needs to be reworked - but is not deprecated completely

template2/genemarks.jinja2

@@ -1,74 +1,50 @@
-# 
-# Copyright 2009 Mark Fiers, Plant & Food Research
-# 
-# This file is part of Moa - http://github.com/mfiers/Moa
-# 
-# Moa is free software: you can redistribute it and/or modify it under
-# the terms of the GNU General Public License as published by the Free
-# Software Foundation, either version 3 of the License, or (at your
-# option) any later version.
-# 
-# Moa is distributed in the hope that it will be useful, but WITHOUT
-# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
-# or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public
-# License for more details.
-# 
-# You should have received a copy of the GNU General Public License
-# along with Moa.  If not, see <http://www.gnu.org/licenses/>.
-#
-
-moa_id = genemarks
-
-#include moabase, if it isn't already done yet..
-include $(MOABASE)/lib/gnumake/core.mk
-#define resultfilesets
-genemarks_input_files = $(wildcard $(genemarks_input_dir)/*.$(genemarks_input_extension))
-
-genemarks_out_files = $(addprefix out/, 										\
-		$(notdir $(patsubst %.$(genemarks_input_extension), %.lst, 				\
-		$(genemarks_input_files))))
-
-genemarks_gff_files = $(addprefix gff/, 										\
-		$(notdir $(patsubst %.$(genemarks_input_extension), %.gff, 				\
-		$(genemarks_input_files))))
-
-genemarks_cds_files = $(addprefix cds/, 										\
-		$(notdir $(patsubst %.$(genemarks_input_extension), %.cds.fasta, 		\
-		$(genemarks_input_files))))
-
-genemarks: $(genemarks_gff_files) $(genemarks_cds_files)
-	@echo "Created $(genemarks_gff_files)"
-	@echo "Via $(genemarks_out_files)"
-	@echo "From $(genemarks_input_files)"
-	@echo "again $(genemarks_input_dir)/*.$(genemarks_input_extension)"
-
-$(genemarks_gff_files): gff/%.gff: out/%.lst
-
-$(genemarks_cds_files): cds/%.cds.fasta: out/%.orf
-	cat $< 											\
-		| grep -v '^;'								\
-		| sed "s/orf_\([0-9]*\)/$*.gms.g\1/" 		\
-		> $@
-
-$(genemarks_out_files): out/%.lst: $(genemarks_input_dir)/%.$(genemarks_input_extension)
-	@echo "working from $< to create $@"
-	cd out; 														\
-		ln -s  $(realpath $<) $*;									\
-		gm -m $(genemarks_matrix) -onq -v $*							\
-
-PHONY: genemarks_prepare
-genemarks_prepare:
-	-mkdir out
-	-mkdir cds
-	-mkdir fasta
-	-mkdir gff
-
-PHONY: genemarks_post
-genemarks_post:
-
-PHONY: genemarks_clean
-genemarks_clean:
-	-rm -rf fasta/
-	-rm -rf cds/
-	-rm -rf gff/
-	-rm -rf out/
+### run
+
+ mkdir out
+ mkdir cds
+ mkdir fasta
+ mkdir gff
+
+#echo "Implement this":
+#echo genemarks_input_files = $(wildcard $(genemarks_input_dir)/*.$(genemarks_input_extension))
+#echo
+#echo genemarks_out_files = $(addprefix out/, 										\
+#echo 		$(notdir $(patsubst %.$(genemarks_input_extension), %.lst, 				\
+#echo 		$(genemarks_input_files))))
+#echo
+#echo genemarks_gff_files = $(addprefix gff/, 										\
+#echo 		$(notdir $(patsubst %.$(genemarks_input_extension), %.gff, 				\
+#echo 		$(genemarks_input_files))))
+#echo
+#echo genemarks_cds_files = $(addprefix cds/, 										\
+#echo 		$(notdir $(patsubst %.$(genemarks_input_extension), %.cds.fasta, 		\
+#echo 		$(genemarks_input_files))))
+#echo
+#echo genemarks: $(genemarks_gff_files) $(genemarks_cds_files)
+#echo 	@#echo "Created $(genemarks_gff_files)"
+#echo 	@#echo "Via $(genemarks_out_files)"
+#echo 	@#echo "From $(genemarks_input_files)"
+#echo 	@#echo "again $(genemarks_input_dir)/*.$(genemarks_input_extension)"
+#echo
+#echo $(genemarks_gff_files): gff/%.gff: out/%.lst
+#echo
+#echo $(genemarks_cds_files): cds/%.cds.fasta: out/%.orf
+#echo 	cat $< 											\
+#echo 		| grep -v '^;'								\
+#echo 		| sed "s/orf_\([0-9]*\)/$*.gms.g\1/" 		\
+#echo 		> $@
+#echo
+#echo $(genemarks_out_files): out/%.lst: $(genemarks_input_dir)/%.$(genemarks_input_extension)
+#echo 	@#echo "working from $< to create $@"
+#echo 	cd out; 														\
+#echo 		ln -s  $(realpath $<) $*;
+#echo 		gm -m $(genemarks_matrix) -onq -v $*							\
+#echo
+#echo
+
+### clean
+
+rm -rf fasta/
+rm -rf cds/
+rm -rf gff/
+rm -rf out/