diff options
Diffstat (limited to 'biology')
| -rw-r--r-- | biology/lucy/DESCR | 6 | ||||
| -rw-r--r-- | biology/lucy/Makefile | 27 | ||||
| -rw-r--r-- | biology/lucy/PLIST | 17 | ||||
| -rw-r--r-- | biology/lucy/distinfo | 6 | ||||
| -rw-r--r-- | biology/lucy/patches/patch-aa | 14 | ||||
| -rw-r--r-- | biology/lucy/patches/patch-ab | 43 |
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); |