From e0a6c7568ff3e06f928deb291a4a60686242f1e0 Mon Sep 17 00:00:00 2001
From: RoanKanninga <roankanninga@gmail.com>
Date: Mon, 15 Feb 2016 13:54:56 +0100
Subject: [PATCH] added config files for automate.sh

---
 automate_demultiplexing/automate.sh               | 15 ++++++++++-----
 automate_demultiplexing/gattaca.cfg               |  5 +++++
 .../zinc-finger.gcc.rug.nl.cfg                    |  5 +++++
 3 files changed, 20 insertions(+), 5 deletions(-)
 create mode 100644 automate_demultiplexing/gattaca.cfg
 create mode 100644 automate_demultiplexing/zinc-finger.gcc.rug.nl.cfg

diff --git a/automate_demultiplexing/automate.sh b/automate_demultiplexing/automate.sh
index 960264d..1e55776 100755
--- a/automate_demultiplexing/automate.sh
+++ b/automate_demultiplexing/automate.sh
@@ -6,11 +6,16 @@ module load ngs-utils
 module load Python
 module list
 
-WORKDIR="/groups/umcg-gaf/scr01/"
-LOGSDIR="${WORKDIR}/logs/"
-NEXTSEQDIR="${WORKDIR}/sequencers/"
-SAMPLESHEETDIR="${WORKDIR}/Samplesheets/"
-ONTVANGER="helpdesk.gcc.groningen@gmail.com"
+##source config file (zinc-finger.gcc.rug.nl.cfg OR gattaca.cfg)
+myhost=$(hostname)
+if [[ $myhost == *"gattaca"* ]]
+then
+	. gattaca.cfg
+else
+	. ${myhost}
+fi
+
+ 
 
 ### Sequencer is writing to this location: $NEXTSEQDIR
 ### Looping through to see if all files
diff --git a/automate_demultiplexing/gattaca.cfg b/automate_demultiplexing/gattaca.cfg
new file mode 100644
index 0000000..d5c8286
--- /dev/null
+++ b/automate_demultiplexing/gattaca.cfg
@@ -0,0 +1,5 @@
+WORKDIR="/groups/umcg-gaf/scr01/"
+LOGSDIR="${WORKDIR}/logs/"
+NEXTSEQDIR="${WORKDIR}/sequencers/"
+SAMPLESHEETDIR="${WORKDIR}/Samplesheets/"
+ONTVANGER="helpdesk.gcc.groningen@gmail.com"
diff --git a/automate_demultiplexing/zinc-finger.gcc.rug.nl.cfg b/automate_demultiplexing/zinc-finger.gcc.rug.nl.cfg
new file mode 100644
index 0000000..88ea830
--- /dev/null
+++ b/automate_demultiplexing/zinc-finger.gcc.rug.nl.cfg
@@ -0,0 +1,5 @@
+WORKDIR="/groups/umcg-gaf/tmp05/"
+LOGSDIR="${WORKDIR}/logs/"
+NEXTSEQDIR="${WORKDIR}/rawdata/nextseq"
+SAMPLESHEETDIR="${WORKDIR}/Samplesheets/"
+ONTVANGER="helpdesk.gcc.groningen@gmail.com"