.user, env.user, install_dir_root))
if self.tool_env['installed'] or self.is_installed():
return common.compose_successful_return(self.tool_env)
print "----- Problem installing Shogun -----"
return self.tool_env
def _install_postgresql():
version = "8.4.4"
url = "http://wwwmaster.postgresql.org/redir/198/h/source/v%s/postgresql-%s.tar.gz" % (version, version)
install_dir = os.path.join(env.install_dir, "postgresql")
with _make_tmp_dir() as work_dir:
with contextlib.nested(cd(work_dir), settings(hide('stdout'))):
run("wget %s" % url)
run("tar xvzf %s" % os.path.split(url)[1])
with cd("postgresql-%s" % version):
run("./configure --prefix=%s" % install_dir)
with settings(hide('stdout')):
print "Making PostgreSQL..."
run("make")
sudo("make install")
sudo("cd %s; stow postgresql" % env.install_dir)
print(green("----- PostgreSQL installed -----"))
def _create_virtual_host(source_folder, site_name):
run('''cd %s && sed "s/SITENAME/%s/g" deploy_tools/nginx.template.conf | sudo tee /etc/nginx/sites-available/%s''' %
(source_folder, site_name, site_name))
with settings(
hide('warnings'),
warn_only=True
):
run('''sudo ln -s /etc/nginx/sites-available/%s /etc/nginx/sites-enabled/%s''' % (site_name, site_name))
def _install_boto():
install_dir = env.install_dir + "/boto"
with contextlib.nested(cd(env.install_dir), settings(hide('stdout'))):
sudo("git clone http://github.com/boto/boto.git")
with cd(install_dir):
sudo("python setup.py install")
version = run('python -c"import boto; print boto.__version__"')
print(green("----- boto %s installed -----" % version))
def install_proftpd(env):
"""Highly configurable GPL-licensed FTP server software.
http://proftpd.org/
"""
version = "1.3.4c"
postgres_ver = "9.1"
url = "ftp://ftp.tpnet.pl/pub/linux/proftpd/distrib/source/proftpd-%s.tar.gz" % version
modules = "mod_sql:mod_sql_postgres:mod_sql_passwd"
extra_modules = env.get("extra_proftp_modules", "") # Comma separated list of extra modules
if extra_modules:
modules = "%s:%s" % (modules, extra_modules.replace(",", ":"))
install_dir = os.path.join(env.install_dir, 'proftpd')
remote_conf_dir = os.path.join(install_dir, "etc")
# Skip install if already available
if env.safe_exists(remote_conf_dir):
env.logger.debug("ProFTPd seems to already be installed in {0}".format(install_dir))
return
with _make_tmp_dir() as work_dir:
with cd(work_dir):
env.safe_run("wget %s" % url)
with settings(hide('stdout')):
env.safe_run("tar xvzf %s" % os.path.split(url)[1])
with cd("proftpd-%s" % version):
env.safe_run("CFLAGS='-I/usr/include/postgresql' ./configure --prefix=%s "
"--disable-auth-file --disable-ncurses --disable-ident --disable-shadow "
"--enable-openssl --with-modules=%s "
"--with-libraries=/usr/lib/postgresql/%s/lib" % (install_dir, modules, postgres_ver))
env.safe_sudo("make")
env.safe_sudo("make install")
env.safe_sudo("make clean")
# Get the init.d startup script
initd_script = 'proftpd.initd'
initd_url = os.path.join(REPO_ROOT_URL, 'conf_files', initd_script)
remote_file = "/etc/init.d/proftpd"
env.safe_sudo("wget --output-document=%s %s" % (remote_file, initd_url))
env.safe_sed(remote_file, 'REPLACE_THIS_WITH_CUSTOM_INSTALL_DIR', install_dir, use_sudo=True)
env.safe_sudo("chmod 755 %s" % remote_file)
# Set the configuration file
conf_file = 'proftpd.conf'
remote_file = os.path.join(remote_conf_dir, conf_file)
if "postgres_port" not in env:
env.postgres_port = '5910'
if "galaxy_ftp_user_password" not in env:
env.galaxy_ftp_user_password = '******'
proftpd_conf = {'galaxy_uid': env.safe_run('id -u galaxy'),
'galaxy_fs': '/mnt/galaxy', # Should be a var but uncertain how to get it
'install_dir': install_dir}
_setup_conf_file(env, remote_file, conf_file, overrides=proftpd_conf,
default_source="proftpd.conf.template")
# Get the custom welcome msg file
welcome_msg_file = 'welcome_msg.txt'
welcome_url = os.path.join(REPO_ROOT_URL, 'conf_files', welcome_msg_file)
env.safe_sudo("wget --output-document=%s %s" %
(os.path.join(remote_conf_dir, welcome_msg_file), welcome_url))
# Stow
env.safe_sudo("cd %s; stow proftpd" % env.install_dir)
env.logger.debug("----- ProFTPd %s installed to %s -----" % (version, install_dir))
def install_proftpd(env):
"""Highly configurable GPL-licensed FTP server software.
