- Respect PORTDOCS/PORTEXAMPLES

Reported by:	QA Tindie
Approved by:	portmgr

2 files changed, 186 insertions, 188 deletions

diff --git a/biology/t_coffee/Makefile b/biology/t_coffee/Makefile
index d670bebaca9f..6bc30c0b47ea 100644
--- a/biology/t_coffee/Makefile
+++ b/biology/t_coffee/Makefile
@@ -29,15 +29,14 @@ do-install:
 
 post-install:
 .if !defined(NOPORTDOCS)
-	@ ${MKDIR} ${DOCSDIR}
+	@ ${MKDIR} ${DOCSDIR}/html
 	${INSTALL_DATA} ${WRKSRC}/doc/* ${DOCSDIR}
+	${INSTALL_DATA} ${WRKSRC}/license.txt ${DOCSDIR}
+	${INSTALL_DATA} ${WRKSRC}/html/* ${DOCSDIR}/html
+.endif
+.if !defined(NOPORTEXAMPLES)
 	@ ${MKDIR} ${EXAMPLESDIR}
-	@ cd ${WRKSRC}/example && ${FIND} * \
-	  | ${CPIO} --quiet -pdum -R ${SHAREOWN}:${SHAREGRP} ${EXAMPLESDIR}
-	@ ${MKDIR} ${DATADIR}
-	${INSTALL_DATA} ${WRKSRC}/license.txt ${DATADIR}
-	@ ${MKDIR} ${DATADIR}/html
-	${INSTALL_DATA} ${WRKSRC}/html/* ${DATADIR}/html
+	cd ${WRKSRC}/example && ${COPYTREE_SHARE} \* ${EXAMPLESDIR}
 .endif
 
 .include <bsd.port.mk>
diff --git a/biology/t_coffee/pkg-plist b/biology/t_coffee/pkg-plist
index c748e86f53cc..21736fc61d28 100644
--- a/biology/t_coffee/pkg-plist
+++ b/biology/t_coffee/pkg-plist
@@ -8,184 +8,183 @@ bin/t_coffee
 %%PORTDOCS%%%%DOCSDIR%%/t_coffee_tutorial.doc
 %%PORTDOCS%%%%DOCSDIR%%/t_coffee_tutorial.htm
 %%PORTDOCS%%%%DOCSDIR%%/t_coffee_tutorial.txt
-%%EXAMPLESDIR%%/2seqs.fas
-%%EXAMPLESDIR%%/3d.aln
-%%EXAMPLESDIR%%/3d.dnd
-%%EXAMPLESDIR%%/3d.fasta
-%%EXAMPLESDIR%%/3d.html
-%%EXAMPLESDIR%%/3d_sample2.fasta
-%%EXAMPLESDIR%%/3d_sample3.fasta
-%%EXAMPLESDIR%%/3d_sample4.aln
-%%EXAMPLESDIR%%/b30.aln
-%%EXAMPLESDIR%%/block1.aln
-%%EXAMPLESDIR%%/block2.aln
-%%EXAMPLESDIR%%/cache
-%%EXAMPLESDIR%%/charge_relay_lib.tc_lib
-%%EXAMPLESDIR%%/clustalw_method.tc_method
-%%EXAMPLESDIR%%/combined_aln.aln
-%%EXAMPLESDIR%%/combined_aln.aln.aln
-%%EXAMPLESDIR%%/combined_aln.aln.html
-%%EXAMPLESDIR%%/command_line.txt
-%%EXAMPLESDIR%%/error_report.T-COFFEE
-%%EXAMPLESDIR%%/g0.aln
-%%EXAMPLESDIR%%/x
-%%EXAMPLESDIR%%/g10.aln
-%%EXAMPLESDIR%%/g15.aln
-%%EXAMPLESDIR%%/g5.aln
-%%EXAMPLESDIR%%/kinases.aln
-%%EXAMPLESDIR%%/marna.tc_lib
-%%EXAMPLESDIR%%/new_profile1_pdb1.aln
-%%EXAMPLESDIR%%/new_profile1_pdb1.html
-%%EXAMPLESDIR%%/newprf.aln
-%%EXAMPLESDIR%%/newprf.html
-%%EXAMPLESDIR%%/p120.aln
-%%EXAMPLESDIR%%/p250
-%%EXAMPLESDIR%%/p350.aln
-%%EXAMPLESDIR%%/prf1.aln
-%%EXAMPLESDIR%%/prf1.dnd
-%%EXAMPLESDIR%%/prf1.fasta
-%%EXAMPLESDIR%%/prf2.aln
-%%EXAMPLESDIR%%/prf2.dnd
-%%EXAMPLESDIR%%/prf2.fasta
-%%EXAMPLESDIR%%/prf3.aln
-%%EXAMPLESDIR%%/prf3.fasta
-%%EXAMPLESDIR%%/profile1_pdb1.aln
-%%EXAMPLESDIR%%/profile1_pdb1.fasta
-%%EXAMPLESDIR%%/profile1_pdb1.html
-%%EXAMPLESDIR%%/seq.fas
-%%EXAMPLESDIR%%/profile1_pdb1_1.aln
-%%EXAMPLESDIR%%/profile1_pdb1_1.html
-%%EXAMPLESDIR%%/profile2_pdb2.aln
-%%EXAMPLESDIR%%/profile2_pdb2.dnd
-%%EXAMPLESDIR%%/profile2_pdb2.fasta
-%%EXAMPLESDIR%%/profile2_pdb2.html
-%%EXAMPLESDIR%%/sample_aln1.aln
-%%EXAMPLESDIR%%/sample_aln1.dnd
-%%EXAMPLESDIR%%/sample_aln1.fasta
-%%EXAMPLESDIR%%/sample_aln1.tc_lib
-%%EXAMPLESDIR%%/sample_aln1_1.aln
-%%EXAMPLESDIR%%/sample_aln1_2.aln
-%%EXAMPLESDIR%%/sample_aln2.aln
-%%EXAMPLESDIR%%/sample_aln2.fasta
-%%EXAMPLESDIR%%/sample_aln2.msf
-%%EXAMPLESDIR%%/sample_aln3.aln
-%%EXAMPLESDIR%%/sample_aln4.aln
-%%EXAMPLESDIR%%/sample_aln5.aln
-%%EXAMPLESDIR%%/sample_aln6.aln
-%%EXAMPLESDIR%%/sample_aln6.cache
-%%EXAMPLESDIR%%/sample_aln6.html
-%%EXAMPLESDIR%%/sample_aln7.aln
-%%EXAMPLESDIR%%/sample_aln7.cache_aln
-%%EXAMPLESDIR%%/sample_dnaseq1.fasta
-%%EXAMPLESDIR%%/sample_lib1.mocca_lib
-%%EXAMPLESDIR%%/sample_lib1.tc_lib
-%%EXAMPLESDIR%%/sample_lib2.tc_lib
-%%EXAMPLESDIR%%/sample_lib3.tc_lib
-%%EXAMPLESDIR%%/sample_lib4.tc_lib02
-%%EXAMPLESDIR%%/sample_lib5.tc_lib
-%%EXAMPLESDIR%%/sample_list1.lib_list
-%%EXAMPLESDIR%%/sample_param_file.param
-%%EXAMPLESDIR%%/sample_profile1.aln
-%%EXAMPLESDIR%%/sample_profile2.aln
-%%EXAMPLESDIR%%/sample_rnaseq1.fasta
-%%EXAMPLESDIR%%/sample_seq1.aln
-%%EXAMPLESDIR%%/sv.aln
-%%EXAMPLESDIR%%/sample_seq1.fasta
-%%EXAMPLESDIR%%/sample_seq2.fasta
-%%EXAMPLESDIR%%/sample_seq3.fasta
-%%EXAMPLESDIR%%/sample_seq4.fasta
-%%EXAMPLESDIR%%/sample_seq5.fasta
-%%EXAMPLESDIR%%/sample_seq6.fasta
-%%EXAMPLESDIR%%/sample_seq7.fasta
-%%EXAMPLESDIR%%/sample_seq8.seq
-%%EXAMPLESDIR%%/sample_tree.dnd
-%%EXAMPLESDIR%%/sample_tree2.dnd
-%%EXAMPLESDIR%%/sample_tree3.dnd
-%%EXAMPLESDIR%%/sproteases.small
-%%EXAMPLESDIR%%/sproteases.small.blosum62mt.sim_file
-%%EXAMPLESDIR%%/sproteases1_small.aln
-%%EXAMPLESDIR%%/sproteases1_small.dnd
-%%EXAMPLESDIR%%/sproteases1_small.fasta
-%%EXAMPLESDIR%%/sproteases2_small.aln
-%%EXAMPLESDIR%%/sproteases2_small.dnd
-%%EXAMPLESDIR%%/sproteases2_small.fasta
-%%EXAMPLESDIR%%/sproteases_chain.fasta
-%%EXAMPLESDIR%%/sproteases_large.aln
