From 162e9b68a8230b9fdd777e9903d556f7726eddf5 Mon Sep 17 00:00:00 2001
From: tflati <tflati@di.uniroma1.it>
Date: Tue, 22 Jan 2019 14:32:01 +0100
Subject: [PATCH] Added an install.sh script and included virtualenv commands
 in scripts.

---
 install.sh             | 9 +++++++++
 parallel_test.sh       | 4 ++--
 parallel_test_slurm.sh | 2 ++
 serial_test.sh         | 4 ++++
 4 files changed, 17 insertions(+), 2 deletions(-)
 create mode 100755 install.sh

diff --git a/install.sh b/install.sh
new file mode 100755
index 0000000..559d912
--- /dev/null
+++ b/install.sh
@@ -0,0 +1,9 @@
+#!/bin/bash
+
+virtualenv ENV
+
+source ENV/bin/activate
+
+pip install -r requirements.txt
+
+deactivate
\ No newline at end of file
diff --git a/parallel_test.sh b/parallel_test.sh
index d8e198c..f6ddb10 100755
--- a/parallel_test.sh
+++ b/parallel_test.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 
 # Parallel test #
-#source ENV/bin/activate
+source ENV/bin/activate
 
 SOURCE_BAM_FILE="test/SRR2135332.chr21.bam"
 REFERENCE="test/chr21.fa"
@@ -17,4 +17,4 @@ COVERAGE_DIR="test_results/coverage/"
 mpirun -np $NUM_CORES src/cineca/parallel_reditools.py -f $SOURCE_BAM_FILE -o $OUTPUT_FILE -r $REFERENCE -t $TEMP_DIR -Z $SIZE_FILE -G $COVERAGE_FILE -D $COVERAGE_DIR
 ./merge.sh $TEMP_DIR $OUTPUT_FILE $NUM_CORES
 
-#deactivate
+deactivate
diff --git a/parallel_test_slurm.sh b/parallel_test_slurm.sh
index 588dcc3..56182cf 100755
--- a/parallel_test_slurm.sh
+++ b/parallel_test_slurm.sh
@@ -94,3 +94,5 @@ echo "[STATS] [MERGE] START="$t1_human" ["$t1"] END="$t2_human" ["$t2"] ELAPSED=
 
 echo "END:"`date`
 echo "OK" > $TEMP_DIR/status.txt
+
+deactivate
diff --git a/serial_test.sh b/serial_test.sh
index 2307ba1..9e47818 100755
--- a/serial_test.sh
+++ b/serial_test.sh
@@ -1,4 +1,8 @@
 #!/bin/bash
 
+source ENV/bin/activate
+
 # Serial test #
 python src/cineca/reditools.py -f test/SRR2135332.chr21.bam -r test/chr21.fa -o serial_table.txt
+
+deactivate