http://proftpd.org/
"""
version = "1.3.4c"
postgres_ver = "9.1"
url = "ftp://ftp.tpnet.pl/pub/linux/proftpd/distrib/source/proftpd-%s.tar.gz" % version
modules = "mod_sql:mod_sql_postgres:mod_sql_passwd"
extra_modules = env.get("extra_proftp_modules", "") # Comma separated list of extra modules
if extra_modules:
modules = "%s:%s" % (modules, extra_modules.replace(",", ":"))
install_dir = os.path.join(env.install_dir, 'proftpd')
remote_conf_dir = os.path.join(install_dir, "etc")
# Skip install if already available
if env.safe_exists(remote_conf_dir):
env.logger.debug("ProFTPd seems to already be installed in {0}".format(install_dir))
return
with _make_tmp_dir() as work_dir:
with cd(work_dir):
env.safe_run("wget %s" % url)
with settings(hide('stdout')):
env.safe_run("tar xvzf %s" % os.path.split(url)[1])
with cd("proftpd-%s" % version):
env.safe_run("CFLAGS='-I/usr/include/postgresql' ./configure --prefix=%s "
"--disable-auth-file --disable-ncurses --disable-ident --disable-shadow "
"--enable-openssl --with-modules=%s "
"--with-libraries=/usr/lib/postgresql/%s/lib" % (install_dir, modules, postgres_ver))
env.safe_sudo("make")
env.safe_sudo("make install")
env.safe_sudo("make clean")
# Get the init.d startup script
initd_script = 'proftpd.initd'
initd_url = os.path.join(REPO_ROOT_URL, 'conf_files', initd_script)
remote_file = "/etc/init.d/proftpd"
env.safe_sudo("wget --output-document=%s %s" % (remote_file, initd_url))
env.safe_sed(remote_file, 'REPLACE_THIS_WITH_CUSTOM_INSTALL_DIR', install_dir, use_sudo=True)
env.safe_sudo("chmod 755 %s" % remote_file)
# Set the configuration file
conf_file = 'proftpd.conf'
remote_file = os.path.join(remote_conf_dir, conf_file)
if "postgres_port" not in env:
env.postgres_port = '5910'
if "galaxy_ftp_user_password" not in env:
env.galaxy_ftp_user_password = '******'
proftpd_conf = {'galaxy_uid': env.safe_run('id -u galaxy'),
'galaxy_fs': '/mnt/galaxy', # Should be a var but uncertain how to get it
'install_dir': install_dir}
_setup_conf_file(env, remote_file, conf_file, overrides=proftpd_conf,
default_source="proftpd.conf.template")
# Get the custom welcome msg file
welcome_msg_file = 'welcome_msg.txt'
welcome_url = os.path.join(REPO_ROOT_URL, 'conf_files', welcome_msg_file)
env.safe_sudo("wget --output-document=%s %s" %
(os.path.join(remote_conf_dir, welcome_msg_file), welcome_url))
# Stow
env.safe_sudo("cd %s; stow proftpd" % env.install_dir)
env.logger.debug("----- ProFTPd %s installed to %s -----" % (version, install_dir))
def install_sge(env):
out_dir = "ge6.2u5"
url = "%s/ge62u5_lx24-amd64.tar.gz" % CDN_ROOT_URL
install_dir = env.install_dir
if exists(os.path.join(install_dir, out_dir)):
return
with _make_tmp_dir() as work_dir:
with contextlib.nested(cd(work_dir), settings(hide('stdout'))):
run("wget %s" % url)
sudo("chown %s %s" % (env.user, install_dir))
run("tar -C %s -xvzf %s" % (install_dir, os.path.split(url)[1]))
def install_sge(env):
out_dir = "ge6.2u5"
url = "%s/ge62u5_lx24-amd64.tar.gz" % CDN_ROOT_URL
install_dir = env.install_dir
if exists(os.path.join(install_dir, out_dir)):
return
with _make_tmp_dir() as work_dir:
with contextlib.nested(cd(work_dir), settings(hide('stdout'))):
run("wget %s" % url)
sudo("chown %s %s" % (env.user, install_dir))
run("tar -C %s -xvzf %s" % (install_dir, os.path.split(url)[1]))
def install_nginx(env):
"""Nginx open source web server.
http://www.nginx.org/
"""
version = "1.2.0"
url = "http://nginx.org/download/nginx-%s.tar.gz" % version
install_dir = os.path.join(env.install_dir, "nginx")
remote_conf_dir = os.path.join(install_dir, "conf")
# Skip install if already present
if exists(remote_conf_dir) and contains(os.path.join(remote_conf_dir, "nginx.conf"), "/cloud"):
env.logger.debug("Nginx already installed; not installing it again.")
return
with _make_tmp_dir() as work_dir:
with contextlib.nested(cd(work_dir), settings(hide('stdout'))):
modules = _get_nginx_modules(env)
module_flags = " ".join(["--add-module=../%s" % x for x in modules])
run("wget %s" % url)
run("tar xvzf %s" % os.path.split(url)[1])
with cd("nginx-%s" % version):
run("./configure --prefix=%s --with-ipv6 %s "
"--user=galaxy --group=galaxy --with-debug "
"--with-http_ssl_module --with-http_gzip_static_module" %
(install_dir, module_flags))
sed("objs/Makefile", "-Werror", "")
run("make")
sudo("make install")
sudo("cd %s; stow nginx" % env.install_dir)
nginx_conf_file = 'nginx.conf'
url = os.path.join(REPO_ROOT_URL, nginx_conf_file)
with cd(remote_conf_dir):
sudo("wget --output-document=%s/%s %s" % (remote_conf_dir, nginx_conf_file, url))
nginx_errdoc_file = 'nginx_errdoc.tar.gz'
url = os.path.join(REPO_ROOT_URL, nginx_errdoc_file)
remote_errdoc_dir = os.path.join(install_dir, "html")
with cd(remote_errdoc_dir):
sudo("wget --output-document=%s/%s %s" % (remote_errdoc_dir, nginx_errdoc_file, url))
sudo('tar xvzf %s' % nginx_errdoc_file)
sudo("mkdir -p %s" % env.install_dir)
if not exists("%s/nginx" % env.install_dir):
sudo("ln -s %s/sbin/nginx %s/nginx" % (install_dir, env.install_dir))
# If the guessed symlinking did not work, force it now
cloudman_default_dir = "/opt/galaxy/sbin"
if not exists(cloudman_default_dir):
sudo("mkdir -p %s" % cloudman_default_dir)
if not exists(os.path.join(cloudman_default_dir, "nginx")):
sudo("ln -s %s/sbin/nginx %s/nginx" % (install_dir, cloudman_default_dir))
env.logger.debug("Nginx {0} installed to {1}".format(version, install_dir))
def install_nginx(env):
"""Nginx open source web server.
