diff --git a/singularity/Makefile b/singularity/Makefile index 4c3c4e7c23038d7e7e2f298b620a38c47982d23f..33ec860442bfa3bcb62ee98df7e292546941c404 100644 --- a/singularity/Makefile +++ b/singularity/Makefile @@ -11,27 +11,27 @@ endif all: run_pipeline install: run_pipeline run_pipeline.sh workflows_shell.sh - install -d $(PREFIX)_$(VERSION)/bin - install run_pipeline $(PREFIX)_$(VERSION)/bin/. - install run_pipeline.sh $(PREFIX)_$(VERSION)/bin/. - install workflows_shell.sh $(PREFIX)_$(VERSION)/bin/. + sudo install -d $(PREFIX)_$(VERSION)/bin + sudo install run_pipeline $(PREFIX)_$(VERSION)/bin/. + sudo install run_pipeline.sh $(PREFIX)_$(VERSION)/bin/. + sudo install workflows_shell.sh $(PREFIX)_$(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 $(PREFIX)_$(VERSION)/bin/run_pipeline.sh $(PREFIX)_$(VERSION)/bin/run_$${datatype}_pipeline; \ + sudo ln -sf $(PREFIX)_$(VERSION)/bin/run_pipeline.sh $(PREFIX)_$(VERSION)/bin/run_$${datatype}_pipeline; \ done - ln -sfn $(PREFIX)_$(VERSION) $(PREFIX) + sudo 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/. + sudo install -d $(TEST_PREFIX)_$(VERSION)/bin + sudo install run_pipeline $(TEST_PREFIX)_$(VERSION)/bin/. + sudo install run_pipeline.sh $(TEST_PREFIX)_$(VERSION)/bin/. + sudo 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_$${datatype}_pipeline; \ + sudo ln -sf $(TEST_PREFIX)_$(VERSION)/bin/run_pipeline.sh $(TEST_PREFIX)_$(VERSION)/bin/run_$${datatype}_pipeline; \ done - ln -sfn $(TEST_PREFIX)_$(VERSION) $(TEST_PREFIX) + sudo 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.