From 614d7a3d9acf8e0856287e5197fa9c90681ca8ba Mon Sep 17 00:00:00 2001
From: kmnip <kamingnip@gmail.com>
Date: Wed, 14 Feb 2018 13:47:17 -0800
Subject: [PATCH] makefile for installing python3 instead of python2

---
 prereqs/makefile3 | 66 +++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 66 insertions(+)
 create mode 100644 prereqs/makefile3

diff --git a/prereqs/makefile3 b/prereqs/makefile3
new file mode 100644
index 0000000..452b9af
--- /dev/null
+++ b/prereqs/makefile3
@@ -0,0 +1,66 @@
+# This make file would install all require software packages except ABySS.
+
+SHELL:=/bin/bash -eu -o pipefail
+
+.DELETE_ON_ERROR:
+
+WORKDIR:=$(shell pwd)
+
+IGRAPH_VERSION:=0.7.1
+PYTHON_VERSION:=3.6.4
+
+all: transabyss transabyss-merge
+	touch $@.COMPLETE
+
+clean: clean_blat clean_python clean_igraph
+	rm -f all.COMPLETE && \
+	rm -rf ./bin ./lib ./include ./share
+
+transabyss: bin blat.COMPLETE python.COMPLETE python-igraph.COMPLETE
+
+transabyss-merge: transabyss
+
+bin:
+	mkdir -p ./bin
+
+blat.COMPLETE: bin
+	wget --quiet --no-check-certificate -N -P ./bin http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/blat && \
+	chmod +x ./bin/blat && \
+	touch $@
+	
+clean_blat:
+	rm -f blat.COMPLETE ./bin/blat
+
+python.COMPLETE: bin
+	wget --quiet --no-check-certificate -N https://www.python.org/ftp/python/$(PYTHON_VERSION)/Python-$(PYTHON_VERSION).tgz && \
+	tar -zxf Python-$(PYTHON_VERSION).tgz && \
+	cd Python-$(PYTHON_VERSION) && \
+	./configure --quiet --prefix=$(WORKDIR) && \
+	make --quiet && \
+	make --quiet install && \
+	cd $(WORKDIR) && \
+	ln -s python3 ./bin/python && \
+	touch $@
+
+clean_python:
+	rm -f python.COMPLETE python-igraph.COMPLETE Python-$(PYTHON_VERSION).tgz && \
+	rm -rf Python-$(PYTHON_VERSION)
+
+igraph.COMPLETE: bin
+	wget --quiet --no-check-certificate -N http://igraph.org/nightly/get/c/igraph-$(IGRAPH_VERSION).tar.gz && \
+	tar -zxf igraph-$(IGRAPH_VERSION).tar.gz && \
+	cd igraph-$(IGRAPH_VERSION) && \
+	./configure --quiet --prefix=$(WORKDIR) && \
+	make --quiet && \
+	make --quiet install && \
+	cd $(WORKDIR) && \
+	touch $@
+
+clean_igraph:
+	rm -f igraph.COMPLETE igraph-$(IGRAPH_VERSION).tar.gz && \
+	rm -rf igraph-$(IGRAPH_VERSION)
+
+python-igraph.COMPLETE: bin python.COMPLETE igraph.COMPLETE
+	export PKG_CONFIG_PATH=$(WORKDIR)/lib/pkgconfig && \
+	./bin/pip3 --quiet install python-igraph && \
+	touch $@