[med-svn] [emboss] 03/05: Imported Upstream version 6.6.0+dfsg
Andreas Tille
tille at debian.org
Tue May 20 06:38:30 UTC 2014
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository emboss.
commit b49dd4d61e05bbc9cdffc751bbd51db1183dd78b
Author: Andreas Tille <tille at debian.org>
Date: Mon May 19 21:13:20 2014 +0200
Imported Upstream version 6.6.0+dfsg
---
doc/manuals/admin.aux | 96 -
doc/manuals/admin.dvi | Bin 144504 -> 0 bytes
doc/manuals/admin.log | 162 -
doc/manuals/admin.pdf | Bin 305395 -> 0 bytes
doc/manuals/admin.ps | 7901 -------------------------------------------------
doc/manuals/admin.tex | 2784 -----------------
doc/manuals/admin.toc | 79 -
7 files changed, 11022 deletions(-)
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-%%EndFont
-%%BeginFont: CMCSC10
-%!PS-AdobeFont-1.1: CMCSC10 1.0
-%%CreationDate: 1991 Aug 18 17:46:49
-% Copyright (C) 1997 American Mathematical Society. All Rights Reserved.
-11 dict begin
-/FontInfo 7 dict dup begin
-/version (1.0) readonly def
-/Notice (Copyright (C) 1997 American Mathematical Society. All Rights Reserved) readonly def
-/FullName (CMCSC10) readonly def
-/FamilyName (Computer Modern) readonly def
-/Weight (Medium) readonly def
-/ItalicAngle 0 def
-/isFixedPitch false def
-end readonly def
-/FontName /CMCSC10 def
-/PaintType 0 def
-/FontType 1 def
-/FontMatrix [0.001 0 0 0.001 0 0] readonly def
-/Encoding 256 array
-0 1 255 {1 index exch /.notdef put} for
-dup 46 /period put
-dup 52 /four put
-dup 65 /A put
-dup 67 /C put
-dup 69 /E put
-dup 71 /G put
-dup 72 /H put
-dup 73 /I put
-dup 76 /L put
-dup 77 /M put
-dup 78 /N put
-dup 79 /O put
-dup 80 /P put
-dup 82 /R put
-dup 83 /S put
-dup 84 /T put
-dup 85 /U put
-dup 89 /Y put
-dup 97 /a put
-dup 98 /b put
-dup 99 /c put
-dup 100 /d put
-dup 101 /e put
-dup 102 /f put
-dup 103 /g put
-dup 104 /h put
-dup 105 /i put
-dup 108 /l put
-dup 109 /m put
-dup 110 /n put
-dup 111 /o put
-dup 112 /p put
-dup 114 /r put
-dup 115 /s put
-dup 116 /t put
-dup 117 /u put
-dup 119 /w put
-dup 120 /x put
-dup 122 /z put
-readonly def
-/FontBBox{14 -250 1077 750}readonly def
-currentdict end
-currentfile eexec
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-% Copyright (C) 1997 American Mathematical Society. All Rights Reserved.
-11 dict begin
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-/FontBBox{-71 -250 1099 780}readonly def
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-%%EndFont
-%%BeginFont: CMR8
-%!PS-AdobeFont-1.1: CMR8 1.0
-%%CreationDate: 1991 Aug 20 16:39:40
-% Copyright (C) 1997 American Mathematical Society. All Rights Reserved.
