From adb64b09cdb55cce932d6028d05c4f6537536459 Mon Sep 17 00:00:00 2001 From: Ai Nagano CRUKcambridge <40435585+cruknagano@users.noreply.github.com> Date: Mon, 26 Nov 2018 15:39:10 +0000 Subject: [PATCH 1/3] Link /roddy/bin/Roddy/dist/runtimeDevel/jre --- Dockerfile | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 4bc15bf..caf50a5 100644 --- a/Dockerfile +++ b/Dockerfile @@ -100,7 +100,10 @@ ADD scripts/combineJsons.py /roddy/bin/combineJsons.py ADD scripts/python_modules /roddy/bin/python_modules -RUN cd /roddy/bin/Roddy/dist/runtimeDevel && ln -sf groovy* groovy && ln -sf jdk* jdk && ln -sf jdk/jre jre; \ +RUN cd /roddy/bin/Roddy/dist/runtimeDevel; + ln -sf groovy2.3.6 groovy; \ + ln -sf jdk1.8.0_20 jdk; \ + ln -sf jdk1.8.0_20/jre jre; \ cd /roddy/bin/Roddy && cp applicationPropertiesAllLocal.ini applicationProperties.ini; \ bash /roddy/sgeResetup.sh; \ qconf -Mc /roddy/bin/sgeConfig.txt; \ From c0553d0956e15872039b857c3ee8c311c1db26cf Mon Sep 17 00:00:00 2001 From: Ai Nagano CRUKcambridge <40435585+cruknagano@users.noreply.github.com> Date: Mon, 26 Nov 2018 15:40:44 +0000 Subject: [PATCH 2/3] Link jre --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index caf50a5..6406500 100644 --- a/Dockerfile +++ b/Dockerfile @@ -100,7 +100,7 @@ ADD scripts/combineJsons.py /roddy/bin/combineJsons.py ADD scripts/python_modules /roddy/bin/python_modules -RUN cd /roddy/bin/Roddy/dist/runtimeDevel; +RUN cd /roddy/bin/Roddy/dist/runtimeDevel; \ ln -sf groovy2.3.6 groovy; \ ln -sf jdk1.8.0_20 jdk; \ ln -sf jdk1.8.0_20/jre jre; \ From 02318090d1086104d70b1a1f9b3cd282cb4d5edf Mon Sep 17 00:00:00 2001 From: Denis Yuen Date: Wed, 28 Nov 2018 09:28:17 -0500 Subject: [PATCH 3/3] Update Dockstore.cwl --- Dockstore.cwl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockstore.cwl b/Dockstore.cwl index 68a738e..6f4a6c8 100644 --- a/Dockstore.cwl +++ b/Dockstore.cwl @@ -14,7 +14,7 @@ dct:contributor: requirements: - class: DockerRequirement - dockerPull: quay.io/pancancer/pcawg-dkfz-workflow:2.0.6_cwl1.0 + dockerPull: quay.io/pancancer/pcawg-dkfz-workflow:2.0.7_cwl1.0 cwlVersion: v1.0