diff --git a/singularity/Makefile b/singularity/Makefile index cc323d461f6b408eec9819ea3ac360289840bc34..4c3c4e7c23038d7e7e2f298b620a38c47982d23f 100644 --- a/singularity/Makefile +++ b/singularity/Makefile @@ -4,6 +4,10 @@ ifeq ($(PREFIX),) PREFIX := /opt/bioinfo_utils endif +ifeq ($(TEST_PREFIX),) + TEST_PREFIX := /opt/test_bioinfo_utils +endif + all: run_pipeline install: run_pipeline run_pipeline.sh workflows_shell.sh @@ -17,6 +21,18 @@ install: run_pipeline run_pipeline.sh workflows_shell.sh done ln -sfn $(PREFIX)_$(VERSION) $(PREFIX) +# To test before replacing "prod" version in $(PREFIX) +install_test: run_pipeline run_pipeline.sh workflows_shell.sh + install -d $(TEST_PREFIX)_$(VERSION)/bin + install run_pipeline $(TEST_PREFIX)_$(VERSION)/bin/. + install run_pipeline.sh $(TEST_PREFIX)_$(VERSION)/bin/. + install workflows_shell.sh $(TEST_PREFIX)_$(VERSION)/bin/. + for datatype in sRNA-seq small_RNA-seq RNA-seq GRO-seq PRO-seq Degradome-seq Ribo-seq iCLIP-seq iCLIP; \ + do \ + ln -sf $(TEST_PREFIX)_$(VERSION)/bin/run_pipeline.sh $(TEST_PREFIX)_$(VERSION)/bin/run_$${datatype}_pipeline; \ + done + ln -sfn $(TEST_PREFIX)_$(VERSION) $(TEST_PREFIX) + # TODO: Bind home on temporary directory at build time in order to decrease "pollution" risks? # Should depend on the rest of the repository. run_pipeline: run_pipeline.def workflows_base.sif