- New port: biology/fasta3, which comprises the FASTA3 suite of DNA and

  protein sequence search programs
- FASTA3 updates only some of the elements of FASTA2, which is why I have
  submitted ports of both versions (as biology/fasta and biology/fasta3)

PR:		24716
Submitted by:	Johann Visagie <johann@egenetics.com>

2 files changed, 69 insertions, 0 deletions

diff --git a/biology/fasta3/files/patch-Makefile b/biology/fasta3/files/patch-Makefile
new file mode 100644
index 000000000000..bdc135f01c97
--- /dev/null
+++ b/biology/fasta3/files/patch-Makefile
@@ -0,0 +1,49 @@
+--- Makefile.orig	Mon Jan 29 13:44:28 2001
++++ Makefile	Mon Jan 29 14:08:43 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
+ #
+ # 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
++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
+ # -I/usr/local/include/mysql -DMYSQL_DB 
+ #(for mySQL databases)  (also requires change to Makefile33.common)
+ 
+@@ -32,11 +32,15 @@
+ HFLAGS= -o
+ NFLAGS= -o
+ 
+-#for DEC Unix V4.0 
+ THR_SUBS = pthr_subs
+-THR_LIBS = -threads
++THR_LIBS = -pthread
+ 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 = ${PREFIX}/bin
+ 
+ # renamed (fasta33)  programs
+-include Makefile33.common
++# include Makefile33.common
+ # conventional (fasta3) names
+-#include Makefile.common
++include Makefile.common
diff --git a/biology/fasta3/files/patch-Makefile.common b/biology/fasta3/files/patch-Makefile.common
new file mode 100644
index 000000000000..395da695e031
--- /dev/null
+++ b/biology/fasta3/files/patch-Makefile.common
@@ -0,0 +1,20 @@
+--- 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)