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1 ---
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2 # Configuration file specifying system details for running an analysis pipeline
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3 # These pipeline apply generally across multiple projects. Adjust them in sample
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4 # specific configuration files when needed.
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5
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6 # -- Base setup
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7
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8 # Define resources to be used for individual programs on multicore machines.
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9 # These can be defined specifically for memory and processor availability.
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10 # - memory: Specify usage for memory intensive programs. The indicated value
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11 # specifies the wanted *per core* usage.
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12 # - cores: Define cores that can be used for multicore programs. The indicated
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13 # value is the maximum cores that should be allocated for a program.
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14 # - jvm_opts: specify details
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15 resources:
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16 # default options, used if other items below are not present
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17 # avoids needing to configure/adjust for every program
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18 default:
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19 memory: 3G
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20 cores: 16
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21 jvm_opts: ["-Xms750m", "-Xmx3500m"]
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22 gatk:
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23 jvm_opts: ["-Xms500m", "-Xmx3500m"]
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24 snpeff:
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25 jvm_opts: ["-Xms750m", "-Xmx3g"]
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26 qualimap:
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27 memory: 4g
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28 express:
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29 memory: 8g
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30 dexseq:
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31 memory: 10g
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32 macs2:
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33 memory: 8g
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34 seqcluster:
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35 memory: 8g
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36
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37 # Location of galaxy configuration file, which has pointers to reference data
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38 # https://bcbio-nextgen.readthedocs.org/en/latest/contents/configuration.html#reference-genome-files
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39 galaxy_config: universe_wsgi.ini
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40
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41
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42 # -- Additional options for specific integration, not required for standalone usage.
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43
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44 # Galaxy integration. Required for retrieving information from Galaxy LIMS.
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45 #galaxy_url: http://your/galaxy/url
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46 #galaxy_api_key: your_galaxy_api_key
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47
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48 # Details for hooking automated processing to a sequencer machine.
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49 # Not required if running standalone pipelines.
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50 # analysis:
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51 # # Can specify a different remote host to initiate
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52 # # the copy from. This is useful for NFS shared filesystems
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53 # # where you want to manage the copy from the base machine.
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54 # copy_user:
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55 # copy_host:
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56 # store_dir: /store4/solexadata
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57 # base_dir: /array0/projects/Sequencing
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58 # worker_program: nextgen_analysis_server.py
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