http://www.nginx.org/
"""
version = "1.2.0"
url = "http://nginx.org/download/nginx-%s.tar.gz" % version
install_dir = os.path.join(env.install_dir, "nginx")
remote_conf_dir = os.path.join(install_dir, "conf")
# Skip install if already present
if exists(remote_conf_dir) and contains(os.path.join(remote_conf_dir, "nginx.conf"), "/cloud"):
env.logger.debug("Nginx already installed; not installing it again.")
return
with _make_tmp_dir() as work_dir:
with contextlib.nested(cd(work_dir), settings(hide('stdout'))):
modules = _get_nginx_modules(env)
module_flags = " ".join(["--add-module=../%s" % x for x in modules])
run("wget %s" % url)
run("tar xvzf %s" % os.path.split(url)[1])
with cd("nginx-%s" % version):
run("./configure --prefix=%s --with-ipv6 %s "
"--user=galaxy --group=galaxy --with-debug "
"--with-http_ssl_module --with-http_gzip_static_module" %
(install_dir, module_flags))
sed("objs/Makefile", "-Werror", "")
run("make")
sudo("make install")
sudo("cd %s; stow nginx" % env.install_dir)
defaults = {"galaxy_home": "/mnt/galaxyTools/galaxy-central"}
_setup_conf_file(env, os.path.join(remote_conf_dir, "nginx.conf"), "nginx.conf", defaults=defaults)
nginx_errdoc_file = 'nginx_errdoc.tar.gz'
url = os.path.join(REPO_ROOT_URL, nginx_errdoc_file)
remote_errdoc_dir = os.path.join(install_dir, "html")
with cd(remote_errdoc_dir):
sudo("wget --output-document=%s/%s %s" % (remote_errdoc_dir, nginx_errdoc_file, url))
sudo('tar xvzf %s' % nginx_errdoc_file)
sudo("mkdir -p %s" % env.install_dir)
if not exists("%s/nginx" % env.install_dir):
sudo("ln -s %s/sbin/nginx %s/nginx" % (install_dir, env.install_dir))
# If the guessed symlinking did not work, force it now
cloudman_default_dir = "/opt/galaxy/sbin"
if not exists(cloudman_default_dir):
sudo("mkdir -p %s" % cloudman_default_dir)
if not exists(os.path.join(cloudman_default_dir, "nginx")):
sudo("ln -s %s/sbin/nginx %s/nginx" % (install_dir, cloudman_default_dir))
env.logger.debug("Nginx {0} installed to {1}".format(version, install_dir))
def install_proftpd(env):
"""Highly configurable GPL-licensed FTP server software.
http://proftpd.org/
"""
version = "1.3.4c"
postgres_ver = "9.1"
url = "ftp://ftp.tpnet.pl/pub/linux/proftpd/distrib/source/proftpd-%s.tar.gz" % version
modules = "mod_sql:mod_sql_postgres:mod_sql_passwd"
extra_modules = env.get("extra_proftp_modules", "") # Comma separated list of extra modules
if extra_modules:
modules = "%s:%s" % (modules, extra_modules.replace(",", ":"))
install_dir = os.path.join(env.install_dir, 'proftpd')
remote_conf_dir = os.path.join(install_dir, "etc")
# skip install if already present
if exists(remote_conf_dir):
env.logger.debug("ProFTPd seems to already be installed in {0}".format(install_dir))
return
with _make_tmp_dir() as work_dir:
with cd(work_dir):
run("wget %s" % url)
with settings(hide('stdout')):
run("tar xvzf %s" % os.path.split(url)[1])
with cd("proftpd-%s" % version):
run("CFLAGS='-I/usr/include/postgresql' ./configure --prefix=%s " \
"--disable-auth-file --disable-ncurses --disable-ident --disable-shadow " \
"--enable-openssl --with-modules=%s " \
"--with-libraries=/usr/lib/postgresql/%s/lib" % (install_dir, modules, postgres_ver))
sudo("make")
sudo("make install")
sudo("make clean")
# Get the init.d startup script
initd_script = 'proftpd.initd'
initd_url = os.path.join(REPO_ROOT_URL, 'conf_files', initd_script)
remote_file = "/etc/init.d/proftpd"
sudo("wget --output-document=%s %s" % (remote_file, initd_url))
sed(remote_file, 'REPLACE_THIS_WITH_CUSTOM_INSTALL_DIR', install_dir, use_sudo=True)
sudo("chmod 755 %s" % remote_file)
# Set the configuration file
conf_file = 'proftpd.conf'
conf_url = os.path.join(REPO_ROOT_URL, 'conf_files', conf_file)
remote_file = os.path.join(remote_conf_dir, conf_file)
sudo("wget --output-document=%s %s" % (remote_file, conf_url))
sed(remote_file, 'REPLACE_THIS_WITH_CUSTOM_INSTALL_DIR', install_dir, use_sudo=True)
# Get the custom welcome msg file
welcome_msg_file = 'welcome_msg.txt'
welcome_url = os.path.join(REPO_ROOT_URL, 'conf_files', welcome_msg_file)
sudo("wget --output-document=%s %s" % (os.path.join(remote_conf_dir, welcome_msg_file), welcome_url))
# Stow
sudo("cd %s; stow proftpd" % env.install_dir)
env.logger.debug("----- ProFTPd %s installed to %s -----" % (version, install_dir))
def _get_sge():
sge_dir = 'ge6.2u5'
url = "%s/ge62u5_lx24-amd64.tar.gz" % CDN_ROOT_URL
install_dir = env.install_dir
if not exists(os.path.join(install_dir, sge_dir, 'ge-6.2u5-bin-lx24-amd64.tar.gz') or \
os.path.join(install_dir, sge_dir, 'ge-6.2u5-common.tar.gz')):
with _make_tmp_dir() as work_dir:
with contextlib.nested(cd(work_dir), settings(hide('stdout'))):
run("wget %s" % url)
sudo("chown %s %s" % (env.user, install_dir))
run("tar -C %s -xvzf %s" % (install_dir, os.path.split(url)[1]))
print(green("----- SGE downloaded and extracted to '%s' -----" % install_dir))
else:
print(green("SGE already exists at '%s'" % install_dir))
def install_sge(env):
"""Sun Grid Engine.
