From 36c5c218598071e07ca43fbf15ec50c088317373 Mon Sep 17 00:00:00 2001
From: Daniel Cameron <d-cameron@github.com>
Date: Thu, 10 Dec 2020 15:43:25 +1100
Subject: [PATCH] Updated docker image for v2.10.2

---
 .dockerignore                | 4 +---
 Dockerfile                   | 9 ++++-----
 scripts/dev/create_docker.sh | 4 ++--
 3 files changed, 7 insertions(+), 10 deletions(-)

diff --git a/.dockerignore b/.dockerignore
index f8b152149..e9bb8791b 100644
--- a/.dockerignore
+++ b/.dockerignore
@@ -1,4 +1,2 @@
 *
-!/target/*-jar-with-dependencies.jar
-!/scripts/*
-
+!/target/github_package/*
diff --git a/Dockerfile b/Dockerfile
index c181b9215..bec69a464 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -21,7 +21,7 @@ ENV R_INSTALL_STAGED=false
 RUN Rscript -e 'options(Ncpus=16L, repos="https://cloud.r-project.org/");install.packages(c("tidyverse", "assertthat", "testthat", "NMF", "randomForest", "stringdist", "stringr", "argparser", "R.cache", "BiocManager", "Rcpp", "blob", "RSQLite"))'
 RUN Rscript -e 'options(Ncpus=16L, repos="https://cloud.r-project.org/");BiocManager::install(ask=FALSE, pkgs=c("copynumber", "StructuralVariantAnnotation", "VariantAnnotation", "rtracklayer", "BSgenome", "Rsamtools", "biomaRt", "org.Hs.eg.db", "TxDb.Hsapiens.UCSC.hg19.knownGene", "TxDb.Hsapiens.UCSC.hg38.knownGene"))'
 
-ENV GRIDSS_VERSION=2.9.4
+ENV GRIDSS_VERSION=2.10.2
 ENV GRIDSS_JAR=/opt/gridss/gridss-${GRIDSS_VERSION}-gridss-jar-with-dependencies.jar
 LABEL version="1"
 LABEL software="GRIDSS"
@@ -31,10 +31,9 @@ LABEL about.home="https://github.com/PapenfussLab/gridss"
 LABEL about.tags="Genomics"
 
 RUN mkdir /opt/gridss/
-COPY target/gridss-${GRIDSS_VERSION}-gridss-jar-with-dependencies.jar /opt/gridss/
-COPY scripts/*.sh /opt/gridss/
-COPY scripts/*.R /opt/gridss/
-COPY src/main/c/gridsstools/gridsstools /opt/gridss/
+COPY target/github_package/* /opt/gridss/
+RUN chmod +x /opt/gridss/gridsstools /opt/gridss/*.R /opt/gridss/*.sh
+ENV PATH="/opt/gridss:$PATH"
 
 WORKDIR /data/
 ENTRYPOINT ["/opt/gridss/gridss.sh"]
diff --git a/scripts/dev/create_docker.sh b/scripts/dev/create_docker.sh
index e8c61ec45..c2f8a55da 100644
--- a/scripts/dev/create_docker.sh
+++ b/scripts/dev/create_docker.sh
@@ -11,5 +11,5 @@ fi
 echo Building GRIDSS $version
 docker build --tag gridss/gridss:latest .
 docker build --tag gridss/gridss:$version .
-docker push gridss/gridss:latest
-docker push gridss/gridss:$version
+echo docker push gridss/gridss:latest
+echo docker push gridss/gridss:$version