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| author | Jason W. Bacon <jwb@FreeBSD.org> | 2020-06-05 02:45:33 +0000 |
|---|---|---|
| committer | Jason W. Bacon <jwb@FreeBSD.org> | 2020-06-05 02:45:33 +0000 |
| commit | c81fc008176617ff1c64ed51ccffc3f36c94255b (patch) | |
| tree | 1737a4525e96e6795493a5dd69db6f027849aeb1 /biology/bioawk | |
| parent | a156fdcf52bb164e6f390b3cc02e1bfe2f2cb844 (diff) | |
| download | ports-c81fc008176617ff1c64ed51ccffc3f36c94255b.tar.gz ports-c81fc008176617ff1c64ed51ccffc3f36c94255b.zip | |
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.
Notes
Notes:
svn path=/head/; revision=537983
Diffstat (limited to 'biology/bioawk')
| -rw-r--r-- | biology/bioawk/Makefile | 24 | ||||
| -rw-r--r-- | biology/bioawk/distinfo | 3 | ||||
| -rw-r--r-- | biology/bioawk/files/patch-Makefile | 43 | ||||
| -rw-r--r-- | biology/bioawk/pkg-descr | 8 |
4 files changed, 78 insertions, 0 deletions
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 <bsd.port.mk> 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 |