"""
out_dir = "ge6.2u5"
url = "%s/ge62u5_lx24-amd64.tar.gz" % CDN_ROOT_URL
install_dir = env.install_dir
if env.safe_exists(os.path.join(install_dir, out_dir)):
return
with _make_tmp_dir() as work_dir:
with contextlib.nested(cd(work_dir), settings(hide('stdout'))):
env.safe_run("wget %s" % url)
env.safe_sudo("chown %s %s" % (env.user, install_dir))
env.safe_run("tar -C %s -xvzf %s" % (install_dir, os.path.split(url)[1]))
env.logger.debug("SGE setup")
def install_sge(env):
"""Sun Grid Engine.
"""
out_dir = "ge6.2u5"
url = "%s/ge62u5_lx24-amd64.tar.gz" % CDN_ROOT_URL
install_dir = env.install_dir
if env.safe_exists(os.path.join(install_dir, out_dir)):
return
with _make_tmp_dir() as work_dir:
with contextlib.nested(cd(work_dir), settings(hide('stdout'))):
env.safe_run("wget %s" % url)
env.safe_sudo("chown %s %s" % (env.user, install_dir))
env.safe_run("tar -C %s -xvzf %s" % (install_dir, os.path.split(url)[1]))
env.logger.debug("SGE setup")
def install_nginx(env):
version = "0.7.67"
upload_module_version = "2.0.12"
upload_url = "http://www.grid.net.ru/nginx/download/" \
"nginx_upload_module-%s.tar.gz" % upload_module_version
url = "http://nginx.org/download/nginx-%s.tar.gz" % version
install_dir = os.path.join(env.install_dir, "nginx")
remote_conf_dir = os.path.join(install_dir, "conf")
# skip install if already present
if exists(remote_conf_dir) and contains(
os.path.join(remote_conf_dir, "nginx.conf"), "/cloud"):
return
with _make_tmp_dir() as work_dir:
with contextlib.nested(cd(work_dir), settings(hide('stdout'))):
run("wget %s" % upload_url)
run("tar -xvzpf %s" % os.path.split(upload_url)[1])
run("wget %s" % url)
run("tar xvzf %s" % os.path.split(url)[1])
with cd("nginx-%s" % version):
run("./configure --prefix=%s --with-ipv6 --add-module=../nginx_upload_module-%s --user=galaxy --group=galaxy --with-http_ssl_module --with-http_gzip_static_module"
% (install_dir, upload_module_version))
run("make")
sudo("make install")
sudo("cd %s; stow nginx" % env.install_dir)
nginx_conf_file = 'nginx.conf'
url = os.path.join(REPO_ROOT_URL, nginx_conf_file)
with cd(remote_conf_dir):
sudo("wget --output-document=%s/%s %s" %
(remote_conf_dir, nginx_conf_file, url))
nginx_errdoc_file = 'nginx_errdoc.tar.gz'
url = os.path.join(REPO_ROOT_URL, nginx_errdoc_file)
remote_errdoc_dir = os.path.join(install_dir, "html")
with cd(remote_errdoc_dir):
sudo("wget --output-document=%s/%s %s" %
(remote_errdoc_dir, nginx_errdoc_file, url))
sudo('tar xvzf %s' % nginx_errdoc_file)
cloudman_default_dir = "/opt/galaxy/sbin"
sudo("mkdir -p %s" % cloudman_default_dir)
if not exists("%s/nginx" % cloudman_default_dir):
sudo("ln -s %s/sbin/nginx %s/nginx" %
(install_dir, cloudman_default_dir))
def _mount_ebs():
with v_settings(host_string=env.hosts[0]):
if not exists(DEST_DATA_DIR):
sudo("mkdir -p %s" % DEST_DATA_DIR)
# Check if DEST_DATA_DIR is empty before attempting to mount
with settings(hide('stderr'), warn_only=True):
result = sudo('[ "$(ls -A %s)" ]' % DEST_DATA_DIR)
if result.failed:
print "Directory '%s' is empty. Good." % DEST_DATA_DIR
if not SNAP_ID:
# If not recreating a volume from a snapshot, create file system before mounting
sudo("mkfs.xfs %s" % env.vol_device)
sudo("mount -t xfs %s %s" % (env.vol_device, DEST_DATA_DIR))
sudo("chown %s %s" % (env.user, DEST_DATA_DIR))
else:
print "ERROR: data dir '%s' is not empty? Did not mount device '%s'" % (DEST_DATA_DIR, env.vol_device)
def install(self, local_env={}, force=False):
""" If not already installed, install given tool and all of its dependencies. """
if self.set_env(local_env):
if (not self.is_installed(local_env=local_env)
and not self.tool_env['fatal_error']) or force:
if not self.tool_env['dependencies_ok']:
if not self.resolve_dependencies():
print "----- ERROR resolving dependencies -----"
return False
# Maybe the dependencies is all that was missing so check if
# the tool can be considered as installed now
if not self.is_installed(local_env=local_env) or force:
print "Trying to install %s %s as user %s" % (
self.tool_env['pkg_name'], self.tool_env['version'],
env.user)
# TODO: Get complete file name list
files = ['datagen.py']
install_cmd = sudo if self.tool_env['use_sudo'] else run
if not exists(self.tool_env['install_dir']):
install_cmd("mkdir -p %s" %
self.tool_env['install_dir'])
install_cmd("chown %s %s" %
(self.tool_env['user'],
self.tool_env['install_dir']))
with nested(cd(self.tool_env['install_dir']),
