| --- nnmake/make.system 2009-01-09 16:07:59.000000000 +0100 |
| +++ nnmake/make.system.new 2009-04-09 10:54:50.000000000 +0200 |
| @@ -62,10 +62,9 @@ |
| FPROFILEFLAGS=-P |
| |
| ifeq ($(COMPILER),gnu) |
| - F77 = g77 |
| - FFLAGS = -finline-functions -funroll-loops -W -ffixed-line-length-132 -Wimplicit |
| - FOPTIMFLAGS = -O -ffast-math -malign-double |
| - FDEBUGFLAGS = -g -Wall -Wimplicit -Wsurprising -Wformat -W |
| + F77 = $(FORTRANC) |
| + FOPTIMFLAGS = |
| + FDEBUGFLAGS = |
| FPROFILEFLAGS = -pg |
| endif |
| |
| --- nnmake/dipolar_nn.f 2009-01-09 16:08:00.000000000 +0100 |
| +++ nnmake/dipolar_nn.f.new 2009-04-09 11:06:24.923302302 +0200 |
| @@ -1396,7 +1396,7 @@ |
| write(0,*)'rejected' |
| write(0,*)x(1,iset),x(2,iset),x(3,iset),x(4,iset),x(5,iset) |
| do i=1,maplength(iset) |
| - write(0,'(i,6f6.3)')i,A(i,1),A(i,2),A(i,3),A(i,4),A(i,5), |
| + write(0,'(i6,6f6.3)')i,A(i,1),A(i,2),A(i,3),A(i,4),A(i,5), |
| # b(i) |
| enddo |
| goto 300 |
| --- nnmake/make.system 2009-04-09 11:10:34.399945087 +0200 |
| +++ nnmake/make.system.new 2009-04-09 11:19:41.287390259 +0200 |
| @@ -55,7 +55,6 @@ |
| |
| # defaults |
| F77=f77 |
| -FFLAGS= |
| FOPTIMFLAGS=-O |
| FDEBUGFLAGS=-g |
| FPROFILEFLAGS=-P |
| --- nnmake/makefile 2009-01-09 16:08:00.000000000 +0100 |
| +++ nnmake/makefile.new 2009-04-09 11:22:43.454037887 +0200 |
| @@ -102,7 +102,7 @@ |
| # rule to compile executable |
| compile: print $(BASE_NAME).$(COMPILER) |
| $(BASE_NAME).$(COMPILER) : ${OBJS} |
| - $(F77) $(FFLAGS) -o $@ $(OBJS) $(LINKFLAGS) |
| + $(F77) $(FFLAGS) $(LDFLAGS) -o $@ $(OBJS) $(LINKFLAGS) |
| |
| coord_compile: print $(COORD_BASE_NAME).$(COMPILER) |
| $(COORD_BASE_NAME).$(COMPILER) : ${COORD_OBJS} |
| --- nnmake/make_fragments.pl 2009-01-09 15:53:33.000000000 +0100 |
| +++ nnmake/make_fragments.pl.new 2009-04-09 13:01:52.987174602 +0200 |
| @@ -19,38 +19,38 @@ |
| |
| my $TAIL = "_v1_3"; |
| |
| -$src_dir = '/work/chu/rosetta/rosetta_C++/rosetta-2.2.0/rosetta_fragments'; |
| -$shareware_dir = '/work/chu/src/shareware'; |
| -$scratch = "/scratch/shared"; |
| +$src_dir = '/'; |
| +$shareware_dir = '$src_dir/usr/share'; |
| +$scratch = "$src_dir/scratch/shared"; |
| |
| # psi-blast |
| #my $BLAST_BIN_DIR = "$shareware_dir/new_blast/blast-2.2.12/bin"; |
| -my $PSIBLAST = "$shareware_dir/blast/bin/blastpgp"; # PSI-BLAST (duh.) |
| -my $NR = "/$scratch/genomes/nr"; # nr blast database filename |
| -my $VALL_BLAST_DB = "/$scratch/nnmake_database/vall.blast.2006-05-05"; # vall blast database filename (cvs respository 'nnmake_database') |
| -my $BLOSUM = "$scratch/nnmake_database/"; # BLOSUM score matrices directory (cvs repository 'nnmake_database') |
| +my $PSIBLAST = "$src_dir/usr/bin/blastpgp"; # PSI-BLAST (duh.) |
| +my $NR = "$shareware_dir/blast-db/nr"; # nr blast database filename |
