Date: Mon, 25 Sep 2006 16:51:21 -0500 From: Bob Zimmermann <rpz@cse.wustl.edu> To: FreeBSD-gnats-submit@FreeBSD.org Subject: ports/103651: port add biology/gmap Message-ID: <1159221081.1946@crossfire.nijibabulu.org> Resent-Message-ID: <200609252200.k8PM0Y6c057813@freefall.freebsd.org>
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>Number: 103651 >Category: ports >Synopsis: port add biology/gmap >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports-bugs >State: open >Quarter: >Keywords: >Date-Required: >Class: change-request >Submitter-Id: current-users >Arrival-Date: Mon Sep 25 22:00:34 GMT 2006 >Closed-Date: >Last-Modified: >Originator: Bob Zimmermann >Release: FreeBSD 6.1-RELEASE i386 >Organization: Washington University in St. Louis >Environment: System: FreeBSD crossfire.nijibabulu.org 6.1-RELEASE FreeBSD 6.1-RELEASE #0: Sun May 7 04:32:43 UTC 2006 root@opus.cse.buffalo.edu:/usr/obj/usr/src/sys/GENERIC i386 >Description: A standalone program for mapping and aligning cDNA sequences to a genome. The program maps and aligns a single sequence with minimal startup time and memory requirements, and provides fast batch processing of large sequence sets. The program generates accurate gene structures, even in the presence of substantial polymorphisms and sequence errors, without using probabilistic splice site models. Methodology underlying the program includes a minimal sampling strategy for genomic mapping, oligomer chaining for approximate alignment, sandwich DP for splice site detection, and microexon identification with statistical significance testing. WWW: http://www.gene.com/share/gmap >How-To-Repeat: (port add, not a bug) >Fix: (port add, not a bug) port shar archive: # This is a shell archive. Save it in a file, remove anything before # this line, and then unpack it by entering "sh file". Note, it may # create directories; files and directories will be owned by you and # have default permissions. # # This archive contains: # # gmap # gmap/files # gmap/files/patch-configure # gmap/Makefile # gmap/pkg-descr # gmap/distinfo # gmap/pkg-plist # echo c - gmap mkdir -p gmap > /dev/null 2>&1 echo c - gmap/files mkdir -p gmap/files > /dev/null 2>&1 echo x - gmap/files/patch-configure sed 's/^X//' >gmap/files/patch-configure << 'END-of-gmap/files/patch-configure' X--- configure.orig Mon Sep 25 21:06:11 2006 X+++ configure Mon Sep 25 21:05:13 2006 X@@ -3365,7 +3365,7 @@ X else X answer="" X fi; X-if test x"$answer" == x; then X+if test x"$answer" = x; then X X EXP_VAR=GMAPDB X FROM_VAR='${prefix}/share' END-of-gmap/files/patch-configure echo x - gmap/Makefile sed 's/^X//' >gmap/Makefile << 'END-of-gmap/Makefile' X# Ports collection makefile for: gmap X# Date created: 24 September 2006 X# Whom: rpz X# X# $FreeBSD$ X# X XPORTNAME= gmap XPORTVERSION= 2006.04.21 XDISTNAME= ${PORTNAME}-`${ECHO} ${PORTVERSION} | ${SED} s/\\\./-/g` XCATEGORIES= biology XMASTER_SITES= http://www.gene.com/share/gmap/src/ X XMAINTAINER= rpz@cse.wustl.edu XCOMMENT= A Genomic Mapping and Alignment Program for mRNA and EST Sequences X XFETCH_DEPENDS= wget:${PORTSDIR}/ftp/wget X XFETCH_CMD= ${LOCALBASE}/bin/wget -c X XUSE_GMAKE= yes XGNU_CONFIGURE= yes XCONFIGURE_TARGET=--build=${MACHINE_ARCH}-portbld-freebsd${OSREL} X X.include <bsd.port.mk> END-of-gmap/Makefile echo x - gmap/pkg-descr sed 's/^X//' >gmap/pkg-descr << 'END-of-gmap/pkg-descr' XA standalone program for mapping and aligning cDNA sequences to a Xgenome. The program maps and aligns a single sequence with minimal Xstartup time and memory requirements, and provides fast batch Xprocessing of large sequence sets. The program generates accurate Xgene structures, even in the presence of substantial polymorphisms Xand sequence errors, without using probabilistic splice site models. XMethodology underlying the program includes a minimal sampling Xstrategy for genomic mapping, oligomer chaining for approximate Xalignment, sandwich DP for splice site detection, and microexon Xidentification with statistical significance testing. X XWWW: http://www.gene.com/share/gmap END-of-gmap/pkg-descr echo x - gmap/distinfo sed 's/^X//' >gmap/distinfo << 'END-of-gmap/distinfo' XMD5 (gmap-2006-04-21.tar.gz) = 197a47e30dac77c93d3f1b99ec805217 XSHA256 (gmap-2006-04-21.tar.gz) = e635884c07d57e9a79e6e6744587dc1459dd0895eb40d6ca4b61f9827e332984 XSIZE (gmap-2006-04-21.tar.gz) = 1282409 END-of-gmap/distinfo echo x - gmap/pkg-plist sed 's/^X//' >gmap/pkg-plist << 'END-of-gmap/pkg-plist' Xbin/gmap Xbin/get-genome Xbin/gmapindex Xbin/iit_store Xbin/iit_get Xbin/iit_dump Xbin/gmap_compress Xbin/gmap_uncompress Xbin/gmap_process Xbin/gmap_setup Xbin/md_coords Xbin/fa_coords END-of-gmap/pkg-plist exit >Release-Note: >Audit-Trail: >Unformatted:
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