Update of /cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv24068
Added Files: tcoffee.info tcoffee.patch Log Message: build-as-nobody fix, new maintainer --- NEW FILE: tcoffee.info --- Package: tcoffee Version: 1.37 Revision: 2 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/%n.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. Previous maintainer: Jason Stajich << 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: Koen van der Drift <[EMAIL PROTECTED]> Homepage: http://igs-server.cnrs-mrs.fr/~cnotred/Projects_home_page/t_coffee_home_page.html --- NEW FILE: tcoffee.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 +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 +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 ------------------------------------------------------- SF.Net email is sponsored by: Discover Easy Linux Migration Strategies from IBM. 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