diff --git a/biology/Makefile b/biology/Makefile index 203e2844731f..5fadbde39170 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -10,6 +10,7 @@ SUBDIR += bamtools SUBDIR += bcftools SUBDIR += bedtools + SUBDIR += bioawk SUBDIR += biococoa SUBDIR += bolt-lmm SUBDIR += bowtie diff --git a/biology/bioawk/Makefile b/biology/bioawk/Makefile new file mode 100644 index 000000000000..6aaaa818e60e --- /dev/null +++ b/biology/bioawk/Makefile @@ -0,0 +1,24 @@ +# $FreeBSD$ + +PORTNAME= bioawk +DISTVERSIONPREFIX= v +DISTVERSION= 1.0-7 +DISTVERSIONSUFFIX= -gfd40150 +CATEGORIES= biology + +MAINTAINER= jwb@FreeBSD.org +COMMENT= BWK awk modified for biological data + +LICENSE= BSD3CLAUSE + +USE_GITHUB= yes + +GH_ACCOUNT= lh3 + +MAKE_JOBS_UNSAFE= yes +ALL_TARGET= bioawk +INSTALL_TARGET= install-strip + +PLIST_FILES= bin/bioawk + +.include diff --git a/biology/bioawk/distinfo b/biology/bioawk/distinfo new file mode 100644 index 000000000000..91f16ed31f6e --- /dev/null +++ b/biology/bioawk/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1591283068 +SHA256 (lh3-bioawk-v1.0-7-gfd40150_GH0.tar.gz) = 4510ee9493d0acef846e66f7b370c83e6e731954437ef6128a2e0b1fa8a38874 +SIZE (lh3-bioawk-v1.0-7-gfd40150_GH0.tar.gz) = 72209 diff --git a/biology/bioawk/files/patch-Makefile b/biology/bioawk/files/patch-Makefile new file mode 100644 index 000000000000..ef4340ba667e --- /dev/null +++ b/biology/bioawk/files/patch-Makefile @@ -0,0 +1,43 @@ +--- Makefile.orig 2017-09-11 13:43:01 UTC ++++ Makefile +@@ -22,14 +22,20 @@ + # THIS SOFTWARE. + # ****************************************************************/ + +-CFLAGS = -g -Wall -O2 ++CFLAGS ?= -g -Wall -O2 + +-CC = gcc ++CC ?= gcc + +-YACC = bison -y ++# YACC = bison -y + YACC = yacc + YFLAGS = -d + ++MKDIR ?= mkdir ++INSTALL ?= install ++DESTDIR ?= . ++PREFIX ?= /usr/local ++STRIP ?= strip ++ + OFILES = b.o main.o parse.o proctab.o tran.o lib.o run.o lex.o addon.o + + SOURCE = awk.h ytab.c ytab.h proto.h awkgram.y lex.c b.c main.c \ +@@ -61,5 +67,15 @@ maketab: ytab.h maketab.c + names: + @echo $(LISTING) + ++.PHONY: intall-strip install clean ++ ++install-strip: install ++ ${STRIP} ${DESTDIR}${PREFIX}/bin/bioawk ++ ++install: ++ ${MKDIR} -p ${DESTDIR}${PREFIX}/bin ++ ${INSTALL} -c bioawk ${DESTDIR}${PREFIX}/bin ++ + clean: +- rm -fr a.out *.o *.obj maketab maketab.exe *.bb *.bbg *.da *.gcov *.gcno *.gcda awk bioawk ytab.* proctab.c *.dSYM ++ rm -fr a.out *.o *.obj maketab maketab.exe *.bb *.bbg *.da *.gcov \ ++ *.gcno *.gcda awk bioawk ytab.* proctab.c *.dSYM diff --git a/biology/bioawk/pkg-descr b/biology/bioawk/pkg-descr new file mode 100644 index 000000000000..41070de842f8 --- /dev/null +++ b/biology/bioawk/pkg-descr @@ -0,0 +1,8 @@ +Bioawk is an extension to Brian Kernighan's awk, adding the support of several +common biological data formats, including optionally gzip'ed BED, GFF, SAM, +VCF, FASTA/Q and TAB-delimited formats with column names. It also adds a few +built-in functions and an command line option to use TAB as the input/output +delimiter. When the new functionality is not used, bioawk is intended to behave +exactly the same as the original BWK awk. + +WWW: https://github.com/lh3/bioawk