settings(hide('stdout'))):
for f in files:
install_cmd("wget --no-check-certificate %s" %
(self.tool_env['url'] + f))
if self.tool_env.has_key('shogun_env_script') and exists(
self.tool_env['shogun_env_script']):
install_cmd("echo '. %s' > %s/env.sh" %
(self.tool_env['shogun_env_script'],
self.tool_env['install_dir']))
install_cmd("chmod +x %s/env.sh" %
self.tool_env['install_dir'])
install_cmd('chown -R %s %s' %
(env.user, self.tool_env['install_dir']))
else:
print "ERROR: Required dependency file for not found (for Shogun)."
self.tool_env['fatal_error'] = True
# Make sure the tool installed correctly
if not self.tool_env['fatal_error'] and (self.tool_env['installed']
or self.is_installed()):
return common.compose_successful_return(self.tool_env)
print "----- Problem installing EasySVM -----"
return self.tool_env
def _install_nginx():
version = "1.2.0"
upload_module_version = "2.2.0"
upload_url = "http://www.grid.net.ru/nginx/download/" \
"nginx_upload_module-%s.tar.gz" % upload_module_version
url = "http://nginx.org/download/nginx-%s.tar.gz" % version
install_dir = os.path.join(env.install_dir, "nginx")
remote_conf_dir = os.path.join(install_dir, "conf")
# skip install if already present
if exists(remote_conf_dir) and contains(os.path.join(remote_conf_dir, "nginx.conf"), "/cloud"):
return
with _make_tmp_dir() as work_dir:
with contextlib.nested(cd(work_dir), settings(hide('stdout'))):
run("wget %s" % upload_url)
run("tar -xvzpf %s" % os.path.split(upload_url)[1])
run("wget %s" % url)
run("tar xvzf %s" % os.path.split(url)[1])
with cd("nginx-%s" % version):
run("./configure --prefix=%s --with-ipv6 --add-module=../nginx_upload_module-%s "
"--user=galaxy --group=galaxy --with-http_ssl_module --with-http_gzip_static_module "
"--with-cc-opt=-Wno-error --with-debug" % (install_dir, upload_module_version))
run("make")
sudo("make install")
with settings(warn_only=True):
sudo("cd %s; stow nginx" % env.install_dir)
nginx_conf_file = 'nginx.conf'
url = os.path.join(REPO_ROOT_URL, nginx_conf_file)
with cd(remote_conf_dir):
sudo("wget --output-document=%s/%s %s" % (remote_conf_dir, nginx_conf_file, url))
nginx_errdoc_file = 'nginx_errdoc.tar.gz'
url = os.path.join(REPO_ROOT_URL, nginx_errdoc_file)
remote_errdoc_dir = os.path.join(install_dir, "html")
with cd(remote_errdoc_dir):
sudo("wget --output-document=%s/%s %s" % (remote_errdoc_dir, nginx_errdoc_file, url))
sudo('tar xvzf %s' % nginx_errdoc_file)
cloudman_default_dir = "/opt/cloudman/sbin"
sudo("mkdir -p %s" % cloudman_default_dir)
if not exists("%s/nginx" % cloudman_default_dir):
sudo("ln -s %s/sbin/nginx %s/nginx" % (install_dir, cloudman_default_dir))
print(green("----- nginx installed and configured -----"))
def install_nginx(env):
version = "0.7.67"
url = "http://nginx.org/download/nginx-%s.tar.gz" % version
install_dir = os.path.join(env.install_dir, "nginx")
remote_conf_dir = os.path.join(install_dir, "conf")
# skip install if already present
if exists(remote_conf_dir) and contains(
os.path.join(remote_conf_dir, "nginx.conf"), "/cloud"):
return
with _make_tmp_dir() as work_dir:
with contextlib.nested(cd(work_dir), settings(hide('stdout'))):
modules = _get_nginx_modules(env)
module_flags = " ".join(
["--add-module=../%s" % x for x in modules])
run("wget %s" % url)
run("tar xvzf %s" % os.path.split(url)[1])
with cd("nginx-%s" % version):
run("./configure --prefix=%s --with-ipv6 %s "
"--user=galaxy --group=galaxy "
"--with-http_ssl_module --with-http_gzip_static_module" %
(install_dir, module_flags))
sed("objs/Makefile", "-Werror", "")
run("make")
sudo("make install")
sudo("cd %s; stow nginx" % env.install_dir)
nginx_conf_file = 'nginx.conf'
url = os.path.join(REPO_ROOT_URL, nginx_conf_file)
with cd(remote_conf_dir):
sudo("wget --output-document=%s/%s %s" %
(remote_conf_dir, nginx_conf_file, url))
nginx_errdoc_file = 'nginx_errdoc.tar.gz'
url = os.path.join(REPO_ROOT_URL, nginx_errdoc_file)
remote_errdoc_dir = os.path.join(install_dir, "html")
with cd(remote_errdoc_dir):
sudo("wget --output-document=%s/%s %s" %
(remote_errdoc_dir, nginx_errdoc_file, url))
sudo('tar xvzf %s' % nginx_errdoc_file)
sudo("mkdir -p %s" % env.install_dir)
if not exists("%s/nginx" % env.install_dir):
sudo("ln -s %s/sbin/nginx %s/nginx" % (install_dir, env.install_dir))
def is_installed(self, local_env={}):
""" Check if the current tool and its dependencies are installed. Optionally,
missing dependencies may be installed."""
