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biology/bioawk: BWK awk modified for biological data
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.
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Notes:
svn2git
2021-03-31 03:12:20 +00:00
svn path=/head/; revision=537983
@ -10,6 +10,7 @@
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SUBDIR += bamtools
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SUBDIR += bcftools
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SUBDIR += bedtools
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SUBDIR += bioawk
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SUBDIR += biococoa
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SUBDIR += bolt-lmm
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SUBDIR += bowtie
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24
biology/bioawk/Makefile
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24
biology/bioawk/Makefile
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# $FreeBSD$
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PORTNAME= bioawk
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DISTVERSIONPREFIX= v
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DISTVERSION= 1.0-7
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DISTVERSIONSUFFIX= -gfd40150
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CATEGORIES= biology
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MAINTAINER= jwb@FreeBSD.org
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COMMENT= BWK awk modified for biological data
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LICENSE= BSD3CLAUSE
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USE_GITHUB= yes
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GH_ACCOUNT= lh3
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MAKE_JOBS_UNSAFE= yes
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ALL_TARGET= bioawk
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INSTALL_TARGET= install-strip
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PLIST_FILES= bin/bioawk
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.include <bsd.port.mk>
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3
biology/bioawk/distinfo
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3
biology/bioawk/distinfo
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TIMESTAMP = 1591283068
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SHA256 (lh3-bioawk-v1.0-7-gfd40150_GH0.tar.gz) = 4510ee9493d0acef846e66f7b370c83e6e731954437ef6128a2e0b1fa8a38874
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SIZE (lh3-bioawk-v1.0-7-gfd40150_GH0.tar.gz) = 72209
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43
biology/bioawk/files/patch-Makefile
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43
biology/bioawk/files/patch-Makefile
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--- Makefile.orig 2017-09-11 13:43:01 UTC
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+++ Makefile
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@@ -22,14 +22,20 @@
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# THIS SOFTWARE.
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# ****************************************************************/
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-CFLAGS = -g -Wall -O2
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+CFLAGS ?= -g -Wall -O2
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-CC = gcc
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+CC ?= gcc
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-YACC = bison -y
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+# YACC = bison -y
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YACC = yacc
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YFLAGS = -d
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+MKDIR ?= mkdir
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+INSTALL ?= install
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+DESTDIR ?= .
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+PREFIX ?= /usr/local
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+STRIP ?= strip
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+
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OFILES = b.o main.o parse.o proctab.o tran.o lib.o run.o lex.o addon.o
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SOURCE = awk.h ytab.c ytab.h proto.h awkgram.y lex.c b.c main.c \
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@@ -61,5 +67,15 @@ maketab: ytab.h maketab.c
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names:
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@echo $(LISTING)
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+.PHONY: intall-strip install clean
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+
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+install-strip: install
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+ ${STRIP} ${DESTDIR}${PREFIX}/bin/bioawk
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+
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+install:
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+ ${MKDIR} -p ${DESTDIR}${PREFIX}/bin
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+ ${INSTALL} -c bioawk ${DESTDIR}${PREFIX}/bin
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+
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clean:
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- rm -fr a.out *.o *.obj maketab maketab.exe *.bb *.bbg *.da *.gcov *.gcno *.gcda awk bioawk ytab.* proctab.c *.dSYM
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+ rm -fr a.out *.o *.obj maketab maketab.exe *.bb *.bbg *.da *.gcov \
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+ *.gcno *.gcda awk bioawk ytab.* proctab.c *.dSYM
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8
biology/bioawk/pkg-descr
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8
biology/bioawk/pkg-descr
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Bioawk is an extension to Brian Kernighan's awk, adding the support of several
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common biological data formats, including optionally gzip'ed BED, GFF, SAM,
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VCF, FASTA/Q and TAB-delimited formats with column names. It also adds a few
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built-in functions and an command line option to use TAB as the input/output
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delimiter. When the new functionality is not used, bioawk is intended to behave
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exactly the same as the original BWK awk.
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WWW: https://github.com/lh3/bioawk
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