svn commit: r537983 - in head/biology: . bioawk bioawk/files

[Jason W. Bacon]

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 at 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