Add a Makefile

Makefile

@@ -0,0 +1,39 @@
+DESTDIR :=
+PREFIX := /usr
+
+CONDA := conda
+PIP := pip
+
+all: scripts contrib/RSEM
+
+contrib/RSEM:
+	$(MAKE) -C $@
+
+scripts:
+	$(MAKE) -C $@
+
+install: install-python install-systemd-units install-RSEM install-scripts install-conda-env
+
+install-scripts:
+	$(MAKE) -C scripts install
+
+install-python:
+	$(PIP) install --prefix="${DESTDIR}${PREFIX}" .
+
+install-systemd-units:
+	mkdir -p "${DESTDIR}/etc/systemd/system/"
+	install data/systemd/rnaseq-pipeline-viewer.service data/systemd/rnaseq-pipeline-worker@.service "${DESTDIR}/etc/systemd/system/"
+	@echo "Remember to run 'systemctl override rnaseq-pipeline-viewer' and 'systemctl override rnaseq-pipeline-worker@' and set CONDA_BIN, CONDA_ENV, GEMMA_USERNAME and GEMMA_PASSWORD environment variables."
+
+install-RSEM:
+	$(MAKE) -C contrib/RSEM install prefix="${DESTDIR}${PREFIX}"
+
+install-conda-env: environment.yml
+	mkdir -p "${DESTDIR}/share/rnaseq-pipeline/"
+	$(CONDA) env create -p "${DESTDIR}${PREFIX}/share/rnaseq-pipeline/conda-env" -f environment.yml
+
+clean:
+	$(MAKE) -C contrib/RSEM clean
+	$(MAKE) -C scripts clean
+
+.PHONY: all scripts contrib/RSEM install install-python install-systemd-unit install-RSEM

scripts/Makefile

@@ -1,2 +1,14 @@
+DESTDIR :=
+PREFIX := /usr
+
 clean-unused-shm-objects: clean-unused-shm-objects.c
-	gcc -o $@ $<
+	$(CC) -o $@ $<
+
+install:
+	mkdir -p "${DESTDIR}${PREFIX}/bin"
+	install clean-unused-shm-objects "${DESTDIR}${PREFIX}/bin"
+
+clean:
+	rm clean-unused-shm-objects
+
+.PHONY: install clean