Update of /cvsroot/fink/dists/10.2/unstable/main/finkinfo/sci
In directory sc8-pr-cvs1:/tmp/cvs-serv7696
Added Files:
tcoffee-1.37-1.info tcoffee-1.37-1.patch
Log Message:
new package from submission tracker #663403
--- NEW FILE: tcoffee-1.37-1.info ---
Package: tcoffee
Version: 1.37
Revision: 1
Source: http://igs-server.cnrs-mrs.fr/~cnotred/Packages/T-COFFEE_distribution.tar.gz
Source-MD5: a947c75871f56e83ccc1e8444495330a
Sourcedirectory: T-COFFEE_distribution_Version_%v
PatchScript: sed 's|@PREFIX@|%p|g' < %a/%f.patch | patch -p1
CompileScript: make
DocFiles: doc/README4T-COFFEE doc/t_coffee.pdf doc/t_coffee_doc.doc
Description: T-Coffee Multiple Sequence Alignment Program
DescDetail: <<
T-Coffee computes multiple sequence alignments for protein or dna/rna
sequences. It is considerably slower than ClustalW but does a better
job aligning more distantly related sequences (<30% identity). There
are also some enhancements for cDNA alignments.
<<
DescUsage: t_coffee
License: Restrictive
DescPackaging: <<
>From the docs: "This program comes with no warranty. The code should
not be modified and/or redistributed without the permissions of the
authors." Therefore I left the license as restrictive.
<<
Maintainer: Jason Stajich <[EMAIL PROTECTED]>
Homepage:
http://igs-server.cnrs-mrs.fr/~cnotred/Projects_home_page/t_coffee_home_page.html
--- NEW FILE: tcoffee-1.37-1.patch ---
diff -r -Naur T-COFFEE_distribution_Version_1.37.orig/Makefile
T-COFFEE_distribution_Version_1.37/Makefile
--- T-COFFEE_distribution_Version_1.37.orig/Makefile 1969-12-31 19:00:00.000000000
-0500
+++ T-COFFEE_distribution_Version_1.37/Makefile 2003-01-07 10:20:53.000000000 -0500
@@ -0,0 +1,12 @@
+
+all:
+ (cd t_coffee_source; make)
+ (cd lalign; make)
+
+clean:
+ (cd t_coffee_source; make clean)
+ (cd lalign; make clean)
+
+install: all
+ (cd t_coffee_source; make install)
+ (cd lalign; make install)
diff -r -Naur T-COFFEE_distribution_Version_1.37.orig/lalign/makefile
T-COFFEE_distribution_Version_1.37/lalign/makefile
--- T-COFFEE_distribution_Version_1.37.orig/lalign/makefile 2001-07-11
17:40:15.000000000 -0400
+++ T-COFFEE_distribution_Version_1.37/lalign/makefile 2003-01-07 10:21:31.000000000
+-0500
@@ -4,9 +4,9 @@
# use the compiler option that invokes signed char's.
#
#sun (bsd)
-CC= cc
+CC= cc
# for MIPS: CFLAGS= -O -DUNIX -DBIGMEM -DSFCHAR="':'" -signed
-CFLAGS= -O -DUNIX -DBIGMEM -DSFCHAR="':'"
+CFLAGS= -O3 -DUNIX -DBIGMEM -DSFCHAR="':'"
LFLAGS= -o
#NRAND= nrand
#IBM RS/6000
@@ -15,21 +15,29 @@
#HZ=60 for sun, mips, 100 for rs/6000, SGI
HZ=60
+#
+# Where to put things
+#
+prefix = @PREFIX@
+bindir = $(prefix)/bin
+
+INSTALL = /usr/bin/install -o root -g admin
+CFLAGS = -c -O3 -DUNIX -DBIGMEM -DSFCHAR="':'"
+LFLAGS = -O3 -lm
PROGS= lalign2list
+
.c.o:
$(CC) $(CFLAGS) -c $<
+
all : $(PROGS)
-clean :
- rm *.o
lalign2list : lalign.o pam.o lsim.o lgetaa.o ndispn.o time.o
- $(CC) lalign.o pam.o lsim.o lgetaa.o ndispn.o time.o $(LFLAGS) lalign2list
- mv lalign2list $(USER_BIN)/lalign2list
+ $(CC) -o $@ lalign.o pam.o lsim.o lgetaa.o ndispn.o time.o $(LFLAGS)
lalign.o : lalign.c upam.gbl
pam.o : uascii.gbl upam.gbl
lsim.o : lsim.c zzgmata.gbl upam.gbl
- $(CC) $(CFLAGS) -c lsim.c
+ $(CC) $(CFLAGS) -c lsim.c
lgetaa.o : nxgetaa.c upam.gbl uascii.gbl altlib.h
$(CC) $(CFLAGS) -DNOLIB -c nxgetaa.c
mv nxgetaa.o lgetaa.o
@@ -37,3 +45,11 @@
time.o : time.c
$(CC) $(CFLAGS) -DHZ=$(HZ) -c time.c
+install: $(PROGS)
+ $(INSTALL) -d -m 755 $(bindir)
+ $(INSTALL) -c -m 755 $(PROGS) $(bindir)
