Updating building/caching scripts for how dependencies are checked

Author: skchronicles

resources/builder

@@ -122,6 +122,21 @@ function check(){
 }
 
 
+function require(){
+  # Requires an executable is in $PATH, as a last resort it will attempt to load
+  # the executable or dependency as a module
+  # @INPUT $@ = List of dependencies or executables to check
+
+  for exe in "${@}"; do
+    # Check if executable is in $PATH
+    command -V ${exe} &> /dev/null && continue;
+    # Try to load exe as lua module
+    module load ${exe} &> /dev/null || \
+      fatal "Failed to find or load '${exe}', not installed on target system."
+  done
+}
+
+
 function submit(){
   # Submit jobs to the defined job scheduler or executor (i.e. slurm)
   # INPUT $1 = Snakemake Mode of execution
@@ -131,19 +146,9 @@ function submit(){
   # INPUT $5 = Singularity cache directory
   # INPUT $6 = Temporary directory for output files
 
-  # SLURM inherits the environment from which the job was launched
-  # Try to purge modules all modules from environment
-  command -V module &> /dev/null && module purge
-
-  # Check if singularity in $PATH
+  # Check if singularity and snakemake are in $PATH
   # If not, try to module load singularity as a last resort
-  command -V singularity &> /dev/null || module load singularity || \
-    fatal "Fail to find or load 'singularity', not installed on target system."
-
-  # Check if snakemake in $PATH
-  # If not, try to module load snakemake as a last resort
-  command -V snakemake &> /dev/null || module load snakemake || \
-    fatal "Fail to find or load 'snakemake', not installed on target system."
+  require singularity snakemake
 
   # Snakemake executor
   executor=${1}
@@ -248,3 +253,4 @@ function main(){
 
 # Main: check usage, parse args, and run pipeline
 main "$@"
+

resources/cacher

@@ -102,6 +102,21 @@ function check(){
 }
 
 
+function require(){
+  # Requires an executable is in $PATH, as a last resort it will attempt to load
+  # the executable or dependency as a module
+  # @INPUT $@ = List of dependencies or executables to check
+
+  for exe in "${@}"; do
+    # Check if executable is in $PATH
+    command -V ${exe} &> /dev/null && continue;
+    # Try to load exe as lua module
+    module load ${exe} &> /dev/null || \
+      fatal "Failed to find or load '${exe}', not installed on target system."
+  done
+}
+
+
 function retry() {
   # Tries to run a cmd 5 times before failing 
   # If a command is successful, it will break out of attempt loop
@@ -138,11 +153,7 @@ function _pull(){
   # INPUT $4 = Images to pull from DockerHub
 
   # Check if singularity in $PATH
-  # If not, try to module load singularity as a last resort
-  command -V singularity &> /dev/null || { 
-    command -V module &> /dev/null && 
-    module purge && module load singularity
-  } || fatal "Fail to find or load 'singularity', not installed on target system."
+  require singularity
 
   # cache executor
   executor=${1}