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Merge pull request #41 from afgane/master

Version updates; add ruffus
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2 parents 6ebf5f9 + b43a4f6 commit a27b3e8567ea518fbd421d610f904c2fa10ddef7 @chapmanb chapmanb committed May 22, 2012
Showing with 13 additions and 9 deletions.
  1. +12 −9 cloudbio/custom/cloudman.py
  2. +1 −0 config/python-libs.yaml
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21 cloudbio/custom/cloudman.py
@@ -24,7 +24,7 @@ def install_cloudman(env):
install_sge(env)
def install_nginx(env):
- version = "0.7.67"
+ version = "1.2.0"
url = "http://nginx.org/download/nginx-%s.tar.gz" % version
install_dir = os.path.join(env.install_dir, "nginx")
@@ -43,7 +43,7 @@ def install_nginx(env):
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 "
+ "--user=galaxy --group=galaxy --with-debug "
"--with-http_ssl_module --with-http_gzip_static_module" %
(install_dir, module_flags))
sed("objs/Makefile", "-Werror", "")
@@ -72,12 +72,12 @@ def install_nginx(env):
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 installed")
+ env.logger.debug("Nginx {0} installed to {1}".format(version, install_dir))
def _get_nginx_modules(env):
"""Retrieve add-on modules compiled along with nginx.
"""
- upload_module_version = "2.0.12"
+ upload_module_version = "2.2.0"
chunk_module_version = "0.22"
chunk_git_version = "b46dd27"
modules = []
@@ -95,9 +95,9 @@ def _get_nginx_modules(env):
return modules
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
+ 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
@@ -109,7 +109,10 @@ def install_proftpd(env):
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))
+ 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")
@@ -126,7 +129,7 @@ def install_proftpd(env):
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)
- env.logger.debug("ProFTPd installed")
+ env.logger.debug("----- ProFTPd %s installed to %s -----" % (version, install_dir))
def install_sge(env):
out_dir = "ge6.2u5"
View
1 config/python-libs.yaml
@@ -36,6 +36,7 @@ pypi:
# science
- biopython
- bcbio-nextgen
+ - ruffus
#- cogent # build error with python 2.7
- DendroPy
- HTSeq

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