-11 dict begin
-/FontInfo 7 dict dup begin
-/version (1.0) readonly def
-/Notice (Copyright (C) 1997 American Mathematical Society. All Rights Reserved) readonly def
-/FullName (CMR8) readonly def
-/FamilyName (Computer Modern) readonly def
-/Weight (Medium) readonly def
-/ItalicAngle 0 def
-/isFixedPitch false def
-end readonly def
-/FontName /CMR8 def
-/PaintType 0 def
-/FontType 1 def
-/FontMatrix [0.001 0 0 0.001 0 0] readonly def
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-dup 39 /quoteright put
-dup 40 /parenleft put
-dup 41 /parenright put
-dup 44 /comma put
-dup 46 /period put
-dup 47 /slash put
-dup 48 /zero put
-dup 49 /one put
-dup 50 /two put
-dup 54 /six put
-dup 58 /colon put
-dup 64 /at put
-dup 65 /A put
-dup 66 /B put
-dup 67 /C put
-dup 68 /D put
-dup 69 /E put
-dup 70 /F put
-dup 71 /G put
-dup 73 /I put
-dup 74 /J put
-dup 75 /K put
-dup 76 /L put
-dup 77 /M put
-dup 78 /N put
-dup 79 /O put
-dup 80 /P put
-dup 81 /Q put
-dup 82 /R put
-dup 83 /S put
-dup 84 /T put
-dup 85 /U put
-dup 86 /V put
-dup 89 /Y put
-dup 97 /a put
-dup 98 /b put
-dup 99 /c put
-dup 100 /d put
-dup 101 /e put
-dup 102 /f put
-dup 103 /g put
-dup 104 /h put
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-dup 115 /s put
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-dup 117 /u put
-dup 118 /v put
-dup 119 /w put
-dup 120 /x put
-dup 121 /y put
-dup 122 /z put
-readonly def
-/FontBBox{-36 -250 1070 750}readonly def
-currentdict end
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-%%EndFont
-%%BeginFont: CMTT10
-%!PS-AdobeFont-1.1: CMTT10 1.00B
-%%CreationDate: 1992 Apr 26 10:42:42
-% Copyright (C) 1997 American Mathematical Society. All Rights Reserved.
-11 dict begin
-/FontInfo 7 dict dup begin
-/version (1.00B) readonly def
-/Notice (Copyright (C) 1997 American Mathematical Society. All Rights Reserved) readonly def
-/FullName (CMTT10) readonly def
-/FamilyName (Computer Modern) readonly def
-/Weight (Medium) readonly def
-/ItalicAngle 0 def
-/isFixedPitch true def
-end readonly def
-/FontName /CMTT10 def
-/PaintType 0 def
-/FontType 1 def
-/FontMatrix [0.001 0 0 0.001 0 0] readonly def
-/Encoding 256 array
-0 1 255 {1 index exch /.notdef put} for
-dup 33 /exclam put
-dup 34 /quotedbl put
-dup 35 /numbersign put
-dup 36 /dollar put
-dup 37 /percent put
-dup 38 /ampersand put
-dup 39 /quoteright put
-dup 40 /parenleft put
-dup 41 /parenright put
-dup 42 /asterisk put
-dup 43 /plus put
-dup 44 /comma put
-dup 45 /hyphen put
-dup 46 /period put
-dup 47 /slash put
-dup 48 /zero put
-dup 49 /one put
-dup 50 /two put
-dup 51 /three put
-dup 52 /four put
-dup 53 /five put
-dup 54 /six put
-dup 55 /seven put
-dup 56 /eight put
-dup 57 /nine put
-dup 58 /colon put
-dup 59 /semicolon put
-dup 61 /equal put
-dup 62 /greater put
-dup 63 /question put
-dup 64 /at put
-dup 65 /A put
-dup 66 /B put
-dup 67 /C put
-dup 68 /D put
-dup 69 /E put
-dup 70 /F put
-dup 71 /G put
-dup 72 /H put
-dup 73 /I put
-dup 74 /J put
-dup 75 /K put
-dup 76 /L put
-dup 77 /M put
-dup 78 /N put
-dup 79 /O put
-dup 80 /P put
-dup 81 /Q put
-dup 82 /R put
-dup 83 /S put
-dup 84 /T put
-dup 85 /U put
-dup 86 /V put
-dup 87 /W put
-dup 88 /X put
-dup 89 /Y put
-dup 90 /Z put
-dup 91 /bracketleft put
-dup 92 /backslash put
-dup 93 /bracketright put
-dup 94 /asciicircum put
-dup 95 /underscore put
-dup 96 /quoteleft put
-dup 97 /a put
-dup 98 /b put
-dup 99 /c put
-dup 100 /d put
-dup 101 /e put
-dup 102 /f put
-dup 103 /g put
-dup 104 /h put
-dup 105 /i put
-dup 106 /j put
-dup 107 /k put
-dup 108 /l put
-dup 109 /m put
-dup 110 /n put
-dup 111 /o put
-dup 112 /p put
-dup 113 /q put
-dup 114 /r put
-dup 115 /s put
-dup 116 /t put
-dup 117 /u put
-dup 118 /v put
-dup 119 /w put
-dup 120 /x put
-dup 121 /y put
-dup 122 /z put
-dup 123 /braceleft put
-dup 124 /bar put
-dup 125 /braceright put
-readonly def
-/FontBBox{-4 -235 731 800}readonly def
-currentdict end
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-%%EndFont
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-%%CreationDate: 1991 Aug 20 17:34:37
-% Copyright (C) 1997 American Mathematical Society. All Rights Reserved.
