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(-)t_coffee/Makefile (-2 / +1 lines)
Lines 7-13 Link Here
7 
#
 7 
#
8 

          8
          

        

        

          9
          
PORTNAME=	t_coffee

          9
          
PORTNAME=	t_coffee

        

          
            

              10
              
PORTVERSION=	4.96


              10
              
PORTVERSION=	5.68

            

        

          11
          
CATEGORIES=	biology

          11
          
CATEGORIES=	biology

        

        

          12
          
MASTER_SITES=	http://www.tcoffee.org/Packages/

          12
          
MASTER_SITES=	http://www.tcoffee.org/Packages/

        

        

          13
          
DISTNAME=	T-COFFEE_distribution_Version_${PORTVERSION}

          13
          
DISTNAME=	T-COFFEE_distribution_Version_${PORTVERSION}

        

  

    
      
            Lines 23-29
          
      
      
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          23
          
		CLUSTALW_4_TCOFFEE=${LOCALBASE}/bin/clustalw

          23
          
		CLUSTALW_4_TCOFFEE=${LOCALBASE}/bin/clustalw

        

        

          24
          

          24
          

        

        

          25
          
MAKEFILE=	makefile

          25
          
MAKEFILE=	makefile

        

            

              26
              
USE_GCC=	3.3

              
              
            

        

          27
          

          26
          

        

        

          28
          
do-install:

          27
          
do-install:

        

        

          29
          
	${INSTALL_PROGRAM} ${WRKSRC}/bin/t_coffee ${PREFIX}/bin

          28
          
	${INSTALL_PROGRAM} ${WRKSRC}/bin/t_coffee ${PREFIX}/bin

        



(-)t_coffee/distinfo
      (-3 / +3 lines)




  

    
      
            Lines 1-3
          
      
      
        Link Here
      
    
  

          
            

              1
              
MD5 (T-COFFEE_distribution_Version_4.96.tar.gz) = ce40b2654663b7c22c1c8427fb5e32db


              1
              
MD5 (T-COFFEE_distribution_Version_5.68.tar.gz) = 77316ccd4790c3c6e1b118681e15c10e

            

            

              2
              
SHA256 (T-COFFEE_distribution_Version_4.96.tar.gz) = 49181acd69a5723fd5b11f579b1efe685b5289bf187985b25b40c514b0af0213


              2
              
SHA256 (T-COFFEE_distribution_Version_5.68.tar.gz) = 137d188cef6f33a42cbd656482eb961d1588fef3091d2457ee0ef23fab16a6de

            

            

              3
              
SIZE (T-COFFEE_distribution_Version_4.96.tar.gz) = 2863327


              3
              
SIZE (T-COFFEE_distribution_Version_5.68.tar.gz) = 2875438

            



(-)t_coffee/pkg-plist
      (-5 / +6 lines)




  

    
      
            Lines 2-8
          
      
      
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          2
          
%%PORTDOCS%%%%DOCSDIR%%/README4T-COFFEE

          2
          
%%PORTDOCS%%%%DOCSDIR%%/README4T-COFFEE

        

        

          3
          
%%PORTDOCS%%%%DOCSDIR%%/aln_compare.doc.txt

          3
          
%%PORTDOCS%%%%DOCSDIR%%/aln_compare.doc.txt

        

        

          4
          
%%PORTDOCS%%%%DOCSDIR%%/seq_reformat.doc.txt

          4
          
%%PORTDOCS%%%%DOCSDIR%%/seq_reformat.doc.txt

        

            

              5
              
%%PORTDOCS%%%%DOCSDIR%%/t_coffee.pdf

              
              
            

        

          6
          
%%PORTDOCS%%%%DOCSDIR%%/t_coffee_technical.doc

          5
          
%%PORTDOCS%%%%DOCSDIR%%/t_coffee_technical.doc

        

        

          7
          
%%PORTDOCS%%%%DOCSDIR%%/t_coffee_technical.htm

          6
          
%%PORTDOCS%%%%DOCSDIR%%/t_coffee_technical.htm

        

        

          8
          
%%PORTDOCS%%%%DOCSDIR%%/t_coffee_technical.txt

          7
          
%%PORTDOCS%%%%DOCSDIR%%/t_coffee_technical.txt

        

