From dc80ccc20e52cd754d7198cf7e91ee94683b5356 Mon Sep 17 00:00:00 2001 From: Kelly Sovacool Date: Tue, 17 Dec 2024 14:48:09 -0500 Subject: [PATCH] docs: note new platform & runmode options --- CHANGELOG.md | 2 ++ README.md | 6 ++++-- charlie | 8 +++++--- 3 files changed, 11 insertions(+), 5 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index f65f38f..8da2b20 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,7 @@ ## CHARLIE development version +- Support Eddie (The University of Edinburgh's HPC cluster) with `--platform=eddie` and `--runmode=qsub`. (#136, @kelly-sovacool) + ## CHARLIE 0.11.1 - CHARLIE was falsely throwing a file permissions error for tempdir values containing bash variables. (#118, @kelly-sovacool) diff --git a/README.md b/README.md index 343da1d..ce4630e 100644 --- a/README.md +++ b/README.md @@ -164,7 +164,8 @@ Required Arguments: 2. RUNMODE : [Type: String] Valid options: * init : initialize workdir * dryrun : dry run snakemake to generate DAG - * run : run with slurm + * run : run by submitting the job with slurm + * qsub : run by submitting the job with qsub * runlocal : run without submitting to sbatch ADVANCED RUNMODES (use with caution!!) * unlock : unlock WORKDIR if locked by snakemake NEVER UNLOCK WORKDIR WHERE PIPELINE IS CURRENTLY RUNNING! @@ -172,6 +173,7 @@ Required Arguments: * reset : DELETE workdir dir and re-init it (debugging option) EDITS TO ALL FILES IN WORKDIR WILL BE LOST! * printbinds: print singularity binds (paths) * local : same as runlocal + * slurm : same as run (run with slurm) Optional Arguments: @@ -181,7 +183,7 @@ Optional Arguments: --viruses|-v : supply comma-separated list of viruses at command line (--runmode=init only) --manifest|-s : absolute path to samples.tsv. This will be copied to output folder (--runmode=init only) --changegrp|-z : change group to "Ziegelbauer_lab" before running anything. Biowulf-only. Useful for correctly setting permissions. ---platform : set the HPC platform (biowulf, fnlcr, eddie). If not set, CHARLIE will try to detect the platform with scontrol. +--platform : set the HPC platform (biowulf, fnlcr, eddie). If not set, CHARLIE will try to detect the platform with `scontrol`. --help|-h : print this help diff --git a/charlie b/charlie index d0e5186..c6f4377 100755 --- a/charlie +++ b/charlie @@ -110,7 +110,7 @@ Required Arguments: * init : initialize workdir * dryrun : dry run snakemake to generate DAG * run : run by submitting the job with slurm - * runqsub : run by submitting the job with qsub + * qsub : run by submitting the job with qsub * runlocal : run locally without submitting the job to a scheduler ADVANCED RUNMODES (use with caution!!) * unlock : unlock WORKDIR if locked by snakemake NEVER UNLOCK WORKDIR WHERE PIPELINE IS CURRENTLY RUNNING! @@ -118,6 +118,7 @@ Required Arguments: * reset : DELETE workdir dir and re-init it (debugging option) EDITS TO ALL FILES IN WORKDIR WILL BE LOST! * printbinds: print singularity binds (paths) * local : same as runlocal + * slurm : same as run (run with slurm) Optional Arguments: @@ -641,12 +642,13 @@ function main(){ dryrun) dryrun && exit 0;; unlock) unlock && exit 0;; run) runslurm && exit 0;; - runqsub) runqsub && exit 0;; + slurm) runslurm && exit 0;; # same as run + qsub) runqsub && exit 0;; runlocal) runlocal && exit 0;; + local) runlocal && exit 0;; # hidden option reset) reset && exit 0;; touch) touch && exit 0;; dry) dryrun && exit 0;; # hidden option - local) runlocal && exit 0;; # hidden option reconfig) reconfig && exit 0;; # hidden option for debugging printbinds) printbinds && exit 0;; # hidden option help) usage && exit 0;; # print help