From 43ec501eff940204d4ec00bc02a4d249953055fc Mon Sep 17 00:00:00 2001 From: Blaise Li <blaise.li__git@nsup.org> Date: Wed, 10 Jul 2024 12:33:14 +0200 Subject: [PATCH] Install with sudo. --- singularity/Makefile | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/singularity/Makefile b/singularity/Makefile index 4c3c4e7..33ec860 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. -- GitLab