diff options
Diffstat (limited to 'sci-biology/t-coffee/files')
3 files changed, 43 insertions, 21 deletions
diff --git a/sci-biology/t-coffee/files/t-coffee-11.00-cxx11.patch b/sci-biology/t-coffee/files/t-coffee-11.00-cxx11.patch new file mode 100644 index 000000000000..17817d30eca2 --- /dev/null +++ b/sci-biology/t-coffee/files/t-coffee-11.00-cxx11.patch @@ -0,0 +1,21 @@ +--- a/t_coffee_source/programmes_define.h ++++ b/t_coffee_source/programmes_define.h +@@ -390,12 +390,12 @@ + #define XMLSIMPLE_language2 "Perl" + #define XMLSIMPLE_source "empty" + #define XMLSIMPLE_mode "psicoffee,expresso,accurate" +-#define x3dna-ssr_4_TCOFFEE "x3dna" +-#define x3dna-ssr_type "RNA_secondarystructure_predictor" +-#define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" +-#define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" +-#define x3dna-ssr_mode "saracoffee" +-#define x3dna-ssr_update_action "never" ++#define x3dna_ssr_4_TCOFFEE "x3dna" ++#define x3dna_ssr_type "RNA_secondarystructure_predictor" ++#define x3dna_ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ++#define x3dna_ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ++#define x3dna_ssr_mode "saracoffee" ++#define x3dna_ssr_update_action "never" + //TclinkdbEnd + /*New Methods*/ + /********************************************/ diff --git a/sci-biology/t-coffee/files/t-coffee-11.00-gcc7.patch b/sci-biology/t-coffee/files/t-coffee-11.00-gcc7.patch new file mode 100644 index 000000000000..64afc04a4b50 --- /dev/null +++ b/sci-biology/t-coffee/files/t-coffee-11.00-gcc7.patch @@ -0,0 +1,22 @@ +--- a/t_coffee_source/util_lib/aln_convertion_util.c ++++ b/t_coffee_source/util_lib/aln_convertion_util.c +@@ -5592,7 +5592,7 @@ + + list=string2list (H->seq_comment[n]); + if ( list==NULL || atoi(list[0])==1)continue; +- S->seq_comment[a]='\0'; ++ S->seq_comment[a]=NULL; + sprintf (S->name[a], "%s%s%s",H->name[n], list[1], list[2]); + vfree ( S->seq_comment[a]);S->seq_comment[a]=(char*)vcalloc ( strlen (H->seq_comment[n])+1, sizeof (char)); + for (b=3; b< atoi(list[0]); b++)S->seq_comment[a]=strcat (S->seq_comment[a], list[b]); +--- a/t_coffee_source/util_lib/util.c ++++ b/t_coffee_source/util_lib/util.c +@@ -5946,7 +5946,7 @@ + val_array[a]=(char*)vrealloc (val_array[a], strlen (v)+1); + sprintf (val_array[a],"%s",v); + } +- else val_array[a]='\0'; ++ else val_array[a]=NULL; + return v; + } + } diff --git a/sci-biology/t-coffee/files/t-coffee-9.03.1318-flags.patch b/sci-biology/t-coffee/files/t-coffee-9.03.1318-flags.patch deleted file mode 100644 index 5b15108b3bfa..000000000000 --- a/sci-biology/t-coffee/files/t-coffee-9.03.1318-flags.patch +++ /dev/null @@ -1,21 +0,0 @@ - t_coffee_source/makefile | 4 ++-- - 1 file changed, 2 insertions(+), 2 deletions(-) - -diff --git a/t_coffee_source/makefile b/t_coffee_source/makefile -index 9e01ba0..026b714 100644 ---- a/t_coffee_source/makefile -+++ b/t_coffee_source/makefile -@@ -1,6 +1,6 @@ - - t_coffee: util_constraints_list.o util_job_handling.o util_dps.o util_domain_constraints_list.o util_analyse_constraints_list.o util_aln_analyze.o aln_convertion_util.o util_declare.o hsearch.o random.o util_make_tree.o util.o reformat_struc.o reformat.o aln_compare.o io_func.o pb_util_read_sequence.o pb_util_read_seq_util.o tree_util.o util_graph_maln.o util_dp_clean_maln.o util_dp_ssec_pwaln.o util_dp_sim.o util_dp_mm_nw.o util_dp_gotoh_nw.o util_dp_suboptimal_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 fsa_dp.o pavie_dp.o dev1.o dev2.o dev3.o dev4.o fastal.o parttree.o tree.o diagonal.o fastal_opt_parsing.o scoring.o iteration.o Stack.o Vector.o classes.o km_util.o kmeans.o km_coffee.o t_coffee.o -- $(CC) $(CFLAGS) -o t_coffee util_constraints_list.o util_job_handling.o util_dps.o util_domain_constraints_list.o util_analyse_constraints_list.o util_aln_analyze.o aln_convertion_util.o util_declare.o hsearch.o random.o util_make_tree.o util.o reformat_struc.o reformat.o aln_compare.o io_func.o pb_util_read_sequence.o pb_util_read_seq_util.o tree_util.o util_graph_maln.o util_dp_clean_maln.o util_dp_ssec_pwaln.o util_dp_sim.o util_dp_mm_nw.o util_dp_gotoh_nw.o util_dp_suboptimal_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 fsa_dp.o pavie_dp.o dev1.o dev2.o dev3.o dev4.o fastal.o parttree.o tree.o diagonal.o fastal_opt_parsing.o scoring.o iteration.o Stack.o Vector.o classes.o km_util.o kmeans.o km_coffee.o t_coffee.o -lm -+ $(CC) $(CFLAGS) $(LDFLAGS) -o t_coffee util_constraints_list.o util_job_handling.o util_dps.o util_domain_constraints_list.o util_analyse_constraints_list.o util_aln_analyze.o aln_convertion_util.o util_declare.o hsearch.o random.o util_make_tree.o util.o reformat_struc.o reformat.o aln_compare.o io_func.o pb_util_read_sequence.o pb_util_read_seq_util.o tree_util.o util_graph_maln.o util_dp_clean_maln.o util_dp_ssec_pwaln.o util_dp_sim.o util_dp_mm_nw.o util_dp_gotoh_nw.o util_dp_suboptimal_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 fsa_dp.o pavie_dp.o dev1.o dev2.o dev3.o dev4.o fastal.o parttree.o tree.o diagonal.o fastal_opt_parsing.o scoring.o iteration.o Stack.o Vector.o classes.o km_util.o kmeans.o km_coffee.o t_coffee.o -lm - - all: t_coffee TMalign - -@@ -8,4 +8,4 @@ clean: - rm *.o - - TMalign: -- $(FCC) TMalign.f -o TMalign -+ $(FC) $(FCLAGS) $(LDFLAGS) TMalign.f -o TMalign |