From 1c7d639abe661b90fa337d1af395869561ac5266 Mon Sep 17 00:00:00 2001
From: naumenko-sa <sergey_bulk@list.ru>
Date: Fri, 2 Jun 2017 17:57:44 -0400
Subject: [PATCH] 	new file:   bcbio.prepare_family1.sh

---
 bcbio.prepare_family1.sh | 32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)
 create mode 100755 bcbio.prepare_family1.sh

diff --git a/bcbio.prepare_family1.sh b/bcbio.prepare_family1.sh
new file mode 100755
index 0000000..7c08ffd
--- /dev/null
+++ b/bcbio.prepare_family1.sh
@@ -0,0 +1,32 @@
+#!/bin/bash
+
+#prepare family for bcbio run when input files are family_sample.bam or family_sample_1/2.fq.gz
+
+family=$1
+
+cd $family
+
+cp ~/cre/bcbio.sample_sheet_header.csv $family.csv
+
+cd input
+
+ls | sed s/.bam// | sed s/.bai// | sed s/"_1.fq.gz"// | sed s/"_2.fq.gz"// | sort | uniq > ../samples.txt
+
+
+cd ..
+
+while read sample
+do
+    echo $sample","$sample","$family",,," >> $family.csv
+done < samples.txt
+
+bcbio_nextgen.py -w template ~/cre/bcbio.templates.exome.yaml $family.csv input/*
+
+mkdir config
+mkdir work
+
+cp $family/config/$family.yaml config
+
+cd ..
+
+