From 0f6b8f5b0425c11db9847f9b106dbba4874324ba Mon Sep 17 00:00:00 2001
From: Verity Hill <veh3@login2.mccleary.ycrc.yale.edu>
Date: Fri, 11 Aug 2023 11:41:07 -0400
Subject: [PATCH] add path to python calls in mapper script

---
 denv_pipeline/scripts/mapper.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/denv_pipeline/scripts/mapper.sh b/denv_pipeline/scripts/mapper.sh
index 59abe12..e9dbf00 100755
--- a/denv_pipeline/scripts/mapper.sh
+++ b/denv_pipeline/scripts/mapper.sh
@@ -58,9 +58,9 @@ while IFS= read -r virustype || [[ -n "$virustype" ]]; do
     echo "----->>>>>Calculating percentage coverage against serotype "${virustype}" cps reference sequence"
     which python
     if [ -s ${trimbed} ]; then
-        python ${serotype_caller} --alignment ${tempdir}/${fname}.${virustype}.${depth}.out.aln --bed-file ${trimbed} --outfile ${tempdir}/${fname}_all_virustype_info.txt
+        $CONDA_PREFIX/bin/python ${serotype_caller} --alignment ${tempdir}/${fname}.${virustype}.${depth}.out.aln --bed-file ${trimbed} --outfile ${tempdir}/${fname}_all_virustype_info.txt
     else
-        python ${serotype_caller}  --alignment ${tempdir}/${fname}.${virustype}.${depth}.out.aln --outfile ${tempdir}/${fname}_all_virustype_info.txt
+        $CONDA_PREFIX/bin/python ${serotype_caller}  --alignment ${tempdir}/${fname}.${virustype}.${depth}.out.aln --outfile ${tempdir}/${fname}_all_virustype_info.txt
     fi
 
     echo "----->>>>>Identifying variants"