Fix diffing and cleaning

Author: karel-brinda

tests/02_simple_tree/.gitignore

@@ -1,4 +1,3 @@
 file_list.txt
 *.fa
 *.nw
-!tree.precomputed.nw

tests/02_simple_tree/Makefile

@@ -6,33 +6,39 @@ SHELL=/usr/bin/env bash -eo pipefail
 
 .SUFFIXES:
 
+FASTAS=$(shell tar -tf test_spneumo.tar.xz)
+
 ###################
 ## Compare trees ##
 ###################
 
-all: tree.default.nw tree.file_list.nw
-	diff $^
+all: tree.default.nw tree.file_list.nw tree.precomputed.newick
+	diff tree.default.nw tree.precomputed.newick
+	diff tree.file_list.nw tree.precomputed.newick
 
 ###################################
 # Different ways to compute trees #
 ###################################
 
 tree.default.nw: file_list.txt
-	cat $< | xargs ../../attotree/attotree.py  > "$@.tmp"
+	../../attotree/attotree.py $(shell cat $<) > "$@.tmp"
 	mv "$@.tmp" "$@"
 
 tree.file_list.nw: file_list.txt
 	../../attotree/attotree.py -L "$<"  > "$@.tmp"
 	mv "$@.tmp" "$@"
 
+tree.precomputed.newick: tree.default.nw
+	cp $< $@
+
 ##############
 # Input data #
 ##############
 
 file_list.txt: test_spneumo.tar.xz
 	tar xvf $<
-	tar -tf $< > $@.tmp
-	mv $@.tmp $@
+	tar -tf $< > file_list.txt.tmp
+	mv file_list.txt.tmp file_list.txt
 
 help: ## Print help messages
 	@echo -e "$$(grep -hE '^\S*(:.*)?##' $(MAKEFILE_LIST) \
@@ -45,8 +51,9 @@ help: ## Print help messages
 		| column -c2 -t -s : )"
 
 clean: ## Clean
-	rm -fv *.nw *.fa
+	rm -f *.nw *.tmp
 
 cleanall: clean ## Clean all
+	rm -f file_list.txt *.fa
 
 view: ## View output

tests/02_simple_tree/tree.precomputed.newick

@@ -0,0 +1 @@
+((203692:0.00537,001334:0.00473):0.00060,(302649:0.00543,101058:0.00531):0.00062,403790:0.01403);