kpriv/freebsd-ports
1
0
Fork 0
Code Issues Pull requests Projects Releases Packages Wiki Activity

Update to 34.t25.d4.

Browse source 
PR:		ports/93052
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
This commit is contained in:
Sam Lawrance 2006-02-10 09:37:02 +00:00
parent c6004c8778
commit f4cdc25a87
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=155633
11 changed files with 156 additions and 168 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

38
biology/fasta3/Makefile
View file

@ -1,3 +1,4 @@
# ex:ts=8
# New ports collection makefile for: fasta3
# Date created: 29 January 2001
# Whom: Johann Visagie <johann@egenetics.com>
@ -6,21 +7,25 @@
#
PORTNAME= fasta3
PORTVERSION= 33.t08.d4
PORTVERSION= 34.t25.d4
CATEGORIES= biology
MASTER_SITES= ftp://ftp.virginia.edu/pub/fasta/
DISTNAME= fasta${PORTVERSION:S/.//g}
EXTRACT_SUFX= .shar.Z
MAINTAINER= fernan@iib.unsam.edu.ar
COMMENT= A collection of programs for searching DNA and protein databases, v3
COMMENT= A collection of programs for searching DNA and protein databases
NO_CDROM= May not be sold or incorporated into a commercial product
WRKSRC= ${WRKDIR}/fasta3
PKGMESSAGE= ${WRKDIR}/pkg-message
FASTA3_DOCDIR= ${PREFIX}/share/doc/fasta3
FASTA3_DOCS= 00README.1st README COPYRIGHT fasta3x.me fasta3x.doc \
readme.*
NO_CDROM= "May not be sold or incorporated into a commercial product"
WRKSRC= ${WRKDIR}/${PORTNAME}
SUB_FILES= pkg-message
MAKE_ENV+= THR_LIBS=${PTHREAD_LIBS}
FASTA3_DOCS= README COPYRIGHT FASTA_LIST fasta3x.me fasta3x.doc \
fasta20.doc fasta_func.doc readme.* fasta.defaults
DATA= *.mat
EXAMPLES= *.aa *.lc *.seq
MAN1= fasta3.1 fastf3.1 fasts3.1 map_db.1 prss3.1
MLINKS= fasta3.1 tfasta3.1 fasta3.1 fastx3.1 fasta3.1 tfastx3.1 \
@ -35,19 +40,24 @@ do-extract:
done
post-install:
@ ${INSTALL_DATA} ${WRKSRC}/fastlibs ${PREFIX}/etc/fastlibs.sample
${INSTALL_DATA} ${WRKSRC}/fastlibs ${PREFIX}/etc/fastlibs.sample
@ ${MKDIR} ${DATADIR}
.for data in ${DATA}
${INSTALL_DATA} ${WRKSRC}/${data} ${DATADIR}
.endfor
@ ${MKDIR} ${EXAMPLESDIR}
.for ex in ${EXAMPLES}
${INSTALL_DATA} ${WRKSRC}/${ex} ${EXAMPLESDIR}
.endfor
.for manpage in ${MAN1}
@ ${INSTALL_MAN} ${WRKSRC}/${manpage} ${MAN1PREFIX}/man/man1/
.endfor
.if !defined(NOPORTDOCS)
@ ${MKDIR} ${FASTA3_DOCDIR}
@ ${MKDIR} ${DOCSDIR}
.for docfile in ${FASTA3_DOCS}
@ ${INSTALL_DATA} ${WRKSRC}/${docfile} ${FASTA3_DOCDIR}
@ ${INSTALL_DATA} ${WRKSRC}/${docfile} ${DOCSDIR}
.endfor
.endif
.if !defined(BATCH)
@ ${SED} -e 's#%%PREFIX%%#${PREFIX}#' ${.CURDIR}/pkg-message > ${PKGMESSAGE}
@ ${CAT} ${PKGMESSAGE}
.endif
.include <bsd.port.mk>

6
biology/fasta3/distinfo
View file

@ -1,3 +1,3 @@
MD5 (fasta33t08d4.shar.Z) = e6217268e122b2ca7c51b443425e40e3
SHA256 (fasta33t08d4.shar.Z) = f2eb329393cd330c6848cff2a147fcc2c2f74dff6033cf7ba70177ab4bcca231
SIZE (fasta33t08d4.shar.Z) = 685912
MD5 (fasta34t25d4.shar.Z) = 554190cb7bf2488150a96e309651e9c7
SHA256 (fasta34t25d4.shar.Z) = 4d901bc738074c6c72d568b3852cf7e8a91a71ca25a1b2d74b8b1ae997d956fe
SIZE (fasta34t25d4.shar.Z) = 799416

68
biology/fasta3/files/patch-Makefile
View file

@ -1,49 +1,33 @@
--- Makefile.orig Mon May 7 11:36:23 2001
+++ Makefile Mon May 7 11:40:36 2001
@@ -12,13 +12,13 @@
# use -DBIG_LIB64 to generate 64-bit offsets in map_db .xin files
-CC= cc -O -std1
+#CC= cc -O -std1
#CC= insure -g -DDEBUG
#CC= cc -g -DDEBUG -std1
#CC= gcc -g -Wall
--- Makefile.orig Thu Feb 9 12:03:37 2006
+++ Makefile Thu Feb 9 12:07:21 2006
@@ -7,7 +7,7 @@
# in dropnfa.c (wrp 3/19/1998)
#
# standard line for normal searching
-CFLAGS= -DM10_CONS -DUNIX -DTIMES -DHZ=60 -DBIGMEM -DMAX_WORKERS=4 -DTHR_EXIT=pthread_exit -DPROGRESS -DFASTA_HOST='"fasta.bioch.virginia.edu/fasta/cgi"' -DIS_LITTLE_ENDIAN -DUSE_MMAP
+CFLAGS+= -DM10_CONS -DUNIX -DTIMES -DHZ=60 -DBIGMEM -DMAX_WORKERS=4 -DTHR_EXIT=pthread_exit -DPROGRESS -DFASTA_HOST='"fasta.bioch.virginia.edu/fasta/cgi"' -DIS_LITTLE_ENDIAN -DUSE_MMAP
-CC= gcc -g -O3
+#CC= gcc -g -O3
#CC=gcc -Wall -pedantic -ansi -g -O
#CC = gcc -g -DDEBUG
#CC= /opt/parasoft/bin.linux2/insure -g -pg -DDEBUG
@@ -21,7 +21,7 @@
#CFLAGS= -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DSFCHAR="'|'" -c -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DSUPERFAMNUM -DUSE_MMAP -D_REENTRANT -DBIG_LIB64 -D_LARGE_FILE_SOURCE -DUSE_FSEEKO -D_FILE_OFFSET_BITS=64 -DHAS_INTTYPES -DSAMP_STATS
# standard options
-CFLAGS= -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DSFCHAR="':'" -c -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DFASTA_HOST='"wrpx00.bioch.virginia.edu/fasta/cgi"' -DUSE_MMAP -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC
+CFLAGS+= -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DSFCHAR="':'" -c -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DFASTA_HOST='"wrpx00.bioch.virginia.edu/fasta/cgi"' -DUSE_MMAP -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC
# -I/usr/local/include/mysql -DMYSQL_DB
#(for mySQL databases) (also requires change to Makefile33.common)
#
#(for mySQL databases) (also requires change to Makefile34.common)
@@ -35,10 +35,10 @@
@@ -32,11 +32,15 @@
HFLAGS= -o
NFLAGS= -o
-#for DEC Unix V4.0
THR_SUBS = pthr_subs
-THR_LIBS = -threads
+THR_LIBS = -pthread
# for Linux
THR_SUBS = pthr_subs2
-THR_LIBS = -lpthread
+#THR_LIBS = -lpthread
THR_CC =
+#for DEC Unix V4.0
+#THR_SUBS = pthr_subs
+#THR_LIBS = -threads
+#THR_CC =
+#
#for Sun
#THR_SUBS = uthr_subs
#THR_LIBS = -lthread
@@ -53,9 +57,9 @@
#THR_LIBS = -lpthreads
#THR_CC =
-XDIR = /seqprg/slib/bin
-XDIR = /seqprg/bin
+XDIR = ${PREFIX}/bin
# renamed (fasta33) programs
-include Makefile33.common
+#include Makefile33.common
# conventional (fasta3) names
-#include Makefile.common
+include Makefile.common
DROPNFA_O = drop_nfa.o
DROPGSW_O = dropgsw.o

20
biology/fasta3/files/patch-Makefile.common
View file

@ -1,20 +0,0 @@
--- Makefile.common.orig Mon Jan 29 12:42:32 2001
+++ Makefile.common Mon Jan 29 13:44:06 2001
@@ -46,7 +46,7 @@
XTPROGS = fastx33_t tfastx33_t fasty33_t tfasty33_t
XPROGS = fastx33 tfastx33 fasty33 tfasty33
-PROGS = $(SPROGS) $(TPROGS)
+PROGS = $(SPROGS) $(TPROGS) $(APROGS) $(XTPROGS) $(XPROGS)
all : $(PROGS)
@@ -60,7 +60,7 @@
rm -f *.o $(PROGS)
install:
- cp $(PROGS) $(XDIR)
+ $(BSD_INSTALL_PROGRAM) $(PROGS) $(XDIR)
sinstall:
cp $(SPROGS) $(XDIR)

11
biology/fasta3/files/patch-comp_thr.c
View file

@ -1,11 +0,0 @@
--- comp_thr.c.orig Thu Aug 22 20:32:10 2002
+++ comp_thr.c Thu Aug 22 20:32:25 2002
@@ -16,7 +16,7 @@
#include <time.h>
#ifdef UNIX
-#if !defined(__NetBSD__) && !defined(MacOSX)
+#if !defined(__FreeBSD__) && !defined(__NetBSD__) && !defined(MacOSX)
#include <values.h>
#else
#include <limits.h>

11
biology/fasta3/files/patch-compacc.c
View file

@ -1,11 +0,0 @@
--- compacc.c.orig Thu Aug 22 20:30:30 2002
+++ compacc.c Thu Aug 22 20:30:43 2002
@@ -11,7 +11,7 @@
#if defined(UNIX) || defined(MSDOS)
#include <sys/types.h>
#endif
-#if !defined(__MWERKS__) && !defined(MacOSX)
+#if !defined(__FreeBSD__) && !defined(__MWERKS__) && !defined(MacOSX)
#include <values.h>
#else
#include <limits.h>

11
biology/fasta3/files/patch-complib.c
View file

@ -1,11 +0,0 @@
--- complib.c.orig Thu Aug 22 20:33:57 2002
+++ complib.c Thu Aug 22 20:34:07 2002
@@ -29,7 +29,7 @@
#include <ctype.h>
#include <time.h>
#ifdef UNIX
-#if !defined(__NetBSD__) && !defined(MacOSX)
+#if !defined(__FreeBSD__) && !defined(__NetBSD__) && !defined(MacOSX)
#include <values.h>
#else
#include <limits.h>

11
biology/fasta3/files/patch-scaleswn.c
View file

@ -1,11 +0,0 @@
--- scaleswn.c.orig Thu Aug 22 20:30:55 2002
+++ scaleswn.c Thu Aug 22 20:31:06 2002
@@ -26,7 +26,7 @@
#include <math.h>
#include <string.h>
-#if !defined(__MWERKS__) && !defined(MacOSX)
+#if !defined(__FreeBSD__) && !defined(__MWERKS__) && !defined(MacOSX)
#include <values.h>
#else
#include <limits.h> /* needed for LONG_MAX */

16
biology/fasta3/files/pkg-message.in Normal file
View file

@ -0,0 +1,16 @@
=============================================================================
The FASTA3 package has been successfully installed.
A sample configuration file has been installed to
%%PREFIX%%/etc
as "fastlibs.sample". This may be renamed to "fastlibs" and edited
to suit the requirements of a particular site.
In order to use the FASTA3 programs, a user must set the environment
variable FASTLIBS to contain the full path of the FASTA3 configuration
file, e.g.:
set FASTLIBS to: "%%PREFIX%%/etc/fastlibs"
==============================================================================

15
biology/fasta3/pkg-message
View file

@ -1,15 +0,0 @@
--------------------------------------------------------------------------
The FASTA3 package has been successfully installed.
NB: A sample configuration file has been installed to %%PREFIX%%/etc as
"fastlibs.sample". This may be renamed to "fastlibs" and edited
to suit the requirements of a particular site.
In order to use the FASTA3 programs, a user must set the environment
variable FASTLIBS to contain the full path of the FASTA3 configuration
file, e.g.:
- set FASTLIBS to: "%%PREFIX%%/etc/fastlibs"
--------------------------------------------------------------------------

117
biology/fasta3/pkg-plist
View file

@ -1,11 +1,41 @@
%%PORTDOCS%%%%DOCSDIR%%/00README.1st
%%PORTDOCS%%%%DOCSDIR%%/COPYRIGHT
bin/fasta34
bin/prss34_t
bin/tfastf34_t
bin/fastf34_t
bin/fastm34_t
bin/tfasts34_t
bin/tfasty34_t
bin/fasty34_t
bin/tfastx34_t
bin/fastx34_t
bin/tfasta34_t
bin/fasts34_t
bin/fasta34_t
bin/ssearch34_t
bin/tfastf34
bin/fastf34
bin/prfx34
bin/prss34
bin/tfastm34
bin/fastm34
bin/tfasts34
bin/tfasty34
bin/fasty34
bin/tfastx34
bin/fastx34
bin/fasts34
bin/tfasta34
bin/ssearch34
bin/prfx34_t
etc/fastlibs.sample
%%PORTDOCS%%%%DOCSDIR%%/README
%%PORTDOCS%%%%DOCSDIR%%/fasta3x.doc
%%PORTDOCS%%%%DOCSDIR%%/COPYRIGHT
%%PORTDOCS%%%%DOCSDIR%%/FASTA_LIST
%%PORTDOCS%%%%DOCSDIR%%/fasta3x.me
%%PORTDOCS%%%%DOCSDIR%%/fasta3x.doc
%%PORTDOCS%%%%DOCSDIR%%/fasta20.doc
%%PORTDOCS%%%%DOCSDIR%%/fasta_func.doc
%%PORTDOCS%%%%DOCSDIR%%/readme.mpi_3.3
%%PORTDOCS%%%%DOCSDIR%%/readme.pvm_2.0
%%PORTDOCS%%%%DOCSDIR%%/readme.pvm_3.0
%%PORTDOCS%%%%DOCSDIR%%/readme.pvm_3.2
%%PORTDOCS%%%%DOCSDIR%%/readme.pvm_3.3
%%PORTDOCS%%%%DOCSDIR%%/readme.pvm_3.4
@ -16,30 +46,57 @@
%%PORTDOCS%%%%DOCSDIR%%/readme.v31t1
%%PORTDOCS%%%%DOCSDIR%%/readme.v32t0
%%PORTDOCS%%%%DOCSDIR%%/readme.v33t0
%%PORTDOCS%%%%DOCSDIR%%/readme.v34t0
%%PORTDOCS%%%%DOCSDIR%%/readme.w32
bin/fasta3
bin/fasta3_t
bin/fastf3
bin/fastf3_t
bin/fasts3
bin/fasts3_t
bin/fastx3
bin/fastx3_t
bin/fasty3
bin/fasty3_t
bin/map_db
bin/prss3
bin/ssearch3
bin/ssearch3_t
bin/tfasta3
bin/tfasta3_t
bin/tfastf3
bin/tfastf3_t
bin/tfasts3
bin/tfasts3_t
bin/tfastx3
bin/tfastx3_t
bin/tfasty3
bin/tfasty3_t
etc/fastlibs.sample
%%PORTDOCS%%%%DOCSDIR%%/fasta.defaults
%%EXAMPLESDIR%%/egmsmg.aa
%%EXAMPLESDIR%%/gtm1_human.aa
%%EXAMPLESDIR%%/gtt1_drome.aa
%%EXAMPLESDIR%%/h10_human.aa
%%EXAMPLESDIR%%/hahu.aa
%%EXAMPLESDIR%%/lcbo.aa
%%EXAMPLESDIR%%/m1r.aa
%%EXAMPLESDIR%%/m2.aa
%%EXAMPLESDIR%%/mchu.aa
%%EXAMPLESDIR%%/mgstm1.aa
%%EXAMPLESDIR%%/ms1.aa
%%EXAMPLESDIR%%/musplfm.aa
%%EXAMPLESDIR%%/mwkw.aa
%%EXAMPLESDIR%%/mwrtc1.aa
%%EXAMPLESDIR%%/n0.aa
%%EXAMPLESDIR%%/n1.aa
%%EXAMPLESDIR%%/n2.aa
%%EXAMPLESDIR%%/n2s.aa
%%EXAMPLESDIR%%/n2t.aa
%%EXAMPLESDIR%%/ngt.aa
%%EXAMPLESDIR%%/ngts.aa
%%EXAMPLESDIR%%/oohu.aa
%%EXAMPLESDIR%%/prio_atepa.aa
%%EXAMPLESDIR%%/qrhuld.aa
%%EXAMPLESDIR%%/xurt8c.aa
%%EXAMPLESDIR%%/xurtg.aa
%%EXAMPLESDIR%%/mgstm1.lc
%%EXAMPLESDIR%%/xurt8c.lc
%%EXAMPLESDIR%%/bovgh.seq
%%EXAMPLESDIR%%/bovprl.seq
%%EXAMPLESDIR%%/gst.seq
%%EXAMPLESDIR%%/hsgstm1b.seq
%%EXAMPLESDIR%%/humgstd.seq
%%EXAMPLESDIR%%/mgstm1.seq
%%EXAMPLESDIR%%/mgtt2_x.seq
%%DATADIR%%/blosum45.mat
%%DATADIR%%/blosum50.mat
%%DATADIR%%/blosum62.mat
%%DATADIR%%/blosum80.mat
%%DATADIR%%/dna.mat
%%DATADIR%%/idn_aa.mat
%%DATADIR%%/md_10.mat
%%DATADIR%%/md_20.mat
%%DATADIR%%/md_40.mat
%%DATADIR%%/pam120.mat
%%DATADIR%%/pam250.mat
%%DATADIR%%/rna.mat
%%DATADIR%%/vtml160.mat
%%PORTDOCS%%@dirrm %%DOCSDIR%%
@dirrm %%EXAMPLESDIR%%
@dirrm %%DATADIR%%