-11 dict begin
-/FontInfo 7 dict dup begin
-/version (1.0) readonly def
-/Notice (Copyright (C) 1997 American Mathematical Society. All Rights Reserved) readonly def
-/FullName (CMSSI10) readonly def
-/FamilyName (Computer Modern) readonly def
-/Weight (Medium) readonly def
-/ItalicAngle -12 def
-/isFixedPitch false def
-end readonly def
-/FontName /CMSSI10 def
-/PaintType 0 def
-/FontType 1 def
-/FontMatrix [0.001 0 0 0.001 0 0] readonly def
-/Encoding 256 array
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-dup 36 /dollar put
-dup 42 /asterisk put
-dup 45 /hyphen put
-dup 46 /period put
-dup 47 /slash put
-dup 48 /zero put
-dup 49 /one put
-dup 50 /two put
-dup 51 /three put
-dup 52 /four put
-dup 53 /five put
-dup 55 /seven put
-dup 58 /colon put
-dup 65 /A put
-dup 66 /B put
-dup 67 /C put
-dup 68 /D put
-dup 69 /E put
-dup 70 /F put
-dup 72 /H put
-dup 73 /I put
-dup 74 /J put
-dup 76 /L put
-dup 77 /M put
-dup 78 /N put
-dup 79 /O put
-dup 80 /P put
-dup 82 /R put
-dup 83 /S put
-dup 84 /T put
-dup 85 /U put
-dup 88 /X put
-dup 89 /Y put
-dup 97 /a put
-dup 98 /b put
-dup 99 /c put
-dup 100 /d put
-dup 101 /e put
-dup 102 /f put
-dup 103 /g put
-dup 104 /h put
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-dup 108 /l put
-dup 109 /m put
-dup 110 /n put
-dup 111 /o put
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-dup 113 /q put
-dup 114 /r put
-dup 115 /s put
-dup 116 /t put
-dup 117 /u put
-dup 118 /v put
-dup 119 /w put
-dup 121 /y put
-dup 122 /z put
-dup 126 /tilde put
-readonly def
-/FontBBox{-97 -250 1077 759}readonly def
-currentdict end
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-%%EndFont
-%%BeginFont: CMBX12
-%!PS-AdobeFont-1.1: CMBX12 1.0
-%%CreationDate: 1991 Aug 20 16:34:54
-% Copyright (C) 1997 American Mathematical Society. All Rights Reserved.