if not self.tool_env['env_set']:
self.set_env(local_env)
print "Checking if %s %s is installed..." % (self.tool_env['pkg_name'], self.tool_env['version'])
if not self.tool_env['dependencies_ok']:
if not self.resolve_dependencies(install=False):
return False
install_cmd = sudo if self.tool_env['use_sudo'] else run
with nested(cd(self.tool_env['install_dir']), settings(hide('stdout'), warn_only=True)):
result = install_cmd("source env.sh; python kirmes.py --help")
if result.return_code == 0:
self.tool_env['installed'] = True
print "%s %s is installed in %s" % (str(self.tool_env['pkg_name']).upper(), self.tool_env['version'], self.tool_env['install_dir'])
return True
print "%s %s is not installed." % (self.tool_env['pkg_name'], self.tool_env['version'])
return False
def install_nginx(env):
version = "0.7.67"
url = "http://nginx.org/download/nginx-%s.tar.gz" % version
install_dir = os.path.join(env.install_dir, "nginx")
remote_conf_dir = os.path.join(install_dir, "conf")
# skip install if already present
if exists(remote_conf_dir) and contains(os.path.join(remote_conf_dir, "nginx.conf"), "/cloud"):
return
with _make_tmp_dir() as work_dir:
with contextlib.nested(cd(work_dir), settings(hide("stdout"))):
modules = _get_nginx_modules(env)
module_flags = " ".join(["--add-module=../%s" % x for x in modules])
run("wget %s" % url)
run("tar xvzf %s" % os.path.split(url)[1])
with cd("nginx-%s" % version):
run(
"./configure --prefix=%s --with-ipv6 %s "
"--user=galaxy --group=galaxy "
"--with-http_ssl_module --with-http_gzip_static_module" % (install_dir, module_flags)
)
sed("objs/Makefile", "-Werror", "")
run("make")
sudo("make install")
sudo("cd %s; stow nginx" % env.install_dir)
nginx_conf_file = "nginx.conf"
url = os.path.join(REPO_ROOT_URL, nginx_conf_file)
with cd(remote_conf_dir):
sudo("wget --output-document=%s/%s %s" % (remote_conf_dir, nginx_conf_file, url))
nginx_errdoc_file = "nginx_errdoc.tar.gz"
url = os.path.join(REPO_ROOT_URL, nginx_errdoc_file)
remote_errdoc_dir = os.path.join(install_dir, "html")
with cd(remote_errdoc_dir):
sudo("wget --output-document=%s/%s %s" % (remote_errdoc_dir, nginx_errdoc_file, url))
sudo("tar xvzf %s" % nginx_errdoc_file)
cloudman_default_dir = "/opt/galaxy/sbin"
sudo("mkdir -p %s" % cloudman_default_dir)
if not exists("%s/nginx" % cloudman_default_dir):
sudo("ln -s %s/sbin/nginx %s/nginx" % (install_dir, cloudman_default_dir))
def install(self, local_env={}, force=False):
""" If not already installed, install given tool and all of its dependencies. """
if self.set_env(local_env):
if (not self.is_installed(local_env=local_env) and not self.tool_env['fatal_error']) or force:
if not self.tool_env['dependencies_ok']:
if not self.resolve_dependencies():
print "----- ERROR resolving dependencies -----"
return False
# Maybe the dependencies is all that was missing so check if
# the tool can be considered as installed now
if not self.is_installed(local_env=local_env) or force:
print "Trying to install %s %s as user %s" % (str(self.tool_env['pkg_name']).upper(), self.tool_env['version'], env.user)
install_cmd = sudo if self.tool_env['use_sudo'] else run
with nested(cd(self.tool_env['install_dir']), settings(hide('stdout'))):
install_cmd("wget %s" % self.tool_env['url'])
install_cmd("wget %s" % self.tool_env['url2'])
install_cmd("tar xfvj %s; rm %s" % (os.path.split(self.tool_env['url'])[1], os.path.split(self.tool_env['url'])[1]))
install_cmd("tar xfvz %s; rm %s" % (os.path.split(self.tool_env['url2'])[1], os.path.split(self.tool_env['url2'])[1]))
install_cmd("mv asp-%s/* .; rm -rf asp-%s" % (self.tool_env['version'], self.tool_env['version']))
