docs: note new platform & runmode options

CCBR · Dec 17, 2024 · dc80ccc · dc80ccc
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Showing 3 changed files with 11 additions and 5 deletions.
diff --git 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
@@ -164,14 +164,16 @@ 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!
     * reconfig  : recreate config file in WORKDIR (debugging option) EDITS TO config.yaml WILL BE LOST!
     * 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
@@ -110,14 +110,15 @@ 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!
     * reconfig  : recreate config file in WORKDIR (debugging option) EDITS TO config.yaml WILL BE LOST!
     * 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