-11 dict begin
-/FontInfo 7 dict dup begin
-/version (1.0) readonly def
-/Notice (Copyright (C) 1997 American Mathematical Society. All Rights Reserved) readonly def
-/FullName (CMBX12) readonly def
-/FamilyName (Computer Modern) readonly def
-/Weight (Bold) readonly def
-/ItalicAngle 0 def
-/isFixedPitch false def
-end readonly def
-/FontName /CMBX12 def
-/PaintType 0 def
-/FontType 1 def
-/FontMatrix [0.001 0 0 0.001 0 0] readonly def
-/Encoding 256 array
-0 1 255 {1 index exch /.notdef put} for
-dup 11 /ff put
-dup 12 /fi put
-dup 13 /fl put
-dup 46 /period put
-dup 48 /zero put
-dup 49 /one put
-dup 50 /two put
-dup 51 /three put
-dup 52 /four put
-dup 53 /five put
-dup 54 /six put
-dup 55 /seven put
-dup 56 /eight put
-dup 57 /nine put
-dup 58 /colon put
-dup 63 /question put
-dup 65 /A put
-dup 66 /B put
-dup 67 /C put
-dup 68 /D put
-dup 69 /E put
-dup 70 /F put
-dup 71 /G put
-dup 73 /I put
-dup 76 /L put
-dup 77 /M put
-dup 78 /N put
-dup 79 /O put
-dup 80 /P put
-dup 82 /R put
-dup 83 /S put
-dup 84 /T put
-dup 85 /U put
-dup 87 /W put
-dup 88 /X put
-dup 89 /Y put
-dup 97 /a put
-dup 98 /b put
-dup 99 /c put
-dup 100 /d put
-dup 101 /e put
-dup 102 /f put
-dup 103 /g put
-dup 104 /h put
-dup 105 /i put
-dup 107 /k put
-dup 108 /l put
-dup 109 /m put
-dup 110 /n put
-dup 111 /o put
-dup 112 /p put
-dup 113 /q put
-dup 114 /r put
-dup 115 /s put
-dup 116 /t put
-dup 117 /u put
-dup 118 /v put
-dup 119 /w put
-dup 120 /x put
-dup 121 /y put
-dup 122 /z put
-readonly def
-/FontBBox{-53 -251 1139 750}readonly def
-currentdict end
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-%%EndFont
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-%%CreationDate: 1992 Feb 19 19:54:06
-% Copyright (C) 1997 American Mathematical Society. All Rights Reserved.
-11 dict begin
-/FontInfo 7 dict dup begin
-/version (1.00B) readonly def
-/Notice (Copyright (C) 1997 American Mathematical Society. All Rights Reserved) readonly def
-/FullName (CMBX10) readonly def
-/FamilyName (Computer Modern) readonly def
-/Weight (Bold) readonly def
-/ItalicAngle 0 def
-/isFixedPitch false def
-end readonly def
-/FontName /CMBX10 def
-/PaintType 0 def
-/FontType 1 def
-/FontMatrix [0.001 0 0 0.001 0 0] readonly def
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-dup 45 /hyphen put
-dup 46 /period put
-dup 48 /zero put
-dup 49 /one put
-dup 50 /two put
-dup 51 /three put
-dup 52 /four put
-dup 53 /five put
-dup 54 /six put
-dup 55 /seven put
-dup 58 /colon put
-dup 65 /A put
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-dup 67 /C put
-dup 68 /D put
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-dup 70 /F put
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-dup 78 /N put
-dup 79 /O put
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-dup 81 /Q put
-dup 82 /R put
-dup 83 /S put
-dup 84 /T put
-dup 85 /U put
-dup 86 /V put
-dup 87 /W put
-dup 88 /X put
-dup 97 /a put
-dup 98 /b put
-dup 99 /c put
-dup 100 /d put
-dup 101 /e put
-dup 102 /f put
-dup 103 /g put
-dup 104 /h put
-dup 105 /i put
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-dup 108 /l put
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-dup 110 /n put
-dup 111 /o put
-dup 112 /p put
-dup 114 /r put
-dup 115 /s put
-dup 116 /t put
-dup 117 /u put
-dup 119 /w put
-dup 121 /y put
-readonly def
-/FontBBox{-301 -250 1164 946}readonly def
-currentdict end
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-%%CreationDate: 1991 Aug 20 16:46:05
-% Copyright (C) 1997 American Mathematical Society. All Rights Reserved.
-11 dict begin
-/FontInfo 7 dict dup begin
-/version (1.0) readonly def
-/Notice (Copyright (C) 1997 American Mathematical Society. All Rights Reserved) readonly def
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-/FamilyName (Computer Modern) readonly def
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-/FontName /CMTT8 def
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-/FontMatrix [0.001 0 0 0.001 0 0] readonly def
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-dup 117 /u put
-dup 118 /v put
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-dup 122 /z put
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-readonly def
-/FontBBox{-5 -232 545 699}readonly def
-currentdict end
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-11 dict begin
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-%%EndFont
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-%%CreationDate: 1992 Feb 19 19:54:52
-% Copyright (C) 1997 American Mathematical Society. All Rights Reserved.
