diff options
| -rw-r--r-- | biology/Makefile | 1 | ||||
| -rw-r--r-- | biology/dna-qc/Makefile | 45 | ||||
| -rw-r--r-- | biology/dna-qc/distinfo | 2 | ||||
| -rw-r--r-- | biology/dna-qc/files/patch-hybridize.c | 12 | ||||
| -rw-r--r-- | biology/dna-qc/pkg-comment | 1 | ||||
| -rw-r--r-- | biology/dna-qc/pkg-descr | 8 | ||||
| -rw-r--r-- | biology/dna-qc/pkg-plist | 25 |
7 files changed, 94 insertions, 0 deletions
diff --git a/biology/Makefile b/biology/Makefile index cfe51b3bff48..982d82bce3dd 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -7,6 +7,7 @@ SUBDIR += clustalw SUBDIR += coalesce SUBDIR += deft + SUBDIR += dna-qc SUBDIR += emboss SUBDIR += fasta SUBDIR += fasta3 diff --git a/biology/dna-qc/Makefile b/biology/dna-qc/Makefile new file mode 100644 index 000000000000..700cc1ca2122 --- /dev/null +++ b/biology/dna-qc/Makefile @@ -0,0 +1,45 @@ +# New ports collection makefile for: dna-qc +# Date created: 25 Novemeber 2001 +# Whom: Tony Maher <tonym@biolateral.com.au> +# +# $FreeBSD$ +# + +PORTNAME= dna-qc +PORTVERSION= 1993.07.26 +CATEGORIES= biology +MASTER_SITES= ftp://ftp.tigr.org/pub/software/qc/ +DISTNAME= qc +EXTRACT_SUFX= .tar.Z + +MAINTAINER= tonym@biolateral.com.au + +NO_WRKSUBDIR= true + +EXAMPLES= README script.compare script.limits \ + bact.all chromosomeIII.all human.all worm.all +PROGRAMS= counter hybridize normalize random_clip random_line + +post-patch: + @${PERL} -pi -e 's,^CFLAGS,#CFLAGS,' ${WRKSRC}/Makefile + @${PERL} -pi -e 's,malloc.h,stdlib.h,' ${WRKSRC}/normalize.c + @${PERL} -pi -e 's,fname\*,fname,' ${WRKSRC}/random_line.c + @${PERL} -pi -e 's,static void allocate_pool,void allocate_pool,' \ + ${WRKSRC}/stringpool.c + +do-install: +.for file in ${PROGRAMS} + ${INSTALL_PROGRAM} ${WRKSRC}/${file} ${PREFIX}/bin + strip ${PREFIX}/bin/${file} +.endfor +.if !defined(NOPORTDOCS) + @${MKDIR} ${DOCSDIR} + ${INSTALL_DATA} ${WRKSRC}/qc_doc/* ${DOCSDIR} + ${INSTALL_DATA} ${WRKSRC}/surprize_doc/* ${DOCSDIR} + @${MKDIR} ${EXAMPLESDIR} +.for file in ${EXAMPLES} + ${INSTALL_DATA} ${WRKSRC}/${file} ${EXAMPLESDIR} +.endfor +.endif + +.include <bsd.port.mk> diff --git a/biology/dna-qc/distinfo b/biology/dna-qc/distinfo new file mode 100644 index 000000000000..7da08044c989 --- /dev/null +++ b/biology/dna-qc/distinfo @@ -0,0 +1,2 @@ +MD5 (qc.tar.Z) = 30dc287fa9c7c8e818d4ce0a34b86422 +MD5 (hyb2dis.txt) = e5b8260c84a822cb0deff264f01331b8 diff --git a/biology/dna-qc/files/patch-hybridize.c b/biology/dna-qc/files/patch-hybridize.c new file mode 100644 index 000000000000..45dae76fc31e --- /dev/null +++ b/biology/dna-qc/files/patch-hybridize.c @@ -0,0 +1,12 @@ +$FreeBSD$ + +--- hybridize.c.orig Sat Nov 24 21:25:04 2001 ++++ hybridize.c Sat Nov 24 21:25:35 2001 +@@ -54,6 +54,7 @@ + extern unsigned array_to_base_4(); + extern unsigned string_to_base_4(); + extern int dna2i(); ++double logl(); + int *read_file(); + + main(argc, argv) diff --git a/biology/dna-qc/pkg-comment b/biology/dna-qc/pkg-comment new file mode 100644 index 000000000000..38f03537d32c --- /dev/null +++ b/biology/dna-qc/pkg-comment @@ -0,0 +1 @@ +A quality control algorithm for DNA sequencing projects diff --git a/biology/dna-qc/pkg-descr b/biology/dna-qc/pkg-descr new file mode 100644 index 000000000000..7018f40d8854 --- /dev/null +++ b/biology/dna-qc/pkg-descr @@ -0,0 +1,8 @@ +"relevant reference: +White, O., T. Dunning, G. Sutton, M. Adams, J. C. Venter, and C. +Fields (1993). A quality control algorithm for DNA sequencing +projects. Nucleic Acids Research (in press)." +- from the README file + +-- +Tony Maher <tonym@biolateral.com.au> diff --git a/biology/dna-qc/pkg-plist b/biology/dna-qc/pkg-plist new file mode 100644 index 000000000000..09192275d6fa --- /dev/null +++ b/biology/dna-qc/pkg-plist @@ -0,0 +1,25 @@ +bin/counter +bin/hybridize +bin/normalize +bin/random_clip +bin/random_line +%%PORTDOCS%%share/doc/dna-qc/qc_algorithm.ps.Z +%%PORTDOCS%%share/doc/dna-qc/qc_fig1.ps.Z +%%PORTDOCS%%share/doc/dna-qc/qc_fig2a.ps.Z +%%PORTDOCS%%share/doc/dna-qc/qc_fig2b.ps.Z +%%PORTDOCS%%share/doc/dna-qc/qc_fig2c.ps.Z +%%PORTDOCS%%share/doc/dna-qc/qc_fig3.ps.Z +%%PORTDOCS%%share/doc/dna-qc/qc_fig4.ps.Z +%%PORTDOCS%%share/doc/dna-qc/qc_fig5.ps.Z +%%PORTDOCS%%share/doc/dna-qc/qc_fig6.ps.Z +%%PORTDOCS%%share/doc/dna-qc/qc_fig7.ps.Z +%%PORTDOCS%%share/doc/dna-qc/surprize.ps.Z +%%PORTDOCS%%share/examples/dna-qc/README +%%PORTDOCS%%share/examples/dna-qc/bact.all +%%PORTDOCS%%share/examples/dna-qc/chromosomeIII.all +%%PORTDOCS%%share/examples/dna-qc/human.all +%%PORTDOCS%%share/examples/dna-qc/script.compare +%%PORTDOCS%%share/examples/dna-qc/script.limits +%%PORTDOCS%%share/examples/dna-qc/worm.all +%%PORTDOCS%%@dirrm share/examples/dna-qc +%%PORTDOCS%%@dirrm share/doc/dna-qc |