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desc
@@


1.10
log
@## SVN ## Exported commit - http://svnweb.freebsd.org/changeset/base/310361
## SVN ## CVS IS DEPRECATED: http://wiki.freebsd.org/CvsIsDeprecated
@
text
@bin/t_coffee
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%%PORTDOCS%%@@dirrm %%DOCSDIR%%/html
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@


1.9
log
@- Respect PORTDOCS/PORTEXAMPLES

Reported by:	QA Tindie
Approved by:	portmgr
@
text
@@


1.8
log
@- Update to 5.68
- Remove gcc version restriction

PR:		ports/122435
Submitted by:	Fernan Aguero <fernan at iib.unsam.edu.ar> (maintainer)
@
text
@d11 180
a190 181
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%%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%%
@


1.7
log
@- Update to 4.96

PR:             110080
Submitted by:   Fernan Aguero<fernan@@iib.unsam.edu.ar> (maintainer)
@
text
@a4 1
%%PORTDOCS%%%%DOCSDIR%%/t_coffee.pdf
d35 1
d55 1
d90 1
d92 1
a94 1
%%EXAMPLESDIR%%/seq.fas
d138 1
a140 1
%%EXAMPLESDIR%%/struc1.pdb
a143 1
%%EXAMPLESDIR%%/sproteases_small.ph
d152 1
a159 1
%%EXAMPLESDIR%%/sv.aln
@


1.6
log
@Replace ugly "@@unexec rmdir %D... 2>/dev/null || true" with @@dirrmtry

Approved by:    krion@@
PR:             ports/88711 (related)
@
text
@d6 9
a14 3
%%PORTDOCS%%%%DOCSDIR%%/t_coffee_doc.doc
%%PORTDOCS%%%%DOCSDIR%%/t_coffee_doc.pdf
%%PORTDOCS%%%%DOCSDIR%%/t_coffee_doc.txt
d16 1
d19 6
d26 3
d30 31
a60 1
%%EXAMPLESDIR%%/error_report.T-COFFEE.3752
d62 1
d72 6
a78 1
%%EXAMPLESDIR%%/struc1.pdb
d84 1
d92 1
d96 3
d100 51
d154 9
d165 2
d170 14
d187 1
a187 1
@@dirrmtry %%DOCSDIR%%
@


1.5
log
@Forced commit to note the port was updated to 3.14 not 3.13
@
text
@d54 2
a55 2
@@unexec rmdir %D/%%DOCSDIR%% 2>/dev/null || true
@@unexec rmdir %D/%%EXAMPLESDIR%% 2>/dev/null || true
d57 1
a57 1
@@unexec rmdir %D/%%DATADIR%% 2>/dev/null || true
@


1.4
log
@- Update to 3.13. It fixes fetching.