-11 dict begin
-/FontInfo 7 dict dup begin
-/version (1.00B) readonly def
-/Notice (Copyright (C) 1997 American Mathematical Society. All Rights Reserved) readonly def
-/FullName (CMR10) readonly def
-/FamilyName (Computer Modern) readonly def
-/Weight (Medium) readonly def
-/ItalicAngle 0 def
-/isFixedPitch false def
-end readonly def
-/FontName /CMR10 def
-/PaintType 0 def
-/FontType 1 def
-/FontMatrix [0.001 0 0 0.001 0 0] readonly def
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-dup 12 /fi put
-dup 13 /fl put
-dup 14 /ffi put
-dup 34 /quotedblright put
-dup 37 /percent put
-dup 39 /quoteright put
-dup 40 /parenleft put
-dup 41 /parenright put
-dup 44 /comma put
-dup 45 /hyphen put
-dup 46 /period put
-dup 47 /slash put
-dup 48 /zero put
-dup 49 /one put
-dup 50 /two put
-dup 51 /three put
-dup 52 /four put
-dup 53 /five put
-dup 54 /six put
-dup 55 /seven put
-dup 56 /eight put
-dup 57 /nine put
-dup 58 /colon put
-dup 59 /semicolon put
-dup 61 /equal put
-dup 63 /question put
-dup 64 /at put
-dup 65 /A put
-dup 66 /B put
-dup 67 /C put
-dup 68 /D put
-dup 69 /E put
-dup 70 /F put
-dup 71 /G put
-dup 72 /H put
-dup 73 /I put
-dup 74 /J put
-dup 75 /K put
-dup 76 /L put
-dup 77 /M put
-dup 78 /N put
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-dup 80 /P put
-dup 81 /Q put
-dup 82 /R put
-dup 83 /S put
-dup 84 /T put
-dup 85 /U put
-dup 86 /V put
-dup 87 /W put
-dup 88 /X put
-dup 89 /Y put
-dup 90 /Z put
-dup 95 /dotaccent put
-dup 96 /quoteleft put
-dup 97 /a put
-dup 98 /b put
-dup 99 /c put
-dup 100 /d put
-dup 101 /e put
-dup 102 /f put
-dup 103 /g put
-dup 104 /h put
-dup 105 /i put
-dup 106 /j put
-dup 107 /k put
-dup 108 /l put
-dup 109 /m put
-dup 110 /n put
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-dup 112 /p put
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-dup 114 /r put
-dup 115 /s put
-dup 116 /t put
-dup 117 /u put
-dup 118 /v put
-dup 119 /w put
-dup 120 /x put
-dup 121 /y put
-dup 122 /z put
-dup 124 /emdash put
-readonly def
-/FontBBox{-251 -250 1009 969}readonly def
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-%%EndFont
-%%BeginFont: CMR12
-%!PS-AdobeFont-1.1: CMR12 1.0
-%%CreationDate: 1991 Aug 20 16:38:05
-% Copyright (C) 1997 American Mathematical Society. All Rights Reserved.