-%%EXAMPLESDIR%%/sproteases_large.code_name
-%%EXAMPLESDIR%%/sproteases_large.coded.fasta
-%%EXAMPLESDIR%%/sproteases_large.dnd
-%%EXAMPLESDIR%%/sproteases_large.fasta
-%%EXAMPLESDIR%%/sproteases_large.fasta.blosum62mt.sim2_file
-%%EXAMPLESDIR%%/sproteases_large.fasta.blosum62mt.sim_file
-%%EXAMPLESDIR%%/sproteases_large.fasta~
-%%EXAMPLESDIR%%/sproteases_large.html
-%%EXAMPLESDIR%%/sproteases_large.muscle
-%%EXAMPLESDIR%%/sproteases_large_muscle_trim.aln
-%%EXAMPLESDIR%%/sproteases_oneseq.fasta
-%%EXAMPLESDIR%%/sproteases_pair.fasta
-%%EXAMPLESDIR%%/sproteases_small.aln
-%%EXAMPLESDIR%%/sproteases_small.b62_aln
-%%EXAMPLESDIR%%/sproteases_small.cw_aln
-%%EXAMPLESDIR%%/sproteases_small.dnd
-%%EXAMPLESDIR%%/sproteases_small.expresso
-%%EXAMPLESDIR%%/sproteases_small.fasta
-%%EXAMPLESDIR%%/sproteases_small.g0.aln
-%%EXAMPLESDIR%%/sproteases_small.g0.cw_aln
-%%EXAMPLESDIR%%/sproteases_small.g10.cw_aln
-%%EXAMPLESDIR%%/sproteases_small.g10.html
-%%EXAMPLESDIR%%/sproteases_small.g10.score_ascii
-%%EXAMPLESDIR%%/sproteases_small.g15.cw_aln
-%%EXAMPLESDIR%%/sproteases_small.ph
-%%EXAMPLESDIR%%/sproteases_small.g15.html
-%%EXAMPLESDIR%%/sproteases_small.html
-%%EXAMPLESDIR%%/sproteases_small.mafft
-%%EXAMPLESDIR%%/sproteases_small.mcoffee
-%%EXAMPLESDIR%%/sproteases_small.muscle
-%%EXAMPLESDIR%%/sproteases_small.probcons
-%%EXAMPLESDIR%%/sproteases_small.score_ascii
-%%EXAMPLESDIR%%/sproteases_small.score_html
-%%EXAMPLESDIR%%/sproteases_small.tc_aln
-%%EXAMPLESDIR%%/sproteases_small.tc_aln.aln
-%%EXAMPLESDIR%%/sproteases_small.tc_aln.html
-%%EXAMPLESDIR%%/sproteases_small.template_file
-%%EXAMPLESDIR%%/sproteases_small_dna.fasta
-%%EXAMPLESDIR%%/struc1.pdb
-%%EXAMPLESDIR%%/struc2.pdb
-%%EXAMPLESDIR%%/struc3.pdb
-%%EXAMPLESDIR%%/struc4.pdb
-%%EXAMPLESDIR%%/struc5.pdb
-%%EXAMPLESDIR%%/struc6.pdb
-%%EXAMPLESDIR%%/struc7.pdb
-%%EXAMPLESDIR%%/struc8.pdb
-%%EXAMPLESDIR%%/sv.dnd
-%%EXAMPLESDIR%%/sv.fasta
-%%EXAMPLESDIR%%/sv.html
-%%EXAMPLESDIR%%/sv.maln
-%%EXAMPLESDIR%%/t_coffee.log
-%%EXAMPLESDIR%%/template_file.template
-%%EXAMPLESDIR%%/template_file6.template
-%%EXAMPLESDIR%%/template_file7.template
-%%EXAMPLESDIR%%/test.lib
-%%EXAMPLESDIR%%/test.tc_lib
-%%EXAMPLESDIR%%/test_lib.tc_lib
-%%EXAMPLESDIR%%/three_pdb.aln
-%%EXAMPLESDIR%%/three_pdb.dnd
-%%EXAMPLESDIR%%/three_pdb.fasta
-%%EXAMPLESDIR%%/three_pdb_two_seq.aln
-%%EXAMPLESDIR%%/three_pdb_two_seq.dnd
-%%EXAMPLESDIR%%/three_pdb_two_seq.fasta
-%%EXAMPLESDIR%%/three_pdb_two_seq.fasta~
-%%EXAMPLESDIR%%/tlara_libraries.tar
-%%EXAMPLESDIR%%/tlara_tRNA_aln10.output
-%%EXAMPLESDIR%%/tlara_tRNA_aln50.output
-%%EXAMPLESDIR%%/tlara_tRNA_aln51.output
-%%EXAMPLESDIR%%/tmp_file_for_extract_from_pdb169168.1
-%%EXAMPLESDIR%%/tmp_file_for_extract_from_pdb89508.1
-%%EXAMPLESDIR%%/two_profiles.template_file
-%%DATADIR%%/license.txt
-%%DATADIR%%/html/t_coffee.html
-%%DATADIR%%/html/t_coffee4html.cgi
-%%PORTDOCS%%@dirrmtry %%DOCSDIR%%
-@dirrmtry %%EXAMPLESDIR%%
-@dirrm %%DATADIR%%/html
-@dirrmtry %%DATADIR%%
+%%PORTDOCS%%%%DOCSDIR%%/license.txt
+%%PORTDOCS%%%%DOCSDIR%%/html/t_coffee.html
+%%PORTDOCS%%%%DOCSDIR%%/html/t_coffee4html.cgi
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/2seqs.fas
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/3d.aln
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/3d.dnd
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/3d.fasta
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/3d.html
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/3d_sample2.fasta
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/3d_sample3.fasta
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/3d_sample4.aln
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/b30.aln
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/block1.aln
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/block2.aln
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cache
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/charge_relay_lib.tc_lib
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/clustalw_method.tc_method
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/combined_aln.aln
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/combined_aln.aln.aln
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/combined_aln.aln.html
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/command_line.txt
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/error_report.T-COFFEE
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/g0.aln
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/x
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/g10.aln
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/g15.aln
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/g5.aln
