Date: Fri, 5 Jun 2020 02:45:33 +0000 (UTC) From: "Jason W. Bacon" <jwb@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r537983 - in head/biology: . bioawk bioawk/files Message-ID: <202006050245.0552jXss006253@repo.freebsd.org>
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Author: jwb Date: Fri Jun 5 02:45:33 2020 New Revision: 537983 URL: https://svnweb.freebsd.org/changeset/ports/537983 Log: 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. Added: head/biology/bioawk/ head/biology/bioawk/Makefile (contents, props changed) head/biology/bioawk/distinfo (contents, props changed) head/biology/bioawk/files/ head/biology/bioawk/files/patch-Makefile (contents, props changed) head/biology/bioawk/pkg-descr (contents, props changed) Modified: head/biology/Makefile Modified: head/biology/Makefile ============================================================================== --- head/biology/Makefile Fri Jun 5 01:55:49 2020 (r537982) +++ head/biology/Makefile Fri Jun 5 02:45:33 2020 (r537983) @@ -10,6 +10,7 @@ SUBDIR += bamtools SUBDIR += bcftools SUBDIR += bedtools + SUBDIR += bioawk SUBDIR += biococoa SUBDIR += bolt-lmm SUBDIR += bowtie Added: head/biology/bioawk/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/bioawk/Makefile Fri Jun 5 02:45:33 2020 (r537983) @@ -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 <bsd.port.mk> Added: head/biology/bioawk/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/bioawk/distinfo Fri Jun 5 02:45:33 2020 (r537983) @@ -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 Added: head/biology/bioawk/files/patch-Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/bioawk/files/patch-Makefile Fri Jun 5 02:45:33 2020 (r537983) @@ -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 Added: head/biology/bioawk/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/bioawk/pkg-descr Fri Jun 5 02:45:33 2020 (r537983) @@ -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
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