Mercurial > repos > dvanzessen > bcbio_nextgen_emc
view bcbio_system.yaml @ 8:2e5223259a56 draft default tip
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author | dvanzessen |
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date | Tue, 21 Apr 2020 11:38:36 +0000 |
parents | 2ed60a09d6b6 |
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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