From b7689d9a550157f7de83588449c454b987d1f82a Mon Sep 17 00:00:00 2001
From: Donald Buczek <buczek@molgen.mpg.de>
Date: Sun, 11 Sep 2022 14:14:33 +0200
Subject: [PATCH] Add location of picard.jar

---
 Adapting_new_script_for_computing_cluster.sh | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/Adapting_new_script_for_computing_cluster.sh b/Adapting_new_script_for_computing_cluster.sh
index 3f090c3..9ec79bb 100755
--- a/Adapting_new_script_for_computing_cluster.sh
+++ b/Adapting_new_script_for_computing_cluster.sh
@@ -1,6 +1,12 @@
 #!/bin/bash
 # Performs alignment and filtering of CUT&Tag data
 
+# FIXME:
+# picard.jar should be available from some
+# program directory.
+# Downloaded from https://github.com/broadinstitute/picard/releases/tag/2.27.4
+PICARD=/project/RNAseq_Mdl_data/Konrad/August/picard.jar
+
 # inputs
 
 fastq_dir=/project/RNAseq_Mdl_data/Konrad/August/fastq # Fastq directory