curation_tool

simple commandline tools to organise curation files using the GRIT JIRA

Installation

Install Crystal
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 on Alpine Linux/x86_64 binaries.

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                     build files based on a merged map
    -h, --help                       show this help

submit_fcs

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

submit_btk

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

Before running, load the required environment:

module load grit

submit_curation_pretext

Usage: submit_curation_pretext --issue JIRA_ID --fasta FASTA --out OUTDIR
    -i JIRA_ID,   --issue JIRA_ID    JIRA ID
    -n,           --no_email         don't send an email
    -c,           --no_name_check    don't check the tolid against the fasta name
    -f FASTA,     --fasta FASTA      input fasta
    -o OUTDIR,    --out OUTDIR       output dir
    -h,           --help             show this help

ascc_stats

Usage: ascc_stats JIRA_ID [JIRA_ID ...]

Compares FCS-GX .contamination calls against the BED-based calls for each issue and prints a tab-separated stats table to stdout.

Contributors

epaule - creator and maintainer