From f7ccc8cce66c0dd1a680a0d74db1f7f3fb033a5c Mon Sep 17 00:00:00 2001 From: dwest77 Date: Thu, 25 Jan 2024 16:08:29 +0000 Subject: [PATCH] Updated execution instructions for single and group running --- docs/source/execution.rst | 75 +++++++++++++++++++++++++++++++++++---- 1 file changed, 69 insertions(+), 6 deletions(-) diff --git a/docs/source/execution.rst b/docs/source/execution.rst index 975c395..bd0f2df 100644 --- a/docs/source/execution.rst +++ b/docs/source/execution.rst @@ -5,14 +5,77 @@ Running the Pipeline Running for a single dataset ============================ -:: +Run all single-dataset processes with the `single-run.py` script. +``` usage: single_run.py [-h] [-w WORKDIR] [-g GROUPDIR] [-G GROUPID] [-p PROJ_DIR] [-n NEW_VERSION] [-m MODE] [-t TIME_ALLOWED] [-b] [-s SUBSET] [-r REPEAT_ID] [-f] [-v] [-d] [-Q] phase proj_code -:: -Required Parameters: -:phase: Pipeline phase to execute -:proj_code: Project code or ID for this dataset execution +positional arguments: + phase Phase of the pipeline to initiate + proj_code Project identifier code + +options: + -h, --help show this help message and exit + -w WORKDIR, --workdir WORKDIR + Working directory for pipeline + -g GROUPDIR, --groupdir GROUPDIR + Group directory for pipeline + -G GROUPID, --groupID GROUPID + Group identifier label + -p PROJ_DIR, --proj_dir PROJ_DIR + Project directory for pipeline + -n NEW_VERSION, --new_version NEW_VERSION + If present, create a new version + -m MODE, --mode MODE Print or record information (log or std) + -t TIME_ALLOWED, --time-allowed TIME_ALLOWED + Time limit for this job + -b, --bypass-errs Bypass all error messages - skip failed jobs + -s SUBSET, --subset SUBSET + Size of subset within group + -r REPEAT_ID, --repeat_id REPEAT_ID + Repeat id (1 if first time running, _ otherwise) + -f Force overwrite of steps if previously done + -v, --verbose Print helpful statements while running + -d, --dryrun Perform dry-run (i.e no new files/dirs created) + -Q, --quality Quality assured checks - thorough run +``` =============================== Running for a group of datasets -=============================== \ No newline at end of file +=============================== + +Run all multi-dataset group processes within the pipeline using the `group_run.py` script. + +``` +usage: group_run.py [-h] [-s SOURCE] [-e VENVPATH] [-w WORKDIR] [-g GROUPDIR] [-p PROJ_DIR] [-n NEW_VERSION] [-m MODE] [-t TIME_ALLOWED] [-b] [-i INPUT] [-S SUBSET] [-r REPEAT_ID] [-f] [-v] [-d] [-Q] phase groupID + +positional arguments: + phase Phase of the pipeline to initiate + groupID Group identifier code + +options: + -h, --help show this help message and exit + -s SOURCE Path to directory containing master scripts (this one) + -e VENVPATH Path to virtual (e)nvironment (excludes /bin/activate) + -w WORKDIR, --workdir WORKDIR + Working directory for pipeline + -g GROUPDIR, --groupdir GROUPDIR + Group directory for pipeline + -p PROJ_DIR, --proj_dir PROJ_DIR + Project directory for pipeline + -n NEW_VERSION, --new_version NEW_VERSION + If present, create a new version + -m MODE, --mode MODE Print or record information (log or std) + -t TIME_ALLOWED, --time-allowed TIME_ALLOWED + Time limit for this job + -b, --bypass-errs Bypass all error messages - skip failed jobs + -i INPUT, --input INPUT + input file (for init phase) + -S SUBSET, --subset SUBSET + Size of subset within group + -r REPEAT_ID, --repeat_id REPEAT_ID + Repeat id (1 if first time running, _ otherwise) + -f Force overwrite of steps if previously done + -v, --verbose Print helpful statements while running + -d, --dryrun Perform dry-run (i.e no new files/dirs created) + -Q, --quality Quality assured checks - thorough run +``` \ No newline at end of file