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# Configuration file specifying system details for running an analysis pipeline
# These pipeline apply generally across multiple projects. Adjust them in sample
# specific configuration files when needed.
# -- Base setup
# Define resources to be used for individual programs on multicore machines.
# These can be defined specifically for memory and processor availability.
# - memory: Specify usage for memory intensive programs. The indicated value
# specifies the wanted *per core* usage.
# - cores: Define cores that can be used for multicore programs. The indicated
# value is the maximum cores that should be allocated for a program.
# - jvm_opts: specify details
resources:
# default options, used if other items below are not present
# avoids needing to configure/adjust for every program
default:
memory: 3G
cores: 16
jvm_opts: ["-Xms750m", "-Xmx3500m"]
gatk:
jvm_opts: ["-Xms500m", "-Xmx3500m"]
snpeff:
jvm_opts: ["-Xms750m", "-Xmx3g"]
qualimap:
memory: 4g
express:
memory: 8g
dexseq:
memory: 10g
macs2:
memory: 8g
seqcluster:
memory: 8g
# Location of galaxy configuration file, which has pointers to reference data
# https://bcbio-nextgen.readthedocs.org/en/latest/contents/configuration.html#reference-genome-files
galaxy_config: universe_wsgi.ini
# -- Additional options for specific integration, not required for standalone usage.
# Galaxy integration. Required for retrieving information from Galaxy LIMS.
#galaxy_url: http://your/galaxy/url
#galaxy_api_key: your_galaxy_api_key
# Details for hooking automated processing to a sequencer machine.
# Not required if running standalone pipelines.
# analysis:
# # Can specify a different remote host to initiate
# # the copy from. This is useful for NFS shared filesystems
# # where you want to manage the copy from the base machine.
# copy_user:
# copy_host:
# store_dir: /store4/solexadata
# base_dir: /array0/projects/Sequencing
# worker_program: nextgen_analysis_server.py