PR:		ports/87264
Submitted by:	maintainer
@
text
@@


1.3
log
@- Update to 2.03
- Pass maintainership to submitter

PR:		ports/74332
Submitted by:	Fernan Aguero <fernan(at)iib.unsam.edu.ar>
@
text
@a1 8
bin/msf_aln2fasta_aln.pl
bin/blast_aln2fasta_aln.pl
bin/fasta_aln2fasta_aln_unique_name.pl
bin/extract_from_pdb
bin/fugue_client
bin/t_coffee_dpa
bin/t_coffee_dpa2
bin/mocca
d3 2
d8 50
a57 148
%%EXAMPLESDIR%%/seq/1aab_ref1.pep
%%EXAMPLESDIR%%/seq/1aboA_ref1.pep
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%%EXAMPLESDIR%%/seq/1ac5_ref1.pep
%%EXAMPLESDIR%%/seq/1ad2_ref1.pep
%%EXAMPLESDIR%%/seq/1ad3_ref1.pep
%%EXAMPLESDIR%%/seq/1adj_ref1.pep
%%EXAMPLESDIR%%/seq/1ag8_ref4.pep
%%EXAMPLESDIR%%/seq/1aho_ref1.pep
%%EXAMPLESDIR%%/seq/1aisB_ref4.pep
%%EXAMPLESDIR%%/seq/1ajsA_ref1.pep
%%EXAMPLESDIR%%/seq/1ajsA_ref2.pep
%%EXAMPLESDIR%%/seq/1ajsA_ref3.pep
%%EXAMPLESDIR%%/seq/1amk_ref1.pep
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%%EXAMPLESDIR%%/seq/1bbt3_ref1.pep
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%%EXAMPLESDIR%%/seq/1cpt_ref1.pep
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%%EXAMPLESDIR%%/seq/1csp_ref1.pep
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%%EXAMPLESDIR%%/seq/1csy_ref1.pep
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%%EXAMPLESDIR%%/seq/1pfc_ref1.pep
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%%EXAMPLESDIR%%/seq/1sesA_ref1.pep
%%EXAMPLESDIR%%/seq/1taq_ref1.pep
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%%EXAMPLESDIR%%/seq/1thm1_ref5.pep
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%%EXAMPLESDIR%%/seq/1thm_ref1.pep
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%%EXAMPLESDIR%%/seq/1tvxA_ref1.pep
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%%EXAMPLESDIR%%/seq/1ubi_ref1.pep
%%EXAMPLESDIR%%/seq/1ubi_ref2.pep
%%EXAMPLESDIR%%/seq/1ubi_ref3.pep
%%EXAMPLESDIR%%/seq/1uky_ref1.pep
%%EXAMPLESDIR%%/seq/1uky_ref2.pep
%%EXAMPLESDIR%%/seq/1uky_ref3.pep
%%EXAMPLESDIR%%/seq/1vln_ref4.pep
%%EXAMPLESDIR%%/seq/1wit_ref1.pep
%%EXAMPLESDIR%%/seq/1wit_ref2.pep
%%EXAMPLESDIR%%/seq/1wit_ref3.pep
%%EXAMPLESDIR%%/seq/1ycc_ref1.pep
%%EXAMPLESDIR%%/seq/1ycc_ref4.pep
%%EXAMPLESDIR%%/seq/1zin_ref1.pep
%%EXAMPLESDIR%%/seq/2ack_ref1.pep
%%EXAMPLESDIR%%/seq/2cba_ref1.pep
%%EXAMPLESDIR%%/seq/2cba_ref5.pep
%%EXAMPLESDIR%%/seq/2fxb_ref1.pep
%%EXAMPLESDIR%%/seq/2hsdA_ref1.pep
%%EXAMPLESDIR%%/seq/2hsdA_ref2.pep
%%EXAMPLESDIR%%/seq/2mhr_ref1.pep
%%EXAMPLESDIR%%/seq/2myr_ref1.pep
%%EXAMPLESDIR%%/seq/2myr_ref2.pep
%%EXAMPLESDIR%%/seq/2myr_ref3.pep
%%EXAMPLESDIR%%/seq/2pia_ref1.pep
%%EXAMPLESDIR%%/seq/2pia_ref2.pep
%%EXAMPLESDIR%%/seq/2pia_ref3.pep
%%EXAMPLESDIR%%/seq/2trx_ref1.pep
%%EXAMPLESDIR%%/seq/2trx_ref2.pep
%%EXAMPLESDIR%%/seq/3cyr_ref1.pep
%%EXAMPLESDIR%%/seq/3grs_ref1.pep
%%EXAMPLESDIR%%/seq/3grs_ref2.pep
%%EXAMPLESDIR%%/seq/3pmg_ref1.pep
%%EXAMPLESDIR%%/seq/451c_ref1.pep
%%EXAMPLESDIR%%/seq/4enl_ref1.pep
%%EXAMPLESDIR%%/seq/4enl_ref2.pep
%%EXAMPLESDIR%%/seq/4enl_ref3.pep
%%EXAMPLESDIR%%/seq/5ptp_ref1.pep
%%EXAMPLESDIR%%/seq/9rnt_ref1.pep
%%EXAMPLESDIR%%/seq/S51_ref5.pep
%%EXAMPLESDIR%%/seq/S52_ref5.pep
%%EXAMPLESDIR%%/seq/actin_ref1.pep
%%EXAMPLESDIR%%/seq/arp_ref1.pep
%%EXAMPLESDIR%%/seq/gal4_ref1.pep
%%EXAMPLESDIR%%/seq/glg_ref1.pep
%%EXAMPLESDIR%%/seq/kinase1_ref4.pep
%%EXAMPLESDIR%%/seq/kinase1_ref5.pep
%%EXAMPLESDIR%%/seq/kinase2_ref4.pep
%%EXAMPLESDIR%%/seq/kinase2_ref5.pep
%%EXAMPLESDIR%%/seq/kinase3_ref5.pep
%%EXAMPLESDIR%%/seq/kinase_ref1.pep
%%EXAMPLESDIR%%/seq/kinase_ref2.pep
%%EXAMPLESDIR%%/seq/kinase_ref3.pep
%%EXAMPLESDIR%%/test/reference_test.aln
%%EXAMPLESDIR%%/test/test.pep
%%PORTDOCS%%@@dirrm %%DOCSDIR%%
@@dirrm %%EXAMPLESDIR%%/seq
@@dirrm %%EXAMPLESDIR%%/test
@@dirrm %%EXAMPLESDIR%%
@