# find a way to provide xmls
if not exists('%s/tools/signals' % self.tool_env['galaxy_dir']):
install_cmd('mkdir %s/tools/signals' % self.tool_env['galaxy_dir'])
with settings(warn_only=True):
install_cmd("sed -i '1i if [ -n \"${PACKAGE_BASE+x}\" ]; then cd %s; fi' %s.sh" % (self.tool_env['install_dir'], self.tool_env['pkg_name']))
install_cmd('mv %s.xml %s.sh %s/tools/signals/' % (self.tool_env['pkg_name'], self.tool_env['pkg_name'], self.tool_env['galaxy_dir']))
install_cmd("chmod +x %s/tools/signals/%s.sh" % (self.tool_env['galaxy_dir'], self.tool_env['pkg_name']))
install_cmd('chown -R %s %s/tools/signals' % (env.user, self.tool_env['galaxy_dir']))
if self.tool_env.has_key('shogun_env_script') and exists(self.tool_env['shogun_env_script']):
install_cmd("echo '. %s' > %s/env.sh" % (self.tool_env['shogun_env_script'], self.tool_env['install_dir']))
install_cmd("echo 'export PATH=%s:$PATH' >> %s/env.sh" % (self.tool_env['install_dir'], self.tool_env['install_dir']))
install_cmd("echo 'export PYTHONPATH=%s:$PYTHONPATH' >> %s/env.sh" % (self.tool_env['install_dir'], self.tool_env['install_dir']))
install_cmd("chmod +x %s/env.sh" % self.tool_env['install_dir'])
install_dir_root = os.path.join(self.tool_env['install_dir_root'], self.tool_env['pkg_name'])
install_cmd('if [ ! -d %s/default ]; then ln -s %s %s/default; fi' % (install_dir_root, self.tool_env['install_dir'], install_dir_root))
install_cmd('chown -R %s %s' % (env.user, install_dir_root))
else:
print "ERROR: Required dependency file for not found (for Shogun)."
self.tool_env['fatal_error'] = True
# Make sure the tool installed correctly
if not self.tool_env['fatal_error'] and (self.tool_env['installed'] or self.is_installed()):
return common.compose_successful_return(self.tool_env)
print "----- Problem installing ASP -----"
return self.tool_env
def install_proftpd(env):
version = "1.3.3d"
postgres_ver = "8.4"
url = "ftp://mirrors.ibiblio.org/proftpd/distrib/source/proftpd-%s.tar.gz" % version
install_dir = os.path.join(env.install_dir, 'proftpd')
remote_conf_dir = os.path.join(install_dir, "etc")
# skip install if already present
if exists(remote_conf_dir):
return
with _make_tmp_dir() as work_dir:
with cd(work_dir):
run("wget %s" % url)
with settings(hide('stdout')):
run("tar xvzf %s" % os.path.split(url)[1])
with cd("proftpd-%s" % version):
run("CFLAGS='-I/usr/include/postgresql' ./configure --prefix=%s --disable-auth-file --disable-ncurses --disable-ident --disable-shadow --enable-openssl --with-modules=mod_sql:mod_sql_postgres:mod_sql_passwd --with-libraries=/usr/lib/postgres/%s/lib"
% (install_dir, postgres_ver))
sudo("make")
sudo("make install")
sudo("make clean")
# Get init.d startup script
initd_script = 'proftpd'
initd_url = os.path.join(REPO_ROOT_URL, 'conf_files',
initd_script)
sudo("wget --output-document=%s %s" %
(os.path.join('/etc/init.d', initd_script), initd_url))
sudo("chmod 755 %s" %
os.path.join('/etc/init.d', initd_script))
# Get configuration files
proftpd_conf_file = 'proftpd.conf'
welcome_msg_file = 'welcome_msg.txt'
conf_url = os.path.join(REPO_ROOT_URL, 'conf_files',
proftpd_conf_file)
welcome_url = os.path.join(REPO_ROOT_URL, 'conf_files',
welcome_msg_file)
sudo("wget --output-document=%s %s" % (os.path.join(
remote_conf_dir, proftpd_conf_file), conf_url))
sudo("wget --output-document=%s %s" % (os.path.join(
remote_conf_dir, welcome_msg_file), welcome_url))
sudo("cd %s; stow proftpd" % env.install_dir)
def is_installed(self, local_env={}, install_dependencies=False):
""" Check if the current tool and its dependencies are installed. Optionally,
missing dependencies may be installed."""
