From e73f02c949d59cb95005fab74fb5ba429ab5aa7f Mon Sep 17 00:00:00 2001
From: Blaise Li <blaise.li__git@nsup.org>
Date: Tue, 20 Jun 2023 11:37:23 +0200
Subject: [PATCH] Prefix for test install in singularity Makefile.
---
singularity/Makefile | 16 ++++++++++++++++
1 file changed, 16 insertions(+)
diff --git a/singularity/Makefile b/singularity/Makefile
index cc323d4..4c3c4e7 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
--
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