pathfile

Makefile

@@ -11,7 +11,7 @@ MAKEDIR := $(dir $(firstword $(MAKEFILE_LIST)))
 DIR := ${CURDIR}
 
 
-all: brew setup download_scripts orthofuser blast spades trinity shannon seqtk busco trimmomatic
+all: setup brew download_scripts orthofuser blast spades trinity shannon seqtk busco trimmomatic transrate postscript
 
 .DELETE_ON_ERROR:
 .PHONY:report
@@ -20,13 +20,14 @@ setup:
 	mkdir -p ${DIR}/scripts
 	mkdir -p ${DIR}/software
 	mkdir -p ${DIR}/shared
+	rm pathfile
 
 
 brew:
 ifeq "$(shell basename $(shell which brew))" "brew"
 	@echo "BREW is already installed"
 else
-	$error("*** BREW MUST BE INSTALLED BEFORE YOU CAN PROCEED, SEE: http://angus.readthedocs.io/en/2016/linuxbrew_install.html ***")
+	$error("*** BREW MUST BE PROPERLY INSTALLED BEFORE YOU CAN PROCEED, SEE: http://angus.readthedocs.io/en/2016/linuxbrew_install.html ***")
 endif
 
 download_scripts:
@@ -39,17 +40,15 @@ ifeq "$(shell basename $(shell which orthofuser.py))" "orthofuser.py"
 else
 	cd ${DIR}/software && \
 	git clone https://github.com/macmanes-lab/OrthoFinder.git
-	export PATH=${DIR}/software/OrthoFinder/orthofinder:$$PATH
 	@echo ${DIR}/software/OrthoFinder/orthofinder | tee -a pathfile
 endif
 
 blast:
-ifeq "$(shell basename $(shell which blastp))" "blastwww"
+ifeq "$(shell basename $(shell which blastp))" "blastww"
 	@echo "BLASTP is already installed"
 else
 	@echo "blastp is not installed, installing now..."
 	cd ${DIR}/software &$ curl -LO ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.6.0+-x64-linux.tar.gz && tar -zxf ncbi-blast-2.6.0+-x64-linux.tar.gz
-	export PATH=${DIR}/software/ncbi-blast-2.6.0+/bin:$$PATH
 	@echo ${DIR}/software/ncbi-blast-2.6.0+/bin | tee -a pathfile
 endif
 
@@ -59,34 +58,34 @@ ifeq "$(shell basename $(shell which spades.py))" "spades.py"
 else
 	cd ${DIR}/software && \
 	curl -LO http://cab.spbu.ru/files/release3.10.1/SPAdes-3.10.1-Linux.tar.gz && tar -zxf SPAdes-3.10.1-Linux.tar.gz && \
-	export PATH=${DIR}/software/SPAdes-3.10.1-Linux/bin:$$PATH
+	@echo ${DIR}/software/SPAdes-3.10.1-Linux/bin | tee -a pathfile
 endif
 
 trinity:
 ifeq "$(shell basename $(shell which Trinity))" "Trinity"
-	@echo "Trinity is already installed"
+	@echo "TRINITY is already installed"
 else
 	cd ${DIR}/software && \
 	git clone https://github.com/trinityrnaseq/trinityrnaseq.git && cd trinityrnaseq && make
-	export PATH=$$PATH:${DIR}/software/trinityrnaseq
+	@echo PATH=$$PATH:${DIR}/software/trinityrnaseq | tee -a pathfile
 endif
 
 shannon:
 ifeq "$(shell basename $(shell which shannon.py))" "shannon.py"
-	@echo "Shannon is already installed"
+	@echo "SHANNON is already installed"
 else
 	cd ${DIR}/software && \
 	git clone https://github.com/sreeramkannan/Shannon.git
-	export PATH=$$PATH:${DIR}/software/Shannon
+	@echo PATH=$$PATH:${DIR}/software/Shannon | tee -a pathfile
 endif
 
 seqtk:
 ifeq "$(shell basename $(shell which seqtk))" "seqtk"
-	@echo "seqtk is already installed"
+	@echo "SEQTK is already installed"
 else
 	cd ${DIR}/software && \
 	git clone https://github.com/lh3/seqtk.git && cd seqtk && make
-	export PATH=$$PATH:${DIR}/software/seqtk
+	@echo PATH=$$PATH:${DIR}/software/seqtk | tee -a pathfile
 endif
 
 busco:
@@ -96,20 +95,25 @@ else
 	cd ${DIR}/software && \
 	git clone https://gitlab.com/ezlab/busco.git && cd busco && python setup.py install --user --prefix=
 	export PATH=$$PATH:${DIR}/software/busco
+	@echo PATH=$$PATH:${DIR}/software/busco | tee -a pathfile
 endif
 
 trimmomatic:
 ifeq "$(shell basename $(shell which trimmomatic))" "trimmomatic"
-	@echo "trimmomatic is already installed"
+	@echo "TRIMMOMATIC is already installed"
 else
 	brew install trimmomatic
 endif
 
 transrate:
 ifeq "$(shell basename $(shell which transrate))" "transrate"
-	@echo "trimmomatic is already installed"
+	@echo "TRANSRATE is already installed"
 else
 	cd ${DIR}/software && \
 	curl -LO https://bintray.com/artifact/download/blahah/generic/transrate-1.0.3-linux-x86_64.tar.gz && tar -zxf transrate-1.0.3-linux-x86_64.tar.gz
-	export PATH=$$PATH:${DIR}/software/transrate-1.0.3-linux-x86_64
+	@echo PATH=$$PATH:${DIR}/software/transrate-1.0.3-linux-x86_64 | tee -a pathfile
 endif
+
+postscript:
+	@echo "\n\n *** The following locations need to be added to your $PATH *** \n\n "
+	cat pathfile