From 31d65d0f18425a5f233bed0b7b73cbd6bef28c69 Mon Sep 17 00:00:00 2001 From: minskim Date: Sat, 26 Mar 2005 17:05:01 +0000 Subject: Import lucy from pkgsrc-wip. Packaged by David Price and modified by me. A Sequence Cleanup Program. Lucy is a utility that prepares raw DNA sequence fragments for sequence assembly,possibly using the TIGR Assembler. The cleanup process includes quality assessment, confidence reassurance, vector trimming and vector removal. The primary advantage of Lucy over other similar utilities is that it is a fully integrated, stand alone program. --- biology/lucy/DESCR | 6 ++++++ biology/lucy/Makefile | 27 +++++++++++++++++++++++++++ biology/lucy/PLIST | 17 +++++++++++++++++ biology/lucy/distinfo | 6 ++++++ biology/lucy/patches/patch-aa | 14 ++++++++++++++ biology/lucy/patches/patch-ab | 43 +++++++++++++++++++++++++++++++++++++++++++ 6 files changed, 113 insertions(+) create mode 100644 biology/lucy/DESCR create mode 100644 biology/lucy/Makefile create mode 100644 biology/lucy/PLIST create mode 100644 biology/lucy/distinfo create mode 100644 biology/lucy/patches/patch-aa create mode 100644 biology/lucy/patches/patch-ab (limited to 'biology') diff --git a/biology/lucy/DESCR b/biology/lucy/DESCR new file mode 100644 index 00000000000..8acb58c97f6 --- /dev/null +++ b/biology/lucy/DESCR @@ -0,0 +1,6 @@ +A Sequence Cleanup Program. Lucy is a utility that prepares raw DNA +sequence fragments for sequence assembly,possibly using the TIGR +Assembler. The cleanup process includes quality assessment, +confidence reassurance, vector trimming and vector removal. The +primary advantage of Lucy over other similar utilities is that it is a +fully integrated, stand alone program. diff --git a/biology/lucy/Makefile b/biology/lucy/Makefile new file mode 100644 index 00000000000..1b8e5a180c6 --- /dev/null +++ b/biology/lucy/Makefile @@ -0,0 +1,27 @@ +# $NetBSD: Makefile,v 1.1.1.1 2005/03/26 17:05:01 minskim Exp $ +# + +DISTNAME= lucy-1.18p +CATEGORIES= biology +MASTER_SITES= ftp://ftp.tigr.org/pub/software/Lucy/ + +MAINTAINER= dprice@cs.nmsu.edu +HOMEPAGE= http://www.tigr.org/software +COMMENT= Sequence Cleanup Program + +PKG_INSTALLATION_TYPES= overwrite pkgviews + +INSTALLATION_DIRS= bin man/man1 + +do-install: + ${INSTALL_PROGRAM} ${WRKSRC}/lucy ${PREFIX}/bin + ${INSTALL_DATA} ${WRKSRC}/lucy.1 ${PREFIX}/man/man1 + ${INSTALL_DATA_DIR} ${PREFIX}/share/examples/lucy +.for EXAMPLE in PUC19 PUC19splice PUC19splice.for PUC19splice.rev \ + atie.seq atie.qul atie.2nd pSPORT1splice pSPORT1vector ARMTM40TR.seq \ + ARMTM40TR.qul lucy.ps lucy.debug + ${INSTALL_DATA} ${WRKSRC}/${EXAMPLE} ${PREFIX}/share/examples/lucy +.endfor + +.include "../../mk/pthread.buildlink3.mk" +.include "../../mk/bsd.pkg.mk" diff --git a/biology/lucy/PLIST b/biology/lucy/PLIST new file mode 100644 index 00000000000..877416e70ac --- /dev/null +++ b/biology/lucy/PLIST @@ -0,0 +1,17 @@ +@comment $NetBSD: PLIST,v 1.1.1.1 2005/03/26 17:05:03 minskim Exp $ +bin/lucy +man/man1/lucy.1.gz +share/examples/lucy/ARMTM40TR.qul +share/examples/lucy/ARMTM40TR.seq +share/examples/lucy/PUC19 +share/examples/lucy/PUC19splice +share/examples/lucy/PUC19splice.for +share/examples/lucy/PUC19splice.rev +share/examples/lucy/atie.2nd +share/examples/lucy/atie.qul +share/examples/lucy/atie.seq +share/examples/lucy/lucy.debug +share/examples/lucy/lucy.ps +share/examples/lucy/pSPORT1splice +share/examples/lucy/pSPORT1vector +@dirrm share/examples/lucy diff --git a/biology/lucy/distinfo b/biology/lucy/distinfo new file mode 100644 index 00000000000..859607a6fcd --- /dev/null +++ b/biology/lucy/distinfo @@ -0,0 +1,6 @@ +$NetBSD: distinfo,v 1.1.1.1 2005/03/26 17:05:03 minskim Exp $ + +SHA1 (lucy-1.18p.tar.gz) = 93ff9002f7eb69815497633007952ede9ca63e66 +Size (lucy-1.18p.tar.gz) = 1456857 bytes +SHA1 (patch-aa) = 89acea1ef9398cb8fefed57e4d28a925644fb9f9 +SHA1 (patch-ab) = 638e512be7fc526cbd37950f9156ccab46b9f228 diff --git a/biology/lucy/patches/patch-aa b/biology/lucy/patches/patch-aa new file mode 100644 index 00000000000..fc9c2ba72cc --- /dev/null +++ b/biology/lucy/patches/patch-aa @@ -0,0 +1,14 @@ +$NetBSD: patch-aa,v 1.1.1.1 2005/03/26 17:05:03 minskim Exp $ + +--- Makefile.orig 2002-08-26 09:46:06.000000000 -0500 ++++ Makefile +@@ -1,6 +1,6 @@ +-CC = cc +-CFLAGS = -O +-LIBS = -lpthread ++CC ?= cc ++CFLAGS ?= -O ++LIBS = -lpthread ${LDFLAGS} + OBJS = lucy.o qual_trim.o abi.o vector.o splice.o poly.o + + all: lucy beep diff --git a/biology/lucy/patches/patch-ab b/biology/lucy/patches/patch-ab new file mode 100644 index 00000000000..bb7cf023d65 --- /dev/null +++ b/biology/lucy/patches/patch-ab @@ -0,0 +1,43 @@ +$NetBSD: patch-ab,v 1.1.1.1 2005/03/26 17:05:03 minskim Exp $ + +--- lucy.c.orig Mon Apr 21 15:08:41 2003 ++++ lucy.c +@@ -147,7 +147,7 @@ Seq *ptr; + /* thread related variables */ + pthread_mutex_t job_lock, acc_lock; + pthread_cond_t job_waiting, job_returning, job_done; +-int thread_count, job_count, job_close, shutdown, *jobs, job_todo, job_pool; ++int thread_count, job_count, job_close, shut, *jobs, job_todo, job_pool; + pthread_t *threads; + void (*work)(); + +@@ -172,9 +172,9 @@ void *worker(arg) + int id=(int)arg; + pthread_mutex_lock(&job_lock); + while (1) { +- while (job_todo<0 && !shutdown) ++ while (job_todo<0 && !shut) + pthread_cond_wait(&job_waiting, &job_lock); +- if (shutdown) { ++ if (shut) { + pthread_mutex_unlock(&job_lock); + pthread_exit(NULL); + } +@@ -515,7 +515,7 @@ char *argv[]; + /******************************************************/ + threads=(pthread_t*)malloc(sizeof(pthread_t)*thread_count); + jobs=(int*)malloc(sizeof(int)*(thread_count+1)); +- job_count=job_close=shutdown=0; job_todo=job_pool=-1; id=thread_count; ++ job_count=job_close=shut=0; job_todo=job_pool=-1; id=thread_count; + + if (pthread_mutex_init(&job_lock, NULL)) + giveup("can't initialize thread mutex job_lock"); +@@ -1018,7 +1018,7 @@ char *argv[]; + /******************************************************/ + /* Phase 0.3: terminate all computing threads */ + /******************************************************/ +- shutdown=1; ++ shut=1; + pthread_cond_broadcast(&job_waiting); + for (i=0; i