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.

6 files changed, 113 insertions, 0 deletions

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<thread_count; i++)
+     pthread_join(threads[i], NULL);