if not self.tool_env['env_set']:
self.set_env(local_env)
print "Checking if %s %s is installed..." % (str(
self.tool_env['pkg_name']).upper(), self.tool_env['version'])
if not self.tool_env['dependencies_ok']:
if not self.resolve_dependencies(install=False):
return False
install_cmd = sudo if self.tool_env['use_sudo'] else run
with nested(cd(self.tool_env['install_dir']),
settings(hide('stdout'), warn_only=True)):
result = install_cmd("source env.sh; asp --organism=Worm dna.fa")
if result.return_code == 0:
self.tool_env['installed'] = True
print "%s %s is installed in %s" % (
str(self.tool_env['pkg_name']).upper(),
self.tool_env['version'], self.tool_env['install_dir'])
return True
print "%s %s is not installed." % (str(
self.tool_env['pkg_name']).upper(), self.tool_env['version'])
return False
def _install_proftpd():
version = "1.3.3d"
postgres_ver = "8.4"
url = "ftp://mirrors.ibiblio.org/proftpd/distrib/source/proftpd-%s.tar.gz" % version
install_dir = os.path.join(env.install_dir, 'proftpd')
remote_conf_dir = os.path.join(install_dir, "etc")
# skip install if already present
if exists(remote_conf_dir):
return
with _make_tmp_dir() as work_dir:
with cd(work_dir):
run("wget %s" % url)
with settings(hide('stdout')):
run("tar xzf %s" % os.path.split(url)[1])
with cd("proftpd-%s" % version):
run("CFLAGS='-I/usr/include/postgresql' ./configure --prefix=%s --disable-auth-file --disable-ncurses --disable-ident --disable-shadow --enable-openssl --with-modules=mod_sql:mod_sql_postgres:mod_sql_passwd --with-libraries=/usr/lib/postgres/%s/lib" % (install_dir, postgres_ver))
run("make")
sudo("make install")
sudo("make clean")
# Get init.d startup script
proftp_initd_script = 'proftpd'
local_proftp_initd_path = os.path.join('conf_files',proftp_initd_script)
remote_proftpd_initd_path = os.path.join('/etc/init.d',proftp_initd_script)
_put_as_user(local_proftp_initd_path,remote_proftpd_initd_path, user='******')
sudo('chmod 755 %s' % remote_proftpd_initd_path)
# Get configuration files
proftpd_conf_file = 'proftpd.conf'
local_conf_path = os.path.join('conf_files',proftpd_conf_file)
remote_conf_path = os.path.join(remote_conf_dir,proftpd_conf_file)
welcome_msg_file = 'welcome_msg.txt'
local_welcome_msg_path = os.path.join('conf_files',welcome_msg_file)
remote_welcome_msg_path = os.path.join(remote_conf_dir, welcome_msg_file)
_put_as_user(local_conf_path,remote_conf_path, user='******')
_put_as_user(local_welcome_msg_path,remote_welcome_msg_path, user='******')
sudo("cd %s; stow proftpd" % env.install_dir)
print(green("----- ProFTPd %s installed to %s -----" % (version, install_dir)))
def install(self, local_env={}, force=False):
""" If not already installed, install given tool and all of its dependencies. """
if self.set_env(local_env):
if (not self.is_installed(local_env=local_env)
and not self.tool_env['fatal_error']) or force:
if not self.tool_env['dependencies_ok']:
if not self.resolve_dependencies():
print "----- ERROR resolving dependencies -----"
return False
# Maybe the dependencies is all that was missing so check if
# the tool can be considered as installed now
if not self.is_installed(local_env=local_env) or force:
print "Trying to install %s %s as user %s" % (
str(self.tool_env['pkg_name']).upper(),
self.tool_env['version'], env.user)
install_cmd = sudo if self.tool_env['use_sudo'] else run
with nested(cd(self.tool_env['install_dir']),
settings(hide('stdout'))):
install_cmd("wget %s" % self.tool_env['url'])
install_cmd("wget %s" % self.tool_env['url2'])
install_cmd("tar xfvj %s; rm %s" %
(os.path.split(self.tool_env['url'])[1],
os.path.split(self.tool_env['url'])[1]))
install_cmd("tar xfvz %s; rm %s" %
(os.path.split(self.tool_env['url2'])[1],
os.path.split(self.tool_env['url2'])[1]))
install_cmd("mv asp-%s/* .; rm -rf asp-%s" %
(self.tool_env['version'],
self.tool_env['version']))
# find a way to provide xmls
if not exists('%s/tools/signals' %
self.tool_env['galaxy_dir']):
install_cmd('mkdir %s/tools/signals' %
self.tool_env['galaxy_dir'])
with settings(warn_only=True):
install_cmd(
"sed -i '1i if [ -n \"${PACKAGE_BASE+x}\" ]; then cd %s; fi' %s.sh"
% (self.tool_env['install_dir'],
self.tool_env['pkg_name']))
install_cmd(
'mv %s.xml %s.sh %s/tools/signals/' %
(self.tool_env['pkg_name'],
self.tool_env['pkg_name'],
self.tool_env['galaxy_dir']))
install_cmd("chmod +x %s/tools/signals/%s.sh" %
(self.tool_env['galaxy_dir'],
self.tool_env['pkg_name']))
install_cmd(
'chown -R %s %s/tools/signals' %
(env.user, self.tool_env['galaxy_dir']))
if self.tool_env.has_key('shogun_env_script') and exists(
self.tool_env['shogun_env_script']):
install_cmd("echo '. %s' > %s/env.sh" %
(self.tool_env['shogun_env_script'],
self.tool_env['install_dir']))
install_cmd(
"echo 'export PATH=%s:$PATH' >> %s/env.sh" %
(self.tool_env['install_dir'],
self.tool_env['install_dir']))
install_cmd(
"echo 'export PYTHONPATH=%s:$PYTHONPATH' >> %s/env.sh"
% (self.tool_env['install_dir'],
self.tool_env['install_dir']))
install_cmd("chmod +x %s/env.sh" %
self.tool_env['install_dir'])
install_dir_root = os.path.join(
self.tool_env['install_dir_root'],
self.tool_env['pkg_name'])
install_cmd(
'if [ ! -d %s/default ]; then ln -s %s %s/default; fi'
% (install_dir_root, self.tool_env['install_dir'],
install_dir_root))
install_cmd('chown -R %s %s' %
(env.user, install_dir_root))
else:
print "ERROR: Required dependency file for not found (for Shogun)."
self.tool_env['fatal_error'] = True
# Make sure the tool installed correctly
if not self.tool_env['fatal_error'] and (self.tool_env['installed']
or self.is_installed()):
return common.compose_successful_return(self.tool_env)
print "----- Problem installing ASP -----"
return self.tool_env