Attachment 76353 Details for Bug 110080 – file.diff

[patch] file.diff

file.diff (text/plain), 8.03 KB, created by Fernan Aguero on 2007-03-08 12:20:04 UTC

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Creator: Fernan Aguero

Created: 2007-03-08 12:20:04 UTC

Size: 8.03 KB

patch

obsolete

>diff --exclude CVS -ruN /usr/ports/biology/t_coffee/Makefile t_coffee/Makefile
>--- /usr/ports/biology/t_coffee/Makefile	Tue Feb  6 16:23:53 2007
>+++ t_coffee/Makefile	Wed Mar  7 15:19:12 2007
>@@ -7,7 +7,7 @@
> #
> 
> PORTNAME=	t_coffee
>-PORTVERSION=	3.27
>+PORTVERSION=	4.96
> CATEGORIES=	biology
> MASTER_SITES=	http://www.tcoffee.org/Packages/
> DISTNAME=	T-COFFEE_distribution_Version_${PORTVERSION}
>diff --exclude CVS -ruN /usr/ports/biology/t_coffee/distinfo t_coffee/distinfo
>--- /usr/ports/biology/t_coffee/distinfo	Fri Feb 10 06:45:28 2006
>+++ t_coffee/distinfo	Wed Mar  7 15:11:20 2007
>@@ -1,3 +1,3 @@
>-MD5 (T-COFFEE_distribution_Version_3.27.tar.gz) = 747d907f4b87e07d7b1e670a2b263e23
>-SHA256 (T-COFFEE_distribution_Version_3.27.tar.gz) = ffb7920919b24a6144492bec71580cda8a3ef4698acf762f76ebadfcae9aa01a
>-SIZE (T-COFFEE_distribution_Version_3.27.tar.gz) = 1295287
>+MD5 (T-COFFEE_distribution_Version_4.96.tar.gz) = ce40b2654663b7c22c1c8427fb5e32db
>+SHA256 (T-COFFEE_distribution_Version_4.96.tar.gz) = 49181acd69a5723fd5b11f579b1efe685b5289bf187985b25b40c514b0af0213
>+SIZE (T-COFFEE_distribution_Version_4.96.tar.gz) = 2863327
>diff --exclude CVS -ruN /usr/ports/biology/t_coffee/pkg-plist t_coffee/pkg-plist
>--- /usr/ports/biology/t_coffee/pkg-plist	Sat Jan 21 22:25:24 2006
>+++ t_coffee/pkg-plist	Wed Mar  7 15:15:18 2007
>@@ -3,16 +3,63 @@
> %%PORTDOCS%%%%DOCSDIR%%/aln_compare.doc.txt
> %%PORTDOCS%%%%DOCSDIR%%/seq_reformat.doc.txt
> %%PORTDOCS%%%%DOCSDIR%%/t_coffee.pdf
>-%%PORTDOCS%%%%DOCSDIR%%/t_coffee_doc.doc
>-%%PORTDOCS%%%%DOCSDIR%%/t_coffee_doc.pdf
>-%%PORTDOCS%%%%DOCSDIR%%/t_coffee_doc.txt
>+%%PORTDOCS%%%%DOCSDIR%%/t_coffee_technical.doc
>+%%PORTDOCS%%%%DOCSDIR%%/t_coffee_technical.htm
>+%%PORTDOCS%%%%DOCSDIR%%/t_coffee_technical.txt
>+%%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.3752
>+%%EXAMPLESDIR%%/error_report.T-COFFEE
>+%%EXAMPLESDIR%%/g0.aln
>+%%EXAMPLESDIR%%/x
>+%%EXAMPLESDIR%%/g10.aln
>+%%EXAMPLESDIR%%/g15.aln
>+%%EXAMPLESDIR%%/g5.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%%/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
>@@ -22,13 +69,19 @@
> %%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%%/struc1.pdb
> %%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
>@@ -36,22 +89,102 @@
> %%EXAMPLESDIR%%/sample_seq1.aln
> %%EXAMPLESDIR%%/sample_seq1.fasta
> %%EXAMPLESDIR%%/sample_seq2.fasta
>+%%EXAMPLESDIR%%/seq.fas
> %%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.g15.html
>+%%EXAMPLESDIR%%/sproteases_small.html
>+%%EXAMPLESDIR%%/struc1.pdb
>+%%EXAMPLESDIR%%/sproteases_small.mafft
>+%%EXAMPLESDIR%%/sproteases_small.mcoffee
>+%%EXAMPLESDIR%%/sproteases_small.muscle
>+%%EXAMPLESDIR%%/sproteases_small.ph
>+%%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%%/struc2.pdb
> %%EXAMPLESDIR%%/struc3.pdb
> %%EXAMPLESDIR%%/struc4.pdb
>+%%EXAMPLESDIR%%/struc5.pdb
>+%%EXAMPLESDIR%%/struc6.pdb
>+%%EXAMPLESDIR%%/struc7.pdb
>+%%EXAMPLESDIR%%/struc8.pdb
>+%%EXAMPLESDIR%%/sv.aln
>+%%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
>-@dirrmtry %%DOCSDIR%%
>+%%PORTDOCS%%@dirrmtry %%DOCSDIR%%
> @dirrmtry %%EXAMPLESDIR%%
> @dirrm %%DATADIR%%/html
> @dirrmtry %%DATADIR%%

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Attachments on bug 110080: 76353