  

    
      
            Lines 33-38
          
      
      
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          33
          
%%EXAMPLESDIR%%/g10.aln

          32
          
%%EXAMPLESDIR%%/g10.aln

        

        

          34
          
%%EXAMPLESDIR%%/g15.aln

          33
          
%%EXAMPLESDIR%%/g15.aln

        

        

          35
          
%%EXAMPLESDIR%%/g5.aln

          34
          
%%EXAMPLESDIR%%/g5.aln

        

            

              
              
              35
              
%%EXAMPLESDIR%%/kinases.aln

            

        

          36
          
%%EXAMPLESDIR%%/marna.tc_lib

          36
          
%%EXAMPLESDIR%%/marna.tc_lib

        

        

          37
          
%%EXAMPLESDIR%%/new_profile1_pdb1.aln

          37
          
%%EXAMPLESDIR%%/new_profile1_pdb1.aln

        

        

          38
          
%%EXAMPLESDIR%%/new_profile1_pdb1.html

          38
          
%%EXAMPLESDIR%%/new_profile1_pdb1.html

        

  

    
      
            Lines 52-57
          
      
      
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          52
          
%%EXAMPLESDIR%%/profile1_pdb1.aln

          52
          
%%EXAMPLESDIR%%/profile1_pdb1.aln

        

        

          53
          
%%EXAMPLESDIR%%/profile1_pdb1.fasta

          53
          
%%EXAMPLESDIR%%/profile1_pdb1.fasta

        

        

          54
          
%%EXAMPLESDIR%%/profile1_pdb1.html

          54
          
%%EXAMPLESDIR%%/profile1_pdb1.html

        

            

              
              
              55
              
%%EXAMPLESDIR%%/seq.fas

            

        

          55
          
%%EXAMPLESDIR%%/profile1_pdb1_1.aln

          56
          
%%EXAMPLESDIR%%/profile1_pdb1_1.aln

        

        

          56
          
%%EXAMPLESDIR%%/profile1_pdb1_1.html

          57
          
%%EXAMPLESDIR%%/profile1_pdb1_1.html

        

        

          57
          
%%EXAMPLESDIR%%/profile2_pdb2.aln

          58
          
%%EXAMPLESDIR%%/profile2_pdb2.aln

        

  

    
      
            Lines 86-95
          
      
      
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          86
          
%%EXAMPLESDIR%%/sample_param_file.param

          87
          
%%EXAMPLESDIR%%/sample_param_file.param

        

        

          87
          
%%EXAMPLESDIR%%/sample_profile1.aln

          88
          
%%EXAMPLESDIR%%/sample_profile1.aln

        

        

          88
          
%%EXAMPLESDIR%%/sample_profile2.aln

          89
          
%%EXAMPLESDIR%%/sample_profile2.aln

        

            

              
              
              90
              
%%EXAMPLESDIR%%/sample_rnaseq1.fasta

            

        

          89
          
%%EXAMPLESDIR%%/sample_seq1.aln

          91
          
%%EXAMPLESDIR%%/sample_seq1.aln

        

            

              
              
              92
              
%%EXAMPLESDIR%%/sv.aln

            

        

          90
          
%%EXAMPLESDIR%%/sample_seq1.fasta

          93
          
%%EXAMPLESDIR%%/sample_seq1.fasta

        

        

          91
          
%%EXAMPLESDIR%%/sample_seq2.fasta

          94
          
%%EXAMPLESDIR%%/sample_seq2.fasta

        

            

              92
              
%%EXAMPLESDIR%%/seq.fas

              
              
            

        

          93
          
%%EXAMPLESDIR%%/sample_seq3.fasta

          95
          
%%EXAMPLESDIR%%/sample_seq3.fasta

        

        

          94
          
%%EXAMPLESDIR%%/sample_seq4.fasta

          96
          
%%EXAMPLESDIR%%/sample_seq4.fasta

        

        

          95
          
%%EXAMPLESDIR%%/sample_seq5.fasta

          97
          
%%EXAMPLESDIR%%/sample_seq5.fasta

        

  

    
      
            Lines 133-145
          
      
      
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          133
          
%%EXAMPLESDIR%%/sproteases_small.g10.html

          135
          
%%EXAMPLESDIR%%/sproteases_small.g10.html

        

