Handle cryosparc2_ vs cryosparc_ in paths

Breaking change: Remove '2' from default worker paths.

Pulling this change into old installations that still us
`cryosparc2_worker` in the path will temporarily break the worker. To
fix, run `dev/update_version.sh` followed by `./connect_all.sh`.

- new dev/update_versions.sh script to fix your config
- use cryosparcm wrapper, which handles alternate CRYOSPARC_HOME
  correctly

connect_all.sh

@@ -1,7 +1,10 @@
 #!/bin/bash
 # Connect all lanes to cryosparc
 
-: "${CRYOSPARCM:=/data/user/$USER/cryosparc/cryosparc2_master/bin/cryosparcm}"
+
+# Path to cryosparcm binary
+# Defaults to the wrapper script, which validates the host and supports $CRYOSPARC_HOME
+: "${CRYOSPARCM:=/data/project/bio/software/cryoSPARC/v2/scripts/cryosparcm.sh}"
 
 if [[ ! -x "$CRYOSPARCM" ]]; then
     echo "ERROR: Unable to find cryosparcm at $CRYOSPARCM" >&2

cpu-daily/cluster_info.json

@@ -1,6 +1,6 @@
 {
     "name" : "cpu-daily",
-    "worker_bin_path" : "/data/user/USERNAME/cryosparc/cryosparc2_worker/bin/cryosparcw",
+    "worker_bin_path" : "/data/user/USERNAME/cryosparc/cryosparc_worker/bin/cryosparcw",
     "cache_path" : "/scratch/",
     "send_cmd_tpl" : "{{ command }}",
     "qsub_cmd_tpl" : "bash -c 'sbatch --parsable --cluster=merlin6 \"{{ script_path_abs }}\" | cut -d \";\" -f 1'",

dev/update_versions.sh

@@ -0,0 +1,23 @@
+#!/bin/bash
+
+# Updates the cluster scripts based on the currently loaded cuda, gcc, and CRYOSPARC_HOME settings
+
+shopt -s failglob
+set -euo pipefail
+
+CRYOSPARC_HOME="${CRYOSPARC_HOME:-/data/user/$USER/cryosparc}"
+if [[ ! -d "$CRYOSPARC_HOME" ]]; then
+	echo "$CRYOSPARC_HOME not found. Set the CRYOSPARC_HOME variable."
+	exit 1
+fi
+
+# support both cryosparc2_master and cryosparc_master directories
+CRYOSPARC_WORKER=$(ls "$CRYOSPARC_HOME"/cryosparc*_worker/bin/cryosparcw | head -1)
+
+echo "Cuda version: ${CUDA_VERSION?Please load the correct cuda module}"
+echo "GCC version:  ${GCC_VERSION?Please load the correct gcc version}"
+echo "Worker path:  ${CRYOSPARC_WORKER}"
+
+sed -ri 's#cuda/[0-9.]+#cuda/'$CUDA_VERSION'#' */cluster_script.sh
+sed -ri 's#gcc/[0-9.]+#gcc/'$GCC_VERSION'#' */cluster_script.sh
+sed -ri 's#worker_bin_path.*#worker_bin_path" : "'$CRYOSPARC_WORKER'",#' */cluster_info.json

gpu-big/cluster_info.json

@@ -1,6 +1,6 @@
 {
     "name" : "gpu-big",
-    "worker_bin_path" : "/data/user/USERNAME/cryosparc/cryosparc2_worker/bin/cryosparcw",
+    "worker_bin_path" : "/data/user/USERNAME/cryosparc/cryosparc_worker/bin/cryosparcw",
     "cache_path" : "/scratch/",
     "send_cmd_tpl" : "{{ command }}",
     "qsub_cmd_tpl" : "bash -c 'sbatch --parsable --cluster=gmerlin6 \"{{ script_path_abs }}\" | cut -d \";\" -f 1'",

gpu-rtx2080ti/cluster_info.json

@@ -1,6 +1,6 @@
 {
     "name" : "gpu-rtx2080ti",
-    "worker_bin_path" : "/data/user/USERNAME/cryosparc/cryosparc2_worker/bin/cryosparcw",
+    "worker_bin_path" : "/data/user/USERNAME/cryosparc/cryosparc_worker/bin/cryosparcw",
     "cache_path" : "/scratch/",
     "send_cmd_tpl" : "{{ command }}",
     "qsub_cmd_tpl" : "bash -c 'sbatch --parsable --cluster=gmerlin6 \"{{ script_path_abs }}\" | cut -d \";\" -f 1'",

gpu-short/cluster_info.json

@@ -1,6 +1,6 @@
 {
     "name" : "gpu-short",
-    "worker_bin_path" : "/data/user/USERNAME/cryosparc/cryosparc2_worker/bin/cryosparcw",
+    "worker_bin_path" : "/data/user/USERNAME/cryosparc/cryosparc_worker/bin/cryosparcw",
     "cache_path" : "/scratch/",
     "send_cmd_tpl" : "{{ command }}",
     "qsub_cmd_tpl" : "bash -c 'sbatch --parsable --cluster=gmerlin6 \"{{ script_path_abs }}\" | cut -d \";\" -f 1'",

gpu/cluster_info.json

@@ -1,6 +1,6 @@
 {
     "name" : "gpu",
-    "worker_bin_path" : "/data/user/USERNAME/cryosparc/cryosparc2_worker/bin/cryosparcw",
+    "worker_bin_path" : "/data/user/USERNAME/cryosparc/cryosparc_worker/bin/cryosparcw",
     "cache_path" : "/scratch/",
     "send_cmd_tpl" : "{{ command }}",
     "qsub_cmd_tpl" : "bash -c 'sbatch --parsable --cluster=gmerlin6 \"{{ script_path_abs }}\" | cut -d \";\" -f 1'",