include LAVA software in r.sif container

comorment · Sep 22, 2021 · 872e9ae · 872e9ae
1 parent 05d174e
commit 872e9ae
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diff --git a/containers/r/Dockerfile b/containers/r/Dockerfile
@@ -38,5 +38,15 @@ COPY /scripts/install_gcta.sh /tmp
 RUN chmod +x /tmp/install_gcta.sh
 RUN bash /tmp/install_gcta.sh
 
+RUN R -e "install.packages('BiocManager')"
+RUN R -e "BiocManager::install('snpStats')"
+RUN R -e "devtools::install_git('https://github.com/josefin-werme/LAVA.git')"
+
+WORKDIR /tools/
+COPY /scripts/install_lava_partitioning.sh /tmp
+RUN chmod +x /tmp/install_lava_partitioning.sh
+RUN bash /tmp/install_lava_partitioning.sh
+
+
 WORKDIR /tools
 
diff --git a/scripts/install_lava_partitioning.sh b/scripts/install_lava_partitioning.sh
@@ -0,0 +1,6 @@
+# the original software is https://github.com/cadeleeuw/lava-partitioning
+# ofrei fork is a minor change in the makefile 
+git clone https://github.com/ofrei/lava-partitioning.git && cd lava-partitioning
+make
+cp ldblock /bin
+