From 8671be5f1be36baba2c85e28fc8a054b822b1174 Mon Sep 17 00:00:00 2001
From: Keiran Raine <kr2@sanger.ac.uk>
Date: Tue, 16 Apr 2019 12:22:47 +0000
Subject: [PATCH] Bump PCAP for faster bamsort

---
 CHANGES.md                   | 5 +++++
 Dockerfile                   | 2 +-
 build/opt-build.sh           | 2 +-
 cwls/mixins/requirements.yml | 2 +-
 4 files changed, 8 insertions(+), 3 deletions(-)

diff --git a/CHANGES.md b/CHANGES.md
index 0b8ec03..7585f04 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -1,5 +1,10 @@
 # CHANGES
 
+## 3.1.4
+
+* Update PCAP-core to 4.3.5
+  * Sppedup bamsort by adding sort helpers
+
 ## 3.1.3
 
 * Update PCAP-core to 4.3.4
diff --git a/Dockerfile b/Dockerfile
index c30a3c0..0e74f00 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -47,7 +47,7 @@ MAINTAINER  cgphelp@sanger.ac.uk
 
 LABEL vendor="Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute"
 LABEL uk.ac.sanger.cgp.description="PCAP-core for dockstore.org"
-LABEL uk.ac.sanger.cgp.version="3.1.3"
+LABEL uk.ac.sanger.cgp.version="3.1.4"
 
 RUN apt-get -yq update
 RUN apt-get install -yq --no-install-recommends \
diff --git a/build/opt-build.sh b/build/opt-build.sh
index a733390..db63175 100755
--- a/build/opt-build.sh
+++ b/build/opt-build.sh
@@ -14,7 +14,7 @@ VER_BIODBHTS="2.10"
 VER_BWA="v0.7.17"
 VER_HTSLIB="1.9"
 VER_SAMTOOLS="1.9"
-VER_PCAP="4.3.4"
+VER_PCAP="4.3.5"
 
 if [ "$#" -lt "1" ] ; then
   echo "Please provide an installation path such as /opt/ICGC"
diff --git a/cwls/mixins/requirements.yml b/cwls/mixins/requirements.yml
index c2e9938..3e0705f 100644
--- a/cwls/mixins/requirements.yml
+++ b/cwls/mixins/requirements.yml
@@ -1,2 +1,2 @@
 class: DockerRequirement
-dockerPull: "quay.io/wtsicgp/dockstore-cgpmap:3.1.3"
+dockerPull: "quay.io/wtsicgp/dockstore-cgpmap:3.1.4"