From 6b2ba94e3aa66a57b40c4e0824e5b82cc46d8374 Mon Sep 17 00:00:00 2001
From: Alice Minotto <i.m.e@hotmail.it>
Date: Wed, 26 Oct 2016 10:25:47 +0100
Subject: [PATCH] Update wrapper.sh

fixed for agave case insensitivity
---
 wrapper/wrapper.sh | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/wrapper/wrapper.sh b/wrapper/wrapper.sh
index 935ac19..c00e9de 100644
--- a/wrapper/wrapper.sh
+++ b/wrapper/wrapper.sh
@@ -1,19 +1,19 @@
 #!/bin/bash
 
-GFILE=(${gFile})
-PFILE=`echo ${PFILE} | sed -e 's/ /, /g'`
-PFILE=(${PFILE})
-MFILE=(${mFile})
-INPUTS="${GFILE[@]:1}, ${PFILE[@]:1}, ${MFILE[@]:1}"
+GFILEU=(${gFile})
+PFILEU=`echo ${pFile} | sed -e 's/ /, /g'`
+PFILEU=(${PFILEU})
+MFILEU=(${mFile})
+INPUTSU="${GFILEU[@]:1}, ${PFILEU[@]:1}, ${MFILEU[@]:1}"
 CMDLINEARG="${gFile} ${pFile} ${mFile} ${PHENOS} ${COVS} --outDir output ${mkplots} ${saveinter}"
-echo inputs are ${INPUTS}
+echo inputs are ${INPUTSU}
 echo arguments are ${CMDLINEARG}
 
 
 echo  universe                = docker >> lib/condorSubmitEdit.htc
 echo docker_image            =  cyverseuk/gwasser:v1.0.0 >> lib/condorSubmitEdit.htc ######
 echo arguments                          = ${CMDLINEARG} >> lib/condorSubmitEdit.htc
-echo transfer_input_files = ${INPUTS} >> lib/condorSubmitEdit.htc
+echo transfer_input_files = ${INPUTSU} >> lib/condorSubmitEdit.htc
 echo transfer_output_files = output >> lib/condorSubmitEdit.htc
 cat /mnt/data/rosysnake/lib/condorSubmit.htc >> lib/condorSubmitEdit.htc