From 35270ee5125762082a794211fed627d24729d651 Mon Sep 17 00:00:00 2001
From: Daniel Cameron <d-cameron@github.com>
Date: Fri, 21 May 2021 17:00:27 +1000
Subject: [PATCH] Fixed gridss_minimal Docker image

---
 Dockerfile                    | 25 ++++++++++++++++++-------
 scripts/dev/create_release.sh |  6 +++---
 scripts/gridss                |  6 +++++-
 3 files changed, 26 insertions(+), 11 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index a2778eb5..f7d87709 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -65,13 +65,23 @@ RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -y \
 	&& rm -rf /var/lib/apt/lists/*
 # Hack a fake Rscript so that insert size metrics dont break when creating the histogram
 RUN echo "!/bin/sh" > /usr/local/bin/Rscript && chmod +x /usr/local/bin/Rscript
-RUN mkdir /opt/gridss/
-# grab the GRIDSS artefacts from the builders
-COPY --from=gridss_builder_c /opt/gridss/gridsstools /opt/gridss/gridsstools
-COPY --from=gridss_builder_java /opt/gridss/*.jar /opt/gridss/
-# just GRIDSS itself
-COPY scripts/gridss /opt/gridss/
 ENV PATH="/opt/gridss/:$PATH"
+# Install GRIDSS
+ARG GRIDSS_VERSION
+ENV GRIDSS_VERSION=${GRIDSS_VERSION}
+ENV GRIDSS_JAR=/opt/gridss/gridss-${GRIDSS_VERSION}-gridss-jar-with-dependencies.jar
+LABEL software="GRIDSS"
+LABEL software.version="$GRIDSS_VERSION"
+LABEL about.summary="Genomic Rearrangement IDentification Software Suite"
+LABEL about.home="https://github.com/PapenfussLab/gridss"
+LABEL about.tags="Genomics"
+RUN mkdir /opt/gridss/ /data
+COPY --from=gridss_builder_c /opt/gridss/gridsstools /opt/gridss/
+COPY --from=gridss_builder_java /opt/gridss/gridss-${GRIDSS_VERSION}-gridss-jar-with-dependencies.jar /opt/gridss/
+COPY scripts/gridss /opt/gridss/
+RUN chmod +x /opt/gridss/*
+WORKDIR /data/
+
 
 FROM gridss_c_build_environment AS gridss
 # Setup CRAN ubuntu package repository
@@ -144,7 +154,6 @@ RUN mkdir /opt/edirect && \
 	wget ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/edirect.tar.gz && \
 	tar zxf edirect.tar.gz && \
 	rm edirect.tar.gz
-
 ENV PATH="/opt/gridss/:/opt/RepeatMasker:/opt/rmblast/:/opt/trf:/opt/kraken2:/opt/blast:/opt/edirect:$PATH"
 # configure repeatmasker
 RUN cd /opt/RepeatMasker && \
@@ -175,6 +184,8 @@ COPY scripts/gridss \
 	scripts/gridss.config.R \
 	scripts/libgridss.R \
 	/opt/gridss/
+RUN chmod +x /opt/gridss/* && \
+	chmod -x /opt/gridss/*.R
 WORKDIR /data/
 
 # Copy build artifact locally
diff --git a/scripts/dev/create_release.sh b/scripts/dev/create_release.sh
index b4d722cf..73bfec50 100644
--- a/scripts/dev/create_release.sh
+++ b/scripts/dev/create_release.sh
@@ -12,11 +12,11 @@ fi
 echo Building GRIDSS $version 2>&1
 rm -rf release/
 mkdir release
-docker build --build-arg GRIDSS_VERSION=$version --target gridss_export_build_artefacts --output type=local,dest=release --progress=plain . && \
-docker build --build-arg GRIDSS_VERSION=$version --target gridss -t gridss:$version -t gridss:latest . && \
+docker build --build-arg GRIDSS_VERSION=$version --target gridss_export_build_artefacts --output type=local,dest=release . # --progress=plain
+docker build --build-arg GRIDSS_VERSION=$version --target gridss -t gridss:$version -t gridss:latest .
 docker build --build-arg GRIDSS_VERSION=$version --target gridss_minimal -t gridss_minimal:$version -t gridss_minimal:latest .
 cd release
-tar czvf gridss-$version.tar.gz *
+tar czf gridss-$version.tar.gz *
 # TODO: update conda?
 echo docker push gridss/gridss:$version gridss/gridss:latest gridss/gridss_minimal:$version gridss/gridss_minimal:latest 
 
diff --git a/scripts/gridss b/scripts/gridss
index 0e20975b..eeaa87bd 100644
--- a/scripts/gridss
+++ b/scripts/gridss
@@ -865,7 +865,11 @@ if [[ $do_preprocess == true ]] ; then
 				fi
 			fi
 			if [[ -f $tmp_prefix.insert_size_metrics ]] ; then
-				$rmcmd $tmp_prefix.insert_size_metrics $tmp_prefix.idsv_metrics $tmp_prefix.insert_size_histogram.pdf
+				$rmcmd $tmp_prefix.insert_size_metrics $tmp_prefix.idsv_metrics
+			fi
+			if [[ -f $tmp_prefix.insert_size_histogram.pdf ]] ; then
+				# pdf does not exist when using gridss_minimal docker image
+				$rmcmd $tmp_prefix.insert_size_histogram.pdf
 			fi
 			if [[ ! -f $prefix.sv.bam ]] ; then
 				write_status "pre-processing failed for $f"