update to caveman 1.15.4

.gitignore

@@ -11,3 +11,4 @@
 /MYMETA.yml
 /reports
 .vstags
+*.sif

CHANGES.md

@@ -1,12 +1,11 @@
 # CHANGES
 
-## 1.19.2
+## 1.19.0
 
-- Update ci to include copying generateCavemanUMNormVCF into the image
+- Update to caveman 1.15.4
+- Update Dockerfile to include copying generateCavemanUMNormVCF into the image, and tweak CI to understand that
+- Update Dockerfile to use setup.sh install method from caveman repo and ensure linasm.so is on LD PATH
 
-## 1.19.1
-
-- Update Dockerfile to include copying generateCavemanUMNormVCF into the image
 
 ## 1.18.3
 

Dockerfile

@@ -5,7 +5,7 @@ USER  root
 # ALL tool versions used by opt-build.sh
 ENV VER_VCFTOOLS="0.1.16"
 ENV VER_CGPVCF="v2.2.1"
-ENV VER_CAVEMAN="1.15.3"
+ENV VER_CAVEMAN="1.15.4"
 ENV VER_BEDTOOLS="2.27.1"
 ENV VER_CGPCAVEPOSTPROC="1.12.0"
 
@@ -20,6 +20,8 @@ RUN apt-get install -yq --no-install-recommends zlib1g-dev
 RUN apt-get install -yq --no-install-recommends libbz2-dev
 RUN apt-get install -yq --no-install-recommends liblzma-dev
 RUN apt-get install -yq --no-install-recommends libcurl4-openssl-dev
+RUN apt-get install -yq --no-install-recommends wget
+RUN apt-get install -yq --no-install-recommends unzip
 
 
 RUN locale-gen en_US.UTF-8
@@ -45,7 +47,7 @@ FROM ubuntu:20.04
 
 LABEL maintainer="[email protected]" \
       uk.ac.sanger.cgp="Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute" \
-      version="1.19.2" \
+      version="1.19.0" \
       description="cgpCaVEManWrapper docker"
 
 

build/opt-build.sh

@@ -50,18 +50,18 @@ export PERL5LIB=`echo $INST_PATH/lib/perl5:$PERL5LIB | perl -pe 's/:\$//;'`
 export C_INCLUDE_PATH=`echo $INST_PATH/include/ | perl -pe 's/:\$//;'`
 set -u
 
-## linasm library required by CaVEMan core
-if [ ! -e $SETUP_DIR/linasm.success ]; then
-  curl -sSL --retry 10 https://sourceforge.net/projects/linasm/files/linasm-1.13%28stable%29.tar.gz/download > distro.tar.gz
-  rm -rf distro/*
-  tar --strip-components 1 -C distro -xzf distro.tar.gz
-  cd distro
-  make
-  make install prefix=$INST_PATH
-  cd $SETUP_DIR
-  rm -rf distro.* distro/*
-  touch $SETUP_DIR/linasm.success.success
-fi
+# ## linasm library required by CaVEMan core
+# if [ ! -e $SETUP_DIR/linasm.success ]; then
+#   curl -sSL --retry 10 https://sourceforge.net/projects/linasm/files/linasm-1.13%28stable%29.tar.gz/download > distro.tar.gz
+#   rm -rf distro/*
+#   tar --strip-components 1 -C distro -xzf distro.tar.gz
+#   cd distro
+#   make
+#   make install prefix=$INST_PATH
+#   cd $SETUP_DIR
+#   rm -rf distro.* distro/*
+#   touch $SETUP_DIR/linasm.success.success
+# fi
 
 
 ## vcftools
@@ -97,13 +97,12 @@ if [ ! -e $SETUP_DIR/CaVEMan.success ]; then
   rm -rf distro/*
   tar --strip-components 1 -C distro -xzf distro.tar.gz
   cd distro
-  mkdir -p c/bin
-
-  make clean
-  make -j$CPU prefix=$INST_PATH
-  cp bin/caveman $INST_PATH/bin/.
-  cp bin/mergeCavemanResults $INST_PATH/bin/.
-  cp bin/generateCavemanUMNormVCF $INST_PATH/bin/.
+  mkdir install
+  ./setup.sh install/
+  cp install/bin/caveman $INST_PATH/bin/.
+  cp install/bin/mergeCavemanResults $INST_PATH/bin/.
+  cp install/bin/generateCavemanUMNormVCF $INST_PATH/bin/.
+  cp -r install/lib/* $INST_PATH/lib
   cd $SETUP_DIR
   rm -rf distro.* distro/*
   touch $SETUP_DIR/CaVEMan.success