def _install_setuptools():
version = "0.6c11"
python_version = "2.6"
url = "http://pypi.python.org/packages/%s/s/setuptools/setuptools-%s-py%s.egg#md5=bfa92100bd772d5a213eedd356d64086" % (python_version, version, python_version)
with _make_tmp_dir() as work_dir:
with cd(work_dir):
run("wget %s" % url)
sudo("sh %s" % os.path.split(url)[1].split('#')[0])
print(green("----- setuptools installed -----"))
def _install_r_packages():
f = tempfile.NamedTemporaryFile()
f.write(r_packages_template)
f.flush()
with _make_tmp_dir() as work_dir:
put(f.name, os.path.join(work_dir, 'install_packages.r'))
with cd(work_dir):
sudo("R --vanilla --slave < install_packages.r")
f.close()
print(green("----- R packages installed -----"))
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_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 _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_proftpd():
version = "1.3.4a"
postgres_ver = "9.1"
url = "ftp://ftp.tpnet.pl/pub/linux/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):
print(green("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=mod_sql:mod_sql_postgres:mod_sql_passwd " \
"--with-libraries=/usr/lib/postgresql/%s/lib" % (install_dir, 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)
print(green("----- ProFTPd %s installed to %s -----" % (version, install_dir)))
def _install_samtools():
version = "0.1.18"
vext = ""
mirror_info = "?use_mirror=cdnetworks-us-1"
url = "http://downloads.sourceforge.net/project/samtools/samtools/%s/" \
"samtools-%s%s.tar.bz2" % (version, version, vext)
install_dir = "/usr/bin"
install_cmd = sudo
if not exists(install_dir):
install_cmd("mkdir -p %s" % install_dir)
with _make_tmp_dir() as work_dir:
with cd(work_dir):
run("wget %s%s -O %s" % (url, mirror_info, os.path.split(url)[-1]))
run("tar -xjvpf %s" % (os.path.split(url)[-1]))
with cd("samtools-%s%s" % (version, vext)):
run("sed -i.bak -r -e 's/-lcurses/-lncurses/g' Makefile")
run("make")
for install in ["samtools", "misc/maq2sam-long"]:
install_cmd("mv -f %s %s" % (install, install_dir))
print "----- SAMtools %s installed to %s -----" % (version, install_dir)