-11 dict begin
-/FontInfo 7 dict dup begin
-/version (1.0) readonly def
-/Notice (Copyright (C) 1997 American Mathematical Society. All Rights Reserved) readonly def
-/FullName (CMR12) readonly def
-/FamilyName (Computer Modern) readonly def
-/Weight (Medium) readonly def
-/ItalicAngle 0 def
-/isFixedPitch false def
-end readonly def
-/FontName /CMR12 def
-/PaintType 0 def
-/FontType 1 def
-/FontMatrix [0.001 0 0 0.001 0 0] readonly def
-/Encoding 256 array
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-dup 40 /parenleft put
-dup 41 /parenright put
-dup 44 /comma put
-dup 46 /period put
-dup 48 /zero put
-dup 50 /two put
-dup 53 /five put
-dup 65 /A put
-dup 66 /B put
-dup 68 /D put
-dup 69 /E put
-dup 71 /G put
-dup 72 /H put
-dup 73 /I put
-dup 75 /K put
-dup 76 /L put
-dup 77 /M put
-dup 78 /N put
-dup 79 /O put
-dup 80 /P put
-dup 82 /R put
-dup 84 /T put
-dup 85 /U put
-dup 97 /a put
-dup 98 /b put
-dup 99 /c put
-dup 100 /d put
-dup 101 /e put
-dup 103 /g put
-dup 104 /h put
-dup 105 /i put
-dup 108 /l put
-dup 110 /n put
-dup 111 /o put
-dup 114 /r put
-dup 115 /s put
-dup 116 /t put
-dup 117 /u put
-dup 118 /v put
-dup 119 /w put
-dup 121 /y put
-readonly def
-/FontBBox{-34 -251 988 750}readonly def
-currentdict end
-currentfile eexec
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-cleartomark
-%%EndFont
-%%BeginFont: CMR17
-%!PS-AdobeFont-1.1: CMR17 1.0
-%%CreationDate: 1991 Aug 20 16:38:24
-% Copyright (C) 1997 American Mathematical Society. All Rights Reserved.
-11 dict begin
-/FontInfo 7 dict dup begin
-/version (1.0) readonly def
-/Notice (Copyright (C) 1997 American Mathematical Society. All Rights Reserved) readonly def
-/FullName (CMR17) readonly def
-/FamilyName (Computer Modern) readonly def
-/Weight (Medium) readonly def
-/ItalicAngle 0 def
-/isFixedPitch false def
-end readonly def
-/FontName /CMR17 def
-/PaintType 0 def
-/FontType 1 def
-/FontMatrix [0.001 0 0 0.001 0 0] readonly def
-/Encoding 256 array
-0 1 255 {1 index exch /.notdef put} for
-dup 39 /quoteright put
-dup 65 /A put
-dup 71 /G put
-dup 84 /T put
-dup 97 /a put
-dup 100 /d put
-dup 101 /e put
-dup 104 /h put
-dup 105 /i put
-dup 109 /m put
-dup 110 /n put
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diff --git a/doc/manuals/admin.tex b/doc/manuals/admin.tex
deleted file mode 100644
index 47f4d4a..0000000
--- a/doc/manuals/admin.tex
+++ /dev/null
@@ -1,2784 +0,0 @@
-\documentclass{report}
-\usepackage{verbatim}
-\usepackage{emboss}
-
-\begin{document}
-\title{The \EMBOSS\ Administrator's Guide}
-\author{David Martin, EMBnet Norway \\
-Peter Rice, LION Bioscience \\
-Alan Bleasby, HGMP (EMBnet UK)}
-\date{This guide relates to \EMBOSS\ 2.5.0}
-
-\maketitle
-
-Copyright (c) 2000, 2002 David Martin, Peter Rice, Alan Bleasby.
-
-Permission is granted to copy, distribute and/or modify this document
-under the terms of the GNU Free Documentation
-License\URL{http://www.gnu.org/copyleft/fdl.html}, Version 1.1 or any
-later version published by the Free Software Foundation; with no
-Invariant Sections, with no Front-Cover Texts, and with no Back-Cover
-Texts. A copy of the license is included in the chapter entitled "GNU
-Free Documentation License".
-
-\tableofcontents
-
-\chapter{Introduction}
-\section{About this document}
-This guide has been written to assist system administrators and
-developers with the installation and configuration of \EMBOSS. If you
-are reading this to find out how to do bioinformatics then you are
-wasting your time. You are referred instead to the Resources chapter
-below where there is a list of more relevant literature and web sites.
-Experienced users may find this document useful for configuring their
-own databases and customising their \EMBOSS\ experience.
-
-
-\subsection{Credits}
-The original author of this guide was David
-Martin\URL{damartin\@@hgmp.mrc.ac.uk} at the Norwegian EMBnet
-node.\URL{http://www.no.embnet.org} It is however the result of a team
-effort. Thanks are due in particular to Johann Visagie for the FreeBSD
-information. Other contributors are acknowledged in the text.
