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## CloudBioLinux install parameters, copy this to fabricrc.txt and
## modify as needed. This file corresponds to my "non-standard" setup
## that is installing tools and Galaxy into /opt/galaxy instead of
## /mnt/galaxyTools. This non-standard setup is also using my
## cloud-galaxy-dist fork of Galaxy that preconfigures various paths
## for cloud-based Galaxy as symbolic links right in the repository,
## setups a configuration directory for easy runtime configuration via
## my CloudMan extensions, etc...
##
##
##
## A more standard CloudMan setup could be accomplished with the
## default CloudBioLinux fabricrc.txt options.
## https://raw.github.com/chapmanb/cloudbiolinux/master/config/fabricrc.txt
distribution = ubuntu
dist_name = precise
edition = cloudbiolinux
is_ec2_image = false
# Global installation directory for packages and standard programs
system_install = /usr
# Local install directory for versioned software that will not
# be included in the path by default
local_install = ~/install
shell_config = ~/.bashrc
shell = /bin/bash -l -c
# Global setting for using sudo; allows installation of custom packages
# by non-privileged users.
# system_install needs to point to a user writeable directory if set to False
use_sudo = true
# details for biological data files and Galaxy
#data_files = /mnt/biodata
#galaxy_base = /mnt/biodata/galaxy
# Picard home
picard_home = /usr/share/java/picard
## Override nginx path to use my hacked nginx.conf that enabled LDAP
## auth. You will not want this.
# nginx_conf_path = /home/john/galaxp-cloudman/nginx.conf
## Enable nginx ldap
nginx_enable_module_ldap = true
## Override galaxy webapp install path (defaults to
## /mnt/galaxyTools/galaxy-central
galaxy_home = /opt/galaxy/web
## Override galaxy tool dir install path (defaults
galaxy_tools_dir = /opt/galaxy/tools
## Override galaxy webapp jars path
galaxy_jars_dir = /opt/galaxy/jars
## Repository to install Galaxy from, if repo includes changesets from
## jmchilton's cloud-galaxy-dist, galaxy_preconfigured_repository
## should be set to true.
galaxy_repository = https://bitbucket.org/jmchilton/cloud-galaxy-dist
galaxy_preconfigured_repository = true
## nfs mounts used by cloudman (defaults to /mnt/galaxyData, /mnt/galaxyIndices, and /mnt/galaxyTools)
galaxy_data_mount = /mnt/galaxyData
galaxy_indices_mount = /mnt/galaxyIndices
galaxy_tools_mount = /opt/galaxy
## Install galaxy dependencies (defaults to false)
galaxy_install_dependencies = true
galaxy_install_r_packages = true