        

          134
          
%%EXAMPLESDIR%%/sproteases_small.g10.score_ascii

          136
          
%%EXAMPLESDIR%%/sproteases_small.g10.score_ascii

        

        

          135
          
%%EXAMPLESDIR%%/sproteases_small.g15.cw_aln

          137
          
%%EXAMPLESDIR%%/sproteases_small.g15.cw_aln

        

            

              
              
              138
              
%%EXAMPLESDIR%%/sproteases_small.ph

            

        

          136
          
%%EXAMPLESDIR%%/sproteases_small.g15.html

          139
          
%%EXAMPLESDIR%%/sproteases_small.g15.html

        

        

          137
          
%%EXAMPLESDIR%%/sproteases_small.html

          140
          
%%EXAMPLESDIR%%/sproteases_small.html

        

            

              138
              
%%EXAMPLESDIR%%/struc1.pdb

              
              
            

        

          139
          
%%EXAMPLESDIR%%/sproteases_small.mafft

          141
          
%%EXAMPLESDIR%%/sproteases_small.mafft

        

        

          140
          
%%EXAMPLESDIR%%/sproteases_small.mcoffee

          142
          
%%EXAMPLESDIR%%/sproteases_small.mcoffee

        

        

          141
          
%%EXAMPLESDIR%%/sproteases_small.muscle

          143
          
%%EXAMPLESDIR%%/sproteases_small.muscle

        

            

              142
              
%%EXAMPLESDIR%%/sproteases_small.ph

              
              
            

        

          143
          
%%EXAMPLESDIR%%/sproteases_small.probcons

          144
          
%%EXAMPLESDIR%%/sproteases_small.probcons

        

        

          144
          
%%EXAMPLESDIR%%/sproteases_small.score_ascii

          145
          
%%EXAMPLESDIR%%/sproteases_small.score_ascii

        

        

          145
          
%%EXAMPLESDIR%%/sproteases_small.score_html

          146
          
%%EXAMPLESDIR%%/sproteases_small.score_html

        

  

    
      
            Lines 148-153
          
      
      
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          148
          
%%EXAMPLESDIR%%/sproteases_small.tc_aln.html

          149
          
%%EXAMPLESDIR%%/sproteases_small.tc_aln.html

        

        

          149
          
%%EXAMPLESDIR%%/sproteases_small.template_file

          150
          
%%EXAMPLESDIR%%/sproteases_small.template_file

        

        

          150
          
%%EXAMPLESDIR%%/sproteases_small_dna.fasta

          151
          
%%EXAMPLESDIR%%/sproteases_small_dna.fasta

        

            

              
              
              152
              
%%EXAMPLESDIR%%/struc1.pdb

            

        

          151
          
%%EXAMPLESDIR%%/struc2.pdb

          153
          
%%EXAMPLESDIR%%/struc2.pdb

        

        

          152
          
%%EXAMPLESDIR%%/struc3.pdb

          154
          
%%EXAMPLESDIR%%/struc3.pdb

        

        

          153
          
%%EXAMPLESDIR%%/struc4.pdb

          155
          
%%EXAMPLESDIR%%/struc4.pdb

        

  

    
      
            Lines 155-161
          
      
      
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          155
          
%%EXAMPLESDIR%%/struc6.pdb

          157
          
%%EXAMPLESDIR%%/struc6.pdb

        

        

          156
          
%%EXAMPLESDIR%%/struc7.pdb

          158
          
%%EXAMPLESDIR%%/struc7.pdb

        

        

          157
          
%%EXAMPLESDIR%%/struc8.pdb

          159
          
%%EXAMPLESDIR%%/struc8.pdb

        

            

              158
              
%%EXAMPLESDIR%%/sv.aln

              
              
            

        

          159
          
%%EXAMPLESDIR%%/sv.dnd

          160
          
%%EXAMPLESDIR%%/sv.dnd

        

        

          160
          
%%EXAMPLESDIR%%/sv.fasta

          161
          
%%EXAMPLESDIR%%/sv.fasta

        

        

          161
          
%%EXAMPLESDIR%%/sv.html

          162
          
%%EXAMPLESDIR%%/sv.html

        






  

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