-
-\subsection{Reproduction}
-The obligatory bit of legalese. The first version of this guide was
-not in the public domain but has been released under the GNU Free
-Documentation License by the original author.
-
-Although 'Free' in this license is usually explained as 'free as in
-freedom, not as in beer' the authors are likely to appreciate offers
-of free drinks should you ever meet them.
-\section{What is \EMBOSS?}
-
-\EMBOSS\ is a freely available suite of bioinformatics applications
-and libraries. It can be downloaded via the internet, copied,
-customised, and passed on under the terms of the various General
-Public Licenses. \EMBOSS\ has been developed in response to the need
-for a powerful, adaptable suite of software that can interface readily
-with many different situations and meet the need of professional
-bioinformaticists, particularly those needing high throughput and/or
-scriptable capabilities.
-
-\EMBOSS\ has primarily been developed by those responsible for the
-public extensions to the GCG package. \EMBOSS\ supercedes much of EGCG
-and includes far better database interaction. \EMBOSS\ also has the
-benefit of freely accessible source code so novel applications can be
-developed rapidly and at minimal cost.
-
-\EMBOSS\ is currently only available for Unix/Linux systems but it has
-been known to compile and run on Windows NT. This document will only
-consider the UNIX version and will assume the reader has some
-familiarity with UNIX system administration.
-
-\subsection{Where to get it?}
-
-\EMBOSS\ is available for download from the primary site at Open-Bio
-by anonymous ftp.\URL{ftp://emboss.open-bio.org/pub/EMBOSS/} This
-directory contains the \EMBOSS\ package and several associated
-packages (collectively known as EMBASSY) that are distributed with
-\EMBOSS. Download these to a suitable location. Documentation is
-available on the WWW at the \EMBOSS\ web
-site.\URL{http://emboss.sf.net/}
-
-FreeBSD distributions from 4.2 onwards now include \EMBOSS\ as an
-optional package maintained by Johann
-Visagie.\URL{johann\@@egenetics.com} Please see section
-\ref{sec:FreeBSD} for more information on installation on FreeBSD.
-
-\chapter{Installation}
-\section{Retrieving \EMBOSS\ by anonymous ftp}
-\subsection{Interactive FTP}
-
-Change directory to the location in which you wish to download the
-\EMBOSS\ source code. In this example we will download the source to
-\filename{/packages/EMBOSS}. Then start your ftp client and point it
-to emboss.open-bio.org.
-
-\begin{verbatim}
-% ftp emboss.open-bio.org
-Connected to emboss.open-bio.org.
-220 (vsFTPd 2.0.1)
-530 Please login with USER and PASS.
-530 Please login with USER and PASS.
-KERBEROS_V4 rejected as an authentication type
-Name (emboss.open-bio.org:someuser):
-\end{verbatim}
-
-We are using anonymous FTP so type the username \ilcomm{anonymous}.
-
-\begin{verbatim}
-Name (emboss.open-bio.org:someuser): anonymous
-331 Guest login ok, send your complete e-mail address as password.
-Password:
-\end{verbatim}
-
-Enter your email address here as the password for user \filename{anonymous}.
-
-\begin{verbatim}
-Password:
-230 Login successful.
-Remote system type is UNIX.
-Using binary mode to transfer files.
-ftp>
-\end{verbatim}
-
-Move to the \EMBOSS\ directory and list the files. The output has been
-truncated a little to save space.
-
-\begin{verbatim}
-ftp> cd /pub/EMBOSS
-ftp> ls
-200 PORT command successful.
-150 Opening BINARY mode data connection for /bin/ls.
