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| author | jeh <jeh@FreeBSD.org> | 2001-02-12 00:28:59 +0800 |
|---|---|---|
| committer | jeh <jeh@FreeBSD.org> | 2001-02-12 00:28:59 +0800 |
| commit | 1575425fa548d42dd928ecc24d27fac8a205edab (patch) | |
| tree | 8f480f0792ef565d5902e4b7ed96a9d0af153e3a /biology/fasta3/files | |
| parent | 8078b1770fc5c9725b1e6aa19d3470acddde5460 (diff) | |
| download | freebsd-ports-graphics-1575425fa548d42dd928ecc24d27fac8a205edab.tar.gz freebsd-ports-graphics-1575425fa548d42dd928ecc24d27fac8a205edab.tar.zst freebsd-ports-graphics-1575425fa548d42dd928ecc24d27fac8a205edab.zip | |
- 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>
Diffstat (limited to 'biology/fasta3/files')
| -rw-r--r-- | biology/fasta3/files/patch-Makefile | 49 | ||||
| -rw-r--r-- | biology/fasta3/files/patch-Makefile.common | 20 |
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 00000000000..bdc135f01c9 --- /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 00000000000..395da695e03 --- /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) |