+
+clean :
+ rm -f *.o $(PROGS)
+
+
diff -r -Naur T-COFFEE_distribution_Version_1.37.orig/t_coffee_source/makefile
T-COFFEE_distribution_Version_1.37/t_coffee_source/makefile
--- T-COFFEE_distribution_Version_1.37.orig/t_coffee_source/makefile 2001-07-11
17:40:30.000000000 -0400
+++ T-COFFEE_distribution_Version_1.37/t_coffee_source/makefile 2003-01-07
+10:21:15.000000000 -0500
@@ -1,9 +1,22 @@
CC=cc
-t_coffee: util_constraints_list.o util_domain_constraints_list.o
util_analyse_constraints_list.o aln_convertion_util.o util_declare.o hsearch.o
random.o util_make_tree.o util.o reformat_struc.o reformat.o io_func.o
pb_util_read_sequence.o pb_util_read_seq_util.o tree_util.o util_dp_clean_maln.o
util_dp_ssec_pwaln.o util_dp_mm_nw.o util_dp_gotoh_nw.o util_dp_cdna_fasta_nw.o
util_dp_generic_fasta_nw.o util_dp_fasta_nw.o util_dp_fasta_sw.o util_dp_gotoh_sw.o
util_dp_est.o util_domain_dp_drivers.o util_dp_drivers.o util_domain_dp.o
CUSTOM_evaluate_for_struc.o evaluate_for_struc.o evaluate_for_domain.o
evaluate_dirichlet.o evaluate.o showpair.o t_coffee.o
- $(CC) -O -o t_coffee util_constraints_list.o util_domain_constraints_list.o
util_analyse_constraints_list.o aln_convertion_util.o util_declare.o hsearch.o
random.o util_make_tree.o util.o reformat_struc.o reformat.o io_func.o
pb_util_read_sequence.o pb_util_read_seq_util.o tree_util.o util_dp_clean_maln.o
util_dp_ssec_pwaln.o util_dp_mm_nw.o util_dp_gotoh_nw.o util_dp_cdna_fasta_nw.o
util_dp_generic_fasta_nw.o util_dp_fasta_nw.o util_dp_fasta_sw.o util_dp_gotoh_sw.o
util_dp_est.o util_domain_dp_drivers.o util_dp_drivers.o util_domain_dp.o
CUSTOM_evaluate_for_struc.o evaluate_for_struc.o evaluate_for_domain.o
evaluate_dirichlet.o evaluate.o showpair.o t_coffee.o -lm
- mv t_coffee ../bin
+prefix = @PREFIX@
+bindir = $(prefix)/bin
+
+INSTALL = /usr/bin/install -o root -g admin
+CFLAGS = -O3
+LFLAGS = -o -O3 -lm
+
+.c.o:
+ $(CC) $(CFLAGS) -c $<
+
+t_coffee: util_constraints_list.o util_domain_constraints_list.o
+util_analyse_constraints_list.o aln_convertion_util.o util_declare.o hsearch.o
+random.o util_make_tree.o util.o reformat_struc.o reformat.o io_func.o
+pb_util_read_sequence.o pb_util_read_seq_util.o tree_util.o util_dp_clean_maln.o
+util_dp_ssec_pwaln.o util_dp_mm_nw.o util_dp_gotoh_nw.o util_dp_cdna_fasta_nw.o
+util_dp_generic_fasta_nw.o util_dp_fasta_nw.o util_dp_fasta_sw.o util_dp_gotoh_sw.o
+util_dp_est.o util_domain_dp_drivers.o util_dp_drivers.o util_domain_dp.o
+CUSTOM_evaluate_for_struc.o evaluate_for_struc.o evaluate_for_domain.o
+evaluate_dirichlet.o evaluate.o showpair.o t_coffee.o
+ $(CC) $(CFLAGS) -o t_coffee util_constraints_list.o
+util_domain_constraints_list.o util_analyse_constraints_list.o aln_convertion_util.o
+util_declare.o hsearch.o random.o util_make_tree.o util.o reformat_struc.o reformat.o
+io_func.o pb_util_read_sequence.o pb_util_read_seq_util.o tree_util.o
+util_dp_clean_maln.o util_dp_ssec_pwaln.o util_dp_mm_nw.o util_dp_gotoh_nw.o
+util_dp_cdna_fasta_nw.o util_dp_generic_fasta_nw.o util_dp_fasta_nw.o
+util_dp_fasta_sw.o util_dp_gotoh_sw.o util_dp_est.o util_domain_dp_drivers.o
+util_dp_drivers.o util_domain_dp.o CUSTOM_evaluate_for_struc.o evaluate_for_struc.o
+evaluate_for_domain.o evaluate_dirichlet.o evaluate.o showpair.o t_coffee.o
all: t_coffee
+install: t_coffee
+ $(INSTALL) -d -m 755 $(bindir)
+ $(INSTALL) -c -m 755 t_coffee $(bindir)
+
clean:
- rm *.o
+ rm -f *.o t_coffee
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