-total 22334
-... 1024 May 26 20:17 .gnu
-... 9079913 May 14 21:37 EMBOSS-2.5.0.tar.gz
-... 19 May 14 21:37 EMBOSS-latest.tar.gz -> EMBOSS-2.5.0.tar.gz
-... 196872 May 12 18:49 EMNU-1.0.5.tar.gz
-... 231485 May 15 13:55 ESIM4-1.0.0.tar.gz
-... 405620 May 12 18:49 HMMER-2.1.1.tar.gz
-... 1024 Jul 25 08:54 Jemboss
-... 264189 May 12 18:49 MEME-2.3.1.tar.gz
-... 251061 Jul 9 19:01 MSE-0.0.4.tar.gz
-... 694450 May 12 18:49 PHYLIP-3.573c.tar.gz
-... 200490 May 12 18:49 TOPO-0.1.tar.gz
-... 1536 Jul 9 19:01 old
-... 512 Jun 27 14:40 patchfiles
-... 512 Feb 22 15:19 tutorials
-226 Transfer complete.
-ftp>
-\end{verbatim}
-
-Now download the source files
-
-\begin{verbatim}
-ftp> get EMBOSS-latest.tar.gz
-200 PORT command successful.
-150 Opening BINARY mode data connection for EMBOSS-latest.tar.gz
-(9079913 bytes).
-...
-ftp>
-\end{verbatim}
-
-And repeat for each file. Or use \ilcomm{mget *gz} to download all the
-files at once. Exit your ftp session with the command \ilcomm{bye}.
-
-\subsection{FTP using \progname{wget}}
-The program \progname{wget} can be used to download a remote directory
-noninteractively. More details on \progname{wget} can be obtained from
-the Free Software Foundation.\URL{http://www.gnu.org} Assuming you
-have \progname{wget} installed, use the following command which
-generates a lot of output on the screen:
-
-\begin{verbatim}
-% wget -m 'ftp://emboss.open-bio.org/pub/EMBOSS'
---15:04:41-- ftp://emboss.open-bio.org:21/pub/EMBOSS
- => `emboss.open-bio.org/pub/.listing'
-Connecting to emboss.open-bio.org:21... connected!
-Logging in as anonymous ... Logged in!
-==> TYPE I ... done. ==> CWD pub ... done.
-==> PORT ... done. ==> LIST ... done.
-
-...
-many pages truncated
-...
-
-FINISHED --15:04:55--
-Downloaded: 2,657,366 bytes in 4 files
-\end{verbatim}
-
-A new directory \filename{emboss.open-bio.org} has been created and
-EMBOSS can be found at \filename{emboss.open-bio.org/pub/EMBOSS}. You
-may wish to create a symbolic link to this from your
-\filename{/packages} directory for convenience.
-
-
-\section{Unpacking}
-
-You will have downloaded the \EMBOSS\ and EMBASSY packages to a
-suitable directory. For this example we will assume you have
-downloaded them to \filename{/packages} so you should now have the
-following files (or similar) and maybe more packages in EMBASSY.
-
-\begin{verbatim}
-% ls
-EMBOSS-latest.tar.gz
-EMNU-1.0.5.tar.gz
-ESIM4-1.0.0.tar.gz
-HMMER-2.1.1.tar.gz
-MEME-2.3.1.tar.gz
-MSE-0.0.4.tar.gz
-PHYLIP-3.573c.tar.gz
-TOPO-0.1.tar.gz
-\end{verbatim}
-
-First unpack the \EMBOSS\ distribution
-
-\begin{verbatim}
-% gunzip EMBOSS-latest.tar.gz
-% tar xf EMBOSS-latest.tar
-\end{verbatim}
-
-This will create a new directory, \filename{EMBOSS-2.5.0} or
-similar. You may wish to use \ilcomm{tar xpf} for unpacking \EMBOSS.
-
-Enter the \EMBOSS\ directory
-
-\begin{verbatim}
-% cd EMBOSS-2.5.0
-\end{verbatim}
-
-create a directory for the EMBASSY packages
-
-\begin{verbatim}
-% mkdir embassy
-\end{verbatim}
-
-Now move the EMBASSY packages to the EMBASSY directory
-
-\begin{verbatim}
-% mv ../MSE-0.0.4.tar.gz PHYLIP-3.573c.tar.gz \
- TOPO-0.1.tar.gz embassy
-\end{verbatim}
-
-Go into the EMBASSY directory and unpack those packages.
-
-