From f5ce8264d09307dd56b11a31b4b7e1993bb394d9 Mon Sep 17 00:00:00 2001
From: Stephen Newhouse <stephen.j.newhouse@gmail.com>
Date: Thu, 17 Sep 2015 06:56:27 +0100
Subject: [PATCH 1/2] dev updates Thu 17 Sep 2015 06:56:27 BST

---
 bin/ngseasy_trimmomatic                     |   4 ++--
 containerized/ngseasy_dockerfiles/.DS_Store | Bin 6148 -> 6148 bytes
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/bin/ngseasy_trimmomatic b/bin/ngseasy_trimmomatic
index 3503442..64dc7ae 100755
--- a/bin/ngseasy_trimmomatic
+++ b/bin/ngseasy_trimmomatic
@@ -409,9 +409,9 @@ fi
 ########################################################################################################
 # adapter_fa : check of this is in palce and exit if not
 ########################################################################################################
-if [[ ${GENOMEBUILD} == "b37" ]]; then
+if [[ "${GENOMEBUILD}" == "b37" ]]; then
     adapter_fa="/home/pipeman/ngs_projects/ngseasy_resources/reference_genomes_b37/contaminant_list.fa"
-elif [[ ${GENOMEBUILD} == "hg19" ]]; then
+elif [[ "${GENOMEBUILD}" == "hg19" ]]; then
     adapter_fa="/home/pipeman/ngs_projects/ngseasy_resources/reference_genomes_hg19/contaminant_list.fa"
 elif [[ "${GENOMEBUILD}" == "hs37d5" ]]; then
     adapter_fa="/home/pipeman/ngs_projects/ngseasy_resources/reference_genomes_hs37d5/contaminant_list.fa"
diff --git a/containerized/ngseasy_dockerfiles/.DS_Store b/containerized/ngseasy_dockerfiles/.DS_Store
index ca25b3ce7611256bd1b13844357ab69fb5875871..6597501f6a351430701d041fcad819b3699873f3 100755
GIT binary patch
delta 101
zcmZoMXfc@J&&a$nU^gQp^JX3<14egVhCGIJhGK?PhD0D)$q>(w38agGyyTSP<ea4Z
n{2WFG1_o}1QidcT&SNM6lJP(`NO>w;$!1697M9KI9Dn%%*8~|_

delta 32
ocmZoMXfc@J&&aqjU^gQp<7OTv1IEo$n2T8^HbiV@=lIJH0HCx9^8f$<


From 58667cdd334d0beab673245844b0bd26074db7ae Mon Sep 17 00:00:00 2001
From: Stephen Newhouse <stephen.j.newhouse@gmail.com>
Date: Thu, 17 Sep 2015 06:56:40 +0100
Subject: [PATCH 2/2] dev updates Thu 17 Sep 2015 06:56:40 BST

---
 containerized/ngseasy_dockerfiles/.DS_Store | Bin 6148 -> 0 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)
 delete mode 100755 containerized/ngseasy_dockerfiles/.DS_Store

diff --git a/containerized/ngseasy_dockerfiles/.DS_Store b/containerized/ngseasy_dockerfiles/.DS_Store
deleted file mode 100755
index 6597501f6a351430701d041fcad819b3699873f3..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

literal 6148
zcmeHKUyIW~5TET;O|J;?9~}6SSD_CT4SCJg^HC^N?hsF6atYUkn3N{59Ho$FKZgH5
zh9LSK{3yQpo89esQhhCl?1Y)$WHPf$e%tJJh)9f@^gfYGL=Kd((}Veo@N?D;>6pk4
zP^d9ts_2X&N+{mQwt>sY0I%ImD(Dm|mtoa@uOHt>B<U5Rr<5g&YL?_>g8ZM!ESFV1
z9R3iUo$i&Z*PPyNpD*{u?u*H^Tukb?ZmLl{f3EIinkB{`$MtmWKP}7r+>et(nJpss
z_M@_>V_9VL3#G?LvPjFtsBDU~I-cn9j$~R-BlpgDp1nrtI4-h7S;<7^vOaTqd`0fw
za_I-b!1H~7HSm@}FdTRf9|WtF`^9nY-t+gLJe#fFynXln!^cmbzkbszB=BQaa?9Wv
zzQeh`L6!t*6-YWstCKvzOL2Lh8hix}l51G~MS#(ZDeF-!S_UiwmVvD^V757@zxA2z
zgq8uzz-4EE_XiKk7#eIfs;vV?wE(~_!b;$CFTpjQ!O&o<5l<jOmjZREFfE4A<%oMG
zFErR{)a4{h^C8U4!gMG?&5rRsl};kmXsu<yGVmt@-1|XXKK~#8yZ={7)>sBC1OF!j
zqI)no7~$Q_*}CzTeAar<mrxeYYc-yiz)?pra``CUgDOGXV+R--Y&9YRv3~><4c1r&
Hw#vXSw<vSE