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/kinases.aln
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/marna.tc_lib
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/new_profile1_pdb1.aln
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/new_profile1_pdb1.html
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/newprf.aln
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/newprf.html
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/p120.aln
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/p250
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/p350.aln
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/prf1.aln
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/prf1.dnd
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/prf1.fasta
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/prf2.aln
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/prf2.dnd
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/prf2.fasta
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/prf3.aln
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/prf3.fasta
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/profile1_pdb1.aln
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/profile1_pdb1.fasta
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/profile1_pdb1.html
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/seq.fas
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/profile1_pdb1_1.aln
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/profile1_pdb1_1.html
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/profile2_pdb2.aln
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/profile2_pdb2.dnd
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/profile2_pdb2.fasta
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/profile2_pdb2.html
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_aln1.aln
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_aln1.dnd
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_aln1.fasta
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_aln1.tc_lib
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_aln1_1.aln
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_aln1_2.aln
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_aln2.aln
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_aln2.fasta
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_aln2.msf
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_aln3.aln
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_aln4.aln
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_aln5.aln
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_aln6.aln
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_aln6.cache
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_aln6.html
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_aln7.aln
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_aln7.cache_aln
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_dnaseq1.fasta
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_lib1.mocca_lib
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_lib1.tc_lib
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_lib2.tc_lib
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_lib3.tc_lib
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_lib4.tc_lib02
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_lib5.tc_lib
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_list1.lib_list
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_param_file.param
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_profile1.aln
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_profile2.aln
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_rnaseq1.fasta
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_seq1.aln
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sv.aln
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_seq1.fasta
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_seq2.fasta
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_seq3.fasta
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_seq4.fasta
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_seq5.fasta
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_seq6.fasta
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_seq7.fasta
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_seq8.seq
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_tree.dnd
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_tree2.dnd
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_tree3.dnd
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases.small
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases.small.blosum62mt.sim_file
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases1_small.aln