| +my $VALL_BLAST_DB = "$shareware_dir/rosetta-fragments/nnmake_database/vall.blast.2006-05-05"; # vall blast database filename (cvs respository 'nnmake_database') |
| +my $BLOSUM = "$shareware_dir/rosetta-fragments/nnmake_database/"; # BLOSUM score matrices directory (cvs repository 'nnmake_database') |
| |
| # psipred |
| -my $FILTNR = "$scratch/genomes/filtnr"; # filtnr blast database filename |
| -my $MAKEMAT = "$shareware_dir/blast/bin/makemat"; # makemat utility (part of NCBI tools) |
| -my $PSIPRED = "$shareware_dir/psipred/bin/psipred"; # psipred |
| -my $PSIPASS2 = "$shareware_dir/psipred/bin/psipass2"; # psipass2 (part of psipred pkg) |
| +my $FILTNR = "$src_dir/tmp/filtnr"; # filtnr blast database filename |
| +my $MAKEMAT = "$src_dir/usr/bin/makemat"; # makemat utility (part of NCBI tools) |
| +my $PSIPRED = "$src_dir/usr/bin/psipred"; # psipred |
| +my $PSIPASS2 = "$src_dir/usr/bin/psipass2"; # psipass2 (part of psipred pkg) |
| my $PSIPRED_DATA = "$shareware_dir/psipred/data"; # dir containing psipred data files. |
| |
| # prof |
| #my $PROF = "$shareware_dir/prof/run_prof.py"; |
| -my $PROF = "$src_dir/nnmake/run_prof.py"; # remember to change prof executable location in run_prof.py |
| +my $PROF = "$src_dir/usr/bin/run_prof.py"; # remember to change prof executable location in run_prof.py |
| |
| # nnmake |
| -my $VALL = "$scratch/nnmake_database"; # dir containing vall database (cvs repository 'nnmake_database') |
| -my $VALL2 = "$scratch/nnmake_database"; # alt dir containing vall database (cvs repository 'nnmake_database') |
| +my $VALL = "$shareware_dir/rosetta-fragments/nnmake_database"; # dir containing vall database (cvs repository 'nnmake_database') |
| +my $VALL2 = "$shareware_dir/rosetta-fragments/nnmake_database"; # alt dir containing vall database (cvs repository 'nnmake_database') |
| my $VALL_NAME = "vall.dat.2006-05-05"; # filename of vall (vall.dat.<id> and vall_cst_coord.dat.<id> must exist) |
| -my $NNMAKE = "$src_dir/nnmake/pNNMAKE.gnu"; # nnmake binary (cvs respository 'nnmake') |
| -my $TRIMLOOPS = "$src_dir/nnmake/trimLoopLibrary.pl"; # trimLoopLibrary.pl (cvs respository 'nnmake') |
| +my $NNMAKE = "$src_dir/usr/bin/pNNMAKE"; # nnmake binary (cvs respository 'nnmake') |
| +my $TRIMLOOPS = "$src_dir/usr/bin/trimLoopLibrary.pl"; # trimLoopLibrary.pl (cvs respository 'nnmake') |
| |
| # chemshift |
| -my $CHEMSHIFT = "$src_dir/chemshift/pCHEMSHIFT.gnu"; # chemshift binary (cvs repository 'chemshift') |
| -my $TALOS_DB = "$scratch/chemshift_database"; # TALOS databases directory (cvs respository 'chemshift_database') |
| +my $CHEMSHIFT = "$src_dir/usr/bin/pCHEMSHIFT"; # chemshift binary (cvs repository 'chemshift') |
| +my $TALOS_DB = "$shareware_dir/rosetta-fragments/chemshift_database"; # TALOS databases directory (cvs respository 'chemshift_database') |
| |
| # jufo (secondary structure prediction software) |
| my $JUFO = "$shareware_dir/jufo/molecule.exe"; # jufo executable |
