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fabricrc.txt
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fabricrc.txt
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# Configuration file for Fabric specifying filesystem information
# This can be adjusted and passed to fab on the commandline as '-c'
#
# For example
#
# fab -f data_fabfile.py -H your_machine -c your_fabricrc.txt install_data_s3:your_biodata.yaml
flavor = GVLFlavor
flavor_dir = gvl.gvlflavor
# -- Details about the operating system
## Ubuntu
distribution = ubuntu
dist_name = precise
## Centos
#distribution = centos
## Debian
#distribution = debian
#dist_name = squeeze
# -- Installation details
# Unset to avoid CloudBioLinux customizations like setup scripts;
# or set to different edition to get specific customizations
edition = cloudbiolinux
# Whether to clean the system for EC2 AMI preparation;
# do not set on vagrant or local machines
is_ec2_image = false
# Global installation directory for packages and standard programs
system_install = /mnt/galaxy/tools
# Used below path when installing image-level tools
# system_install = /usr/local
# Local install directory for versioned software that will not
# be included in the path by default
local_install = ~/install
# Shell to be used by CBL scripts during runtime
shell_config = ~/.bashrc
shell = /bin/bash --noprofile -l -c
# Global setting for using sudo; allows installation of custom packages
# by non-privileged users.
# *Note*: ``system_install`` needs to point to a user-writeable directory if
# ``use_sudo`` is set to ``False``
use_sudo = True
# -- Details about reference data installation
# Path where biological reference data files should be retrieved to
data_files = /mnt/galaxyIndices
# -- Details about installing Galaxy and its dependencies. Values behind the
# comments are the defaults.
# Specify as which user should Galaxy be installed
#galaxy_user = galaxy
# Path where Galaxy application is installed
galaxy_home = /mnt/galaxy/galaxy-app
# URL for the Galaxy application source code repository
galaxy_repository = https://bitbucket.org/galaxy/galaxy-dist#stable
# If ``True``, Galaxy repository will not be custom-configured after being cloned
# The customization details are primarily targeted at a cloud deployment; for
# details, see ``cbl.galaxy.__init__ -> _configure_galaxy_repository``
#galaxy_preconfigured_repository = False
# A path to the binaries for interacting with PostgreSQL
#postgres_bin_dir = /usr/lib/postgresql/9.1/bin
#postrges_user = postgres
postgres_port = 5910
# If ``True``, setup and initialize Postgres database for use by Galaxy
# according to the following options
galaxy_setup_database = True
#galaxy_db_name = galaxy
galaxy_database_path = /mnt/galaxy/db
#galaxy_ftp_user_password = fu5yOj2sn
#galaxy_universe_wsgi_url = https://bitbucket.org/galaxy/cloudman/raw/tip/universe_wsgi.ini.cloud
# If ``True``, setup Galaxy as a system-level service controlled via init.d
#galaxy_setup_service = False
# If ``True``, setup Xvfb as a system-level service via init.d
#galaxy_setup_xvfb = False
# Location of Galaxy's .loc files
#galaxy_loc_files = /mnt/galaxy/galaxy-app/tool-data/
# Location of files required by Galaxy Trackster
# This path needs to match what will be set in Galaxy's universe_wsgi.ini
#galaxy_len_files = /mnt/galaxy/configuration_data/len
# Galaxy requires Java tools to have their jar files places in a specific
# directory, so specify it here.
galaxy_jars_dir = /mnt/galaxy/tools/jars
# If ``True``, install a set of tools considered as Galaxy dependencies
galaxy_install_dependencies = True
# Load Galaxy's default env.sh files so they are available on the command line
autoload_galaxy_tools = True
# Specify a custom location to a YAML file containing a list of tools to
# install as Galaxy dependencies
galaxy_tools_conf = contrib/flavor/gvl/tools.yaml
# Location where (some?!) Galaxy dependency tools should be installed
galaxy_tools_dir = /mnt/galaxy/tools
# If ``True``, install R packages listed in contrib/cloudman/tools.yaml
galaxy_install_r_packages = false
# Paths for respective file systems that will be added to ``/etc/exports``
# and thus exported via NFS when the operating system boots
#galaxy_data_mount = /mnt/galaxyData
#galaxy_tools_mount = /mnt/galaxyTools
#galaxy_indices_mount = /mnt/biodata
#extra_nfs_exports = comma,separate,desired,paths
# Path to the SCF installation
scf_install = /var/www
# -- Tool-specific configurations
# A location of a custom nginx.conf or a comparable template, respectively.
nginx_conf_template_path = contrib/flavor/gvl/nginx.conf.template
#nginx_conf_path = path/to/custom/nginx.conf
nginx_upload_store_path = /mnt/galaxy/upload_store
# Picard home
picard_home = /usr/share/java/picard
# Science Collaboration Framework
scf_dbname = scfdb
scf_username = scfuser
scf_password = scfgv7
scf_dest_dir = www
scf_site_name = GVL