From fc1f32a0c056cd1a7b93838223fa9d7c481aee28 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Wed, 22 Jan 2025 17:21:14 -0500
Subject: [PATCH] fix: add jobby & spooker to path if not available

resolves #152
---
 config/config.yaml |  1 +
 workflow/Snakefile | 24 +++++++++++++-----------
 2 files changed, 14 insertions(+), 11 deletions(-)

diff --git a/config/config.yaml b/config/config.yaml
index f6407d0..2164aef 100644
--- a/config/config.yaml
+++ b/config/config.yaml
@@ -159,6 +159,7 @@ spikein_reference:
 
 adapters: "PIPELINE_HOME/resources/other/adapters.fa"
 
+tools_path: "/data/CCBR_Pipeliner/Tools/ccbr_tools/v0.1/bin/"
 #####################################################################################
 # CONTAINERS
 #####################################################################################
diff --git a/workflow/Snakefile b/workflow/Snakefile
index eef0478..05dd5d4 100644
--- a/workflow/Snakefile
+++ b/workflow/Snakefile
@@ -255,23 +255,25 @@ rule all:
         unpack(get_rose),
         unpack(get_enrichment)
 
-# create jobby tables
-jobby_cmd = 'run_jobby_on_snakemake_log logs/snakemake.log | tee logs/snakemake.log.jobby | cut -f2,3,18 > logs/snakemake.log.jobby.short'
-spook_cmd = f'spooker {WORKDIR} CARLISLE'
+on_complete = f"""
+for cmd in spooker run_jobby_on_snakemake_log; do
+    if ! command -v run_jobby_on_snakemake_log 2>&1 >/dev/null; then
+        export PATH="$PATH:{config['tools_path']}"
+    fi
+done
+run_jobby_on_snakemake_log logs/snakemake.log | tee logs/snakemake.log.jobby | cut -f2,3,18 > logs/snakemake.log.jobby.short
+spooker {WORKDIR} CARLISLE
+"""
 
 onsuccess:
     print("OnSuccess")
-    print(jobby_cmd)
-    shell(jobby_cmd)
-    print(spook_cmd)
-    shell(spook_cmd)
+    print(on_complete)
+    shell(on_complete)
 
 onerror:
     print("OnError")
-    print(jobby_cmd)
-    shell(jobby_cmd)
-    print(spook_cmd)
-    shell(spook_cmd)
+    print(on_complete)
+    shell(on_complete)
 
 """
         ##########################################