...

scripts/build-container.sh

@@ -5,3 +5,4 @@ set -ex
 sudo singularity build center-impute-grex.sif singularity.def
 
 singularity push -U center-impute-grex.sif library://kkmann/default/center-grex-imputation:latest
+

scripts/singularity.def

@@ -3,7 +3,7 @@ Bootstrap: docker
 From: rocker/verse:3.6.2
 
 %files
-    install.R /tmp/install.R
+    install.R install.R
 
 %post
     # non-interactive debconf
@@ -29,10 +29,7 @@ From: rocker/verse:3.6.2
         gcc wget make zlib1g zlib1g-dev libbz2-dev liblzma-dev libcurl4-openssl-dev pv
     wget https://github.com/samtools/bcftools/releases/download/$BCFVER/bcftools-$BCFVER.tar.bz2
     tar -xvjf bcftools-$BCFVER.tar.bz2
-    cd bcftools-$BCFVER
-    ./configure --prefix=/usr/bcftools
-    make
-    make install
+    (cd bcftools-$BCFVER; ./configure --prefix=/usr/bcftools; make; make install)
     (cd /usr/bin; ln -s /usr/bcftools/bin/bcftools bcftools)
 
     # install PrediXcan and python (2) dependencies
@@ -52,4 +49,4 @@ From: rocker/verse:3.6.2
     apt-get -y install bc
 
     # install R packages
-    Rscript /tmp/install.R
+    Rscript install.R