makefiles/sep.mk

   1 INPUTPATH := fqrad
   2 OUTPUTPREFIX := out
   3
   4 INF := $(patsubst %.1.cut.gz,%,$(foreach ONEINPUTPATH,$(INPUTPATH),$(wildcard $(ONEINPUTPATH)/*.1.cut.gz)))
   5
   6 OUTF := $(addprefix $(OUTPUTPREFIX)/,$(INF))
   7 SEP1 := $(addsuffix _000000,$(OUTF))
   8 SEP2 := $(addsuffix _210210,$(OUTF))
   9 SEP3 := $(addsuffix _221210,$(OUTF))
  10
  11 PATHS := $(addprefix $(OUTPUTPREFIX)/,$(INPUTPATH))
  12
  13 NEEDED_COMMANDS := bc grep mkdir free gzip ./src/separatebytag.pl
  14
  15 all: $(SEP1) $(SEP2) $(SEP3)
  16         @echo "[$(OUTF)]" "[$(INF)]" "[$@]" "[$(SAMMEM) $(FREEMEM)]"
  17         date > $(OUTPUTPREFIX)/_alldone.log
  18
  19 check:
  20         @for thecmd in $(NEEDED_COMMANDS); do \
  21         if ! command -v "$${thecmd%% *}" >/dev/null 2>&1; then \
  22                         checkok="0"; \
  23                         echo "[x]'$${thecmd%% *}' not found."; \
  24                 fi; \
  25         done; \
  26         if [ "$${checkok}" == "0" ]; then \
  27                 echo "[!]Please install missing cmd(s) above."; \
  28                 exit -1; \
  29         fi;
  30
  31 $(PATHS): check
  32         mkdir -p $@
  33
  34 $(SEP1): $(PATHS)
  35         $(eval IN := $(patsubst $(OUTPUTPREFIX)/%_000000,%,$@))
  36         echo "$@" "$<" "$(IN)"
  37         ./src/separatebytag.pl tigrad.lst 000000 $(IN).1.cut.gz $(IN).2.cut.gz $(@)
  38         touch $@
  39
  40 $(SEP2): $(SEP1)
  41         $(eval IN := $(patsubst %_210210,%,$@))
  42         ./src/separatebytag.pl tigrad.lst 210210 $(IN)_000000.NA.Unknown.1.fq.gz $(IN)_000000.NA.Unknown.2.fq.gz $(@)
  43         touch $@
  44
  45 $(SEP3): $(SEP2)
  46         $(eval IN := $(patsubst %_221210,%,$@))
  47         ./src/separatebytag.pl tigrad.lst 221210 $(IN)_210210.NA.Unknown.1.fq.gz $(IN)_210210.NA.Unknown.2.fq.gz $(@)
  48         touch $@