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases1_small.dnd
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases1_small.fasta
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases2_small.aln
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases2_small.dnd
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases2_small.fasta
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_chain.fasta
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_large.aln
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_large.code_name
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_large.coded.fasta
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_large.dnd
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_large.fasta
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_large.fasta.blosum62mt.sim2_file
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_large.fasta.blosum62mt.sim_file
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_large.fasta~
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_large.html
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_large.muscle
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_large_muscle_trim.aln
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_oneseq.fasta
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_pair.fasta
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small.aln
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small.b62_aln
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small.cw_aln
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small.dnd
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small.expresso
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small.fasta
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small.g0.aln
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small.g0.cw_aln
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small.g10.cw_aln
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small.g10.html
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small.g10.score_ascii
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small.g15.cw_aln
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small.ph
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small.g15.html
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small.html
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small.mafft
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small.mcoffee
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small.muscle
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small.probcons
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small.score_ascii
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small.score_html
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small.tc_aln
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small.tc_aln.aln
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small.tc_aln.html
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small.template_file
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small_dna.fasta
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/struc1.pdb
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/struc2.pdb
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/struc3.pdb
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/struc4.pdb
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/struc5.pdb
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/struc6.pdb
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/struc7.pdb
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/struc8.pdb
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sv.dnd
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sv.fasta
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sv.html
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sv.maln
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/t_coffee.log
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/template_file.template
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/template_file6.template
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/template_file7.template
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/test.lib
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/test.tc_lib
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/test_lib.tc_lib
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/three_pdb.aln
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/three_pdb.dnd
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/three_pdb.fasta
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/three_pdb_two_seq.aln
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/three_pdb_two_seq.dnd
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