1.2
log
@Cosmetic fix: use %%DOCSDIR%% macro.
No functionally changes.

Submitted by:	Oleg Karachevtsev <ok@@etrust.ru>
A part of PR:	57992
@
text
@d1 9
a12 1
%%PORTDOCS%%%%DOCSDIR%%/t_coffee_doc.html
d14 144
a157 299
%%PORTDOCS%%%%DOCSDIR%%/t_coffee_doc.ps
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%%PORTDOCS%%share/examples/t_coffee/seq/1aboA_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1aboA_ref2.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1ac5_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1ad2_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1ad3_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1adj_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1ag8_ref4.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1aho_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1aisB_ref4.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1ajsA_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1ajsA_ref2.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1ajsA_ref3.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1amk_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1ar1_ref4.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1ar5A_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1au7A_ref4.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1aym3_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1bbt3_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1bgl_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1ckaA_ref4.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1cpt_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1cpt_ref2.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1csp_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1csp_ref4.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1csy_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1csy_ref2.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1dlc_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1dox_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1eft_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1eft_ref5.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1ezm_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1fieA_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1fjlA_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1fkj_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1fmb_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1gdoA_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1gowA_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1gpb_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1gtr_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1havA_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1havA_ref2.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1hfh_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1hpi_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1idy_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1idy_ref2.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1idy_ref3.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1ivy_ref5.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1krn_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1lcf_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1ldg_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1led_ref1.pep
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%%PORTDOCS%%share/examples/t_coffee/seq/1lvl_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1lvl_ref2.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1mfa_ref4.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1mrj_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1pamA_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1pamA_ref2.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1pamA_ref3.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1ped_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1ped_ref2.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1ped_ref3.pep
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%%PORTDOCS%%share/examples/t_coffee/seq/1pgtA_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1pii_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1pkm_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1plc_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1ppn_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1pysA_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1qpg_ref5.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1r69.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1r69_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1r69_ref2.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1r69_ref3.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1rthA_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1sbp_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1sbp_ref2.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1sesA_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1taq_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1tgxA_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1tgxA_ref2.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1thm1_ref5.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1thm2_ref5.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1thm_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1tis_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1ton_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1tvxA_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1tvxA_ref2.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1ubi_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1ubi_ref2.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1ubi_ref3.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1uky_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1uky_ref2.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1uky_ref3.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1vln_ref4.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1wit_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1wit_ref2.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1wit_ref3.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1ycc_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1ycc_ref4.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1zin_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/2ack_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/2cba_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/2cba_ref5.pep
%%PORTDOCS%%share/examples/t_coffee/seq/2fxb_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/2hsdA_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/2hsdA_ref2.pep
%%PORTDOCS%%share/examples/t_coffee/seq/2mhr_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/2myr_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/2myr_ref2.pep
%%PORTDOCS%%share/examples/t_coffee/seq/2myr_ref3.pep
%%PORTDOCS%%share/examples/t_coffee/seq/2pia_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/2pia_ref2.pep
%%PORTDOCS%%share/examples/t_coffee/seq/2pia_ref3.pep
%%PORTDOCS%%share/examples/t_coffee/seq/2trx_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/2trx_ref2.pep
%%PORTDOCS%%share/examples/t_coffee/seq/3cyr_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/3grs_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/3grs_ref2.pep
%%PORTDOCS%%share/examples/t_coffee/seq/3pmg_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/451c_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/4enl_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/4enl_ref2.pep
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@Add t_coffee 1.37, a multiple DNA or protein sequence alignment package.
@
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