From 54a3dd4b38d267ccf1903b96565d62214800320e Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Tue, 10 Sep 2024 12:58:35 -0400
Subject: [PATCH 1/3] fix: set singularity cache dir (fixes #137)

---
 carlisle               | 19 +++++++++++++++++++
 docs/user-guide/run.md | 12 +++++++++++-
 2 files changed, 30 insertions(+), 1 deletion(-)

diff --git a/carlisle b/carlisle
index 367c2ea..9d6488d 100755
--- a/carlisle
+++ b/carlisle
@@ -268,6 +268,8 @@ function run() {
   if [ "$1" == "local" ]; then
     preruncleanup
 
+    $EXPORT_SING_CACHE_DIR_CMD
+
     snakemake -s $SNAKEFILE \
     --directory $WORKDIR \
     --printshellcmds \
@@ -305,6 +307,8 @@ function run() {
 
     cd \$SLURM_SUBMIT_DIR
 
+    $EXPORT_SING_CACHE_DIR_CMD
+
     snakemake -s $SNAKEFILE \
     --directory $WORKDIR \
     --use-singularity \
@@ -384,6 +388,9 @@ function main(){
         -f|--force)
           FORCEFLAG="ON"
         ;;
+        -c=*|--singcache=*)
+          SING_CACHE_DIR="${i#*=}"
+        ;;
         -v|--version)
           get_version && exit 0
         ;;
@@ -398,6 +405,18 @@ function main(){
   WORKDIR=$(readlink -m "$WORKDIR")
   echo "Working Dir: $WORKDIR"
 
+  if [[ -z "$SING_CACHE_DIR" ]]; then
+    echo "singularity cache dir (--singcache) is not set"
+    if [[ -d "/data/$USER" ]]; then
+      SING_CACHE_DIR="/data/$USER/.singularity"
+    else
+      SING_CACHE_DIR="${WORKDIR}/.singularity"
+    fi
+    echo "\tusing ${SING_CACHE_DIR}"
+  fi
+  mkdir -p $SING_CACHE_DIR
+  EXPORT_SING_CACHE_DIR_CMD="export SINGULARITY_CACHEDIR=\"${SING_CACHE_DIR}\""
+
   case $RUNMODE in
     init) init && exit 0;;
     dryrun) dryrun && exit 0;;
diff --git a/docs/user-guide/run.md b/docs/user-guide/run.md
index bd03a45..2deeadd 100644
--- a/docs/user-guide/run.md
+++ b/docs/user-guide/run.md
@@ -2,10 +2,13 @@
 
 ## 3.1 Pipeline Overview
 
-The Snakemake workflow has a multiple options:
+The Snakemake workflow has a multiple options
+
+### Required arguments
 
 ```
 Usage: bash ./data/CCBR_Pipeliner/Pipelines/CARLISLE/carlisle -m/--runmode=<RUNMODE> -w/--workdir=<WORKDIR>
+
 1.  RUNMODE: [Type: String] Valid options:
     *) init : initialize workdir
     *) run : run with slurm
@@ -17,6 +20,13 @@ Usage: bash ./data/CCBR_Pipeliner/Pipelines/CARLISLE/carlisle -m/--runmode=<RUNM
 2.  WORKDIR: [Type: String]: Absolute or relative path to the output folder with write permissions.
 ```
 
+### Optional arguments
+
+--help|-h       : print this help.
+--version|-v    : print the version of carlisle.
+--force|-f      : use the force flag for snakemake to force all rules to run.
+--singcache|-c  : singularity cache directory. Default is `/data/${USER}/.singularity` if available, or falls back to `${WORKDIR}/.singularity`. Use this flag to specify a different singularity cache directory.
+
 ## 3.2 Commands explained
 
 The following explains each of the command options:

From 8345deb920875662fcbd6a000920fe892d9a0c97 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Tue, 10 Sep 2024 13:01:57 -0400
Subject: [PATCH 2/3] chore: update CHANGELOG.md

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index e23fcba..74e358b 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -20,6 +20,7 @@
 - New parameters in the config file to make certain rules optional: (#133, @kelly-sovacool)
   - GO enrichment is controlled by `run_go_enrichment` (default: `false`)
   - ROSE is controlled by `run_rose` (default: `false`)
+- New `--singcache` argument to provide a singularity cache dir location. The singularity cache dir is automatically set inside `/data/$USER/` or `$WORKDIR/` if `--singcache` is not provided. (#143, @kelly-sovacool)
 
 ### Misc
 

From 240afd242d2ad09548af2ee487950a806b520b6d Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Tue, 10 Sep 2024 13:04:30 -0400
Subject: [PATCH 3/3] style: simplify singcache echo statement

---
 carlisle | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/carlisle b/carlisle
index 9d6488d..315622d 100755
--- a/carlisle
+++ b/carlisle
@@ -406,13 +406,12 @@ function main(){
   echo "Working Dir: $WORKDIR"
 
   if [[ -z "$SING_CACHE_DIR" ]]; then
-    echo "singularity cache dir (--singcache) is not set"
     if [[ -d "/data/$USER" ]]; then
       SING_CACHE_DIR="/data/$USER/.singularity"
     else
       SING_CACHE_DIR="${WORKDIR}/.singularity"
     fi
-    echo "\tusing ${SING_CACHE_DIR}"
+    echo "singularity cache dir (--singcache) is not set, using ${SING_CACHE_DIR}"
   fi
   mkdir -p $SING_CACHE_DIR
   EXPORT_SING_CACHE_DIR_CMD="export SINGULARITY_CACHEDIR=\"${SING_CACHE_DIR}\""