dynamic PYTHON_EXEC_PATH depending on env

Author: YuWei-CH

job.py

@@ -23,12 +23,14 @@
 
 def redisjob(target_dir, timestamp, email, chrom, upstream_fasta, downstream_fasta, position, ref_fastaURL, ref_gffURL,
              in_fasta, in_gff):
+    python_exec_path = os.path.expanduser("~/venv/bin/python")
+
     if position:
-        command = "bash ./run.sh {} {} {} {} {} {} {} {} {}".format(target_dir, timestamp, email, chrom,
+        command = "bash ./run.sh {} {} {} {} {} {} {} {} {} {}".format(python_exec_path, target_dir, timestamp, email, chrom,
                                                                     ref_fastaURL, ref_gffURL, in_fasta,
                                                                     in_gff, position)
     else:
-        command = "bash ./run.sh {} {} {} {} {} {} {} {} {} {}".format(target_dir, timestamp, email, chrom,
+        command = "bash ./run.sh {} {} {} {} {} {} {} {} {} {} {}".format(python_exec_path, target_dir, timestamp, email, chrom,
                                                                        ref_fastaURL, ref_gffURL, in_fasta,
                                                                        in_gff, upstream_fasta,
                                                                        downstream_fasta)

run.sh

@@ -1,5 +1,8 @@
 #!/bin/bash
 
+PYTHON_EXEC_PATH="$1"
+shift
+
 target_dir="$1"
 timestamp="$2"
 email="$3"
@@ -87,20 +90,20 @@ fi
 # Run reform.py
 
 if [ ! -z "$position" ]; then
-  echo   /home/reform/venv/bin/python reform.py --chrom $chrom --position $position --in_fasta ./uploads/$timestamp/$in_fasta \
+  echo   $PYTHON_EXEC_PATH reform.py --chrom $chrom --position $position --in_fasta ./uploads/$timestamp/$in_fasta \
   --in_gff ./uploads/$timestamp/$in_gff --ref_fasta "$ref_fasta_path" --ref_gff "$ref_gff_path" \
   --output_dir "./results/$timestamp/"
 
-  /home/reform/venv/bin/python reform.py --chrom $chrom --position $position --in_fasta ./uploads/$timestamp/$in_fasta \
+  $PYTHON_EXEC_PATH reform.py --chrom $chrom --position $position --in_fasta ./uploads/$timestamp/$in_fasta \
   --in_gff ./uploads/$timestamp/$in_gff --ref_fasta "$ref_fasta_path" --ref_gff "$ref_gff_path" \
   --output_dir "./results/$timestamp/" 2>&1 | tee ./results/$timestamp/$timestamp-worker-err.log
 else
-  echo   /home/reform/venv/bin/python reform.py --chrom $chrom --upstream_fasta ./uploads/$timestamp/$upstream_fasta \
+  echo $PYTHON_EXEC_PATH reform.py --chrom $chrom --upstream_fasta ./uploads/$timestamp/$upstream_fasta \
   --downstream_fasta ./uploads/$timestamp/$downstream_fasta --in_fasta ./uploads/$timestamp/$in_fasta \
   --in_gff ./uploads/$timestamp/$in_gff --ref_fasta "$ref_fasta_path" --ref_gff "$ref_gff_path" \
   --output_dir "./results/$timestamp/"
 
-  /home/reform/venv/bin/python reform.py --chrom $chrom --upstream_fasta ./uploads/$timestamp/$upstream_fasta \
+  $PYTHON_EXEC_PATH reform.py --chrom $chrom --upstream_fasta ./uploads/$timestamp/$upstream_fasta \
   --downstream_fasta ./uploads/$timestamp/$downstream_fasta --in_fasta ./uploads/$timestamp/$in_fasta \
   --in_gff ./uploads/$timestamp/$in_gff --ref_fasta "$ref_fasta_path" --ref_gff "$ref_gff_path" \
   --output_dir "./results/$timestamp/" 2>&1 | tee ./results/$timestamp/$timestamp-worker-err.log