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authorSam Lawrance <lawrance@FreeBSD.org>2006-05-07 13:04:20 +0000
committerSam Lawrance <lawrance@FreeBSD.org>2006-05-07 13:04:20 +0000
commit649566ad8c64c8c2ac63a27b742c9cd32e3fb6ac (patch)
tree2f41a5e008570986a8516aa22470ef116827f2c5 /biology
parentb6bdcc8e1e86ec94dc8831f66235df36954e4f26 (diff)
downloadports-649566ad8c64c8c2ac63a27b742c9cd32e3fb6ac.tar.gz
ports-649566ad8c64c8c2ac63a27b742c9cd32e3fb6ac.zip
Notes
Diffstat (limited to 'biology')
-rw-r--r--biology/fasta/Makefile2
-rw-r--r--biology/fasta/distinfo6
-rw-r--r--biology/fasta/files/patch-Makefile14
-rw-r--r--biology/fasta/pkg-descr15
-rw-r--r--biology/fasta/pkg-plist8
5 files changed, 18 insertions, 27 deletions
diff --git a/biology/fasta/Makefile b/biology/fasta/Makefile
index bda68d575347..f6b19905b720 100644
--- a/biology/fasta/Makefile
+++ b/biology/fasta/Makefile
@@ -6,7 +6,7 @@
#
PORTNAME= fasta
-PORTVERSION= 21.u1.d0
+PORTVERSION= 21.u1.d1
CATEGORIES= biology
MASTER_SITES= http://ftp.virginia.edu/pub/fasta/
DISTNAME= fasta${PORTVERSION:S/.//g}
diff --git a/biology/fasta/distinfo b/biology/fasta/distinfo
index e9bfec1bed86..ebee0667f707 100644
--- a/biology/fasta/distinfo
+++ b/biology/fasta/distinfo
@@ -1,3 +1,3 @@
-MD5 (fasta21u1d0.shar.Z) = df423465929b2f8ceaf508dceffa3403
-SHA256 (fasta21u1d0.shar.Z) = b03e11c74bccf42d8319cc98a35df7df02847b8e9f2b45d602220b1e9940a4c0
-SIZE (fasta21u1d0.shar.Z) = 463293
+MD5 (fasta21u1d1.shar.Z) = f7fefbcf6b07e546eed1a1c6df98821e
+SHA256 (fasta21u1d1.shar.Z) = 9b45ffb0ba7111f398f03fffd77d8c823ced6756461ec96428dc36d88d6777f3
+SIZE (fasta21u1d1.shar.Z) = 445052
diff --git a/biology/fasta/files/patch-Makefile b/biology/fasta/files/patch-Makefile
index 39c4b5160c48..e627085fbe70 100644
--- a/biology/fasta/files/patch-Makefile
+++ b/biology/fasta/files/patch-Makefile
@@ -1,7 +1,7 @@
---- Makefile.orig Mon Jan 29 15:10:42 2001
-+++ Makefile Mon Jan 29 15:15:08 2001
-@@ -3,14 +3,14 @@
- # for mips, also use: -mips2 -O2
+--- Makefile.orig Sun May 7 22:29:14 2006
++++ Makefile Sun May 7 22:30:52 2006
+@@ -2,14 +2,14 @@
+ # for SGI also use: -signed
#
-CC= cc -O
@@ -13,13 +13,13 @@
+CFLAGS+= -DUNIX -DBIGMEM -DSFCHAR="':'" -DEXPM1 -DPROGRESS -DGAP_OPEN
LFLAGS= -lm -o
--BIN = /seqprg/slib/bin
+-BIN = /seqprg/bin
+BIN = $(PREFIX)/bin
#NRAND= nrand
#IBM RS/6000
- NRAND= nrand48
+ #NRAND= nrand48
@@ -29,7 +29,7 @@
- sall : $(SPROGS)
+ all : $(PROGS)
install :
- cp $(PROGS) $(BIN)
diff --git a/biology/fasta/pkg-descr b/biology/fasta/pkg-descr
index b5230be12f67..94f0c8464034 100644
--- a/biology/fasta/pkg-descr
+++ b/biology/fasta/pkg-descr
@@ -1,10 +1,11 @@
-Version 2 of the FASTA packages contains many programs for searching DNA and
-protein databases, performing sequence comparisons, producing local
-alignments, and other related tasks.
+Version 2 of the FASTA packages contains many programs for performing
+sequence comparisons, producing local alignments, and other related tasks
+for analysing DNA and proteins.
-Currently, the FASTA2 suite is in maintenance mode. Updated versions of ONLY
-the searching programs are available in version 3 of the FASTA packages,
-which may be found in the port biology/fasta3.
+Currently, the FASTA2 suite is in maintenance mode. This package provides
+the analysis tools from FASTA2. The searching programs are available in
+version 3 of the FASTA packages, which may be found in the port
+biology/fasta3.
FASTA is described in: W. R. Pearson and D. J. Lipman (1988), "Improved
Tools for Biological Sequence Analysis", PNAS 85:2444- 2448, and W. R.
@@ -16,5 +17,3 @@ not be sold or incorporated into a commercial product.
Author: William R Pearson <wrp@virginia.edu>
WWW: http://fasta.bioch.virginia.edu/
-
--- Johann Visagie <johann@egenetics.com>
diff --git a/biology/fasta/pkg-plist b/biology/fasta/pkg-plist
index b92aa3b62a89..7c4d1df211c5 100644
--- a/biology/fasta/pkg-plist
+++ b/biology/fasta/pkg-plist
@@ -16,8 +16,6 @@ bin/align
bin/align0
bin/bestscor
bin/crandseq
-bin/fasta
-bin/fastx
bin/flalign
bin/fromgb
bin/garnier
@@ -26,15 +24,9 @@ bin/lalign
bin/lfasta
bin/plalign
bin/plfasta
-bin/prdf
-bin/prss
bin/psgrease
bin/randseq
bin/relate
bin/revcomp
-bin/ssearch
-bin/tfasta
-bin/tfastx
bin/tgrease
-bin/zs_exp
%%PORTDOCS%%@dirrm %%DOCSDIR%%