curation_tool

simple commandline tools to organise curation files using the GRIT JIRA

Installation

1. Install Crystal

2. Build the project:

git clone git@github.com:Aquatic-Symbiosis-Genomics-Project/curation_tool.git
cd curation_tool
shards build

• You can also get binaries compiled using Github Actions from the Release page. They are statically linked.

Usage

curation_tool

Usage: curation_tool --issue JIRA_ID [options]
    -i JIRA_ID, --issue JIRA_ID      JIRA ID
    -p, --copy_pretext               copy over pretext
    -w, --setup_working_dir          create initial curation files and directory
    -r, --build_release              create pretext and release files
    -q, --copy_qc                    copy from DIR to curation for QC
    -m, --merged                     work on a merged curation & pretext
    -h, --help                       show this help

submit_fcs

Usage: submit_fcs --issue JIRA_ID

don't forget to setup your environment:

export MODULEPATH=/software/treeoflife/shpc/current/views/grit:/software/treeoflife/custom-installs/modules:/software/modules
module load nextflow/23.04.0-5857
module load ISG/singularity/3.10.0
module load ISG/python/

the options are:
    -i JIRA_ID, --issue JIRA_ID      JIRA ID
    -h, --help                       show this help

Usage: submit_fcs --issue JIRA_ID 
    -i JIRA_ID, --issue JIRA_ID      JIRA ID
    -h, --help                       show this help

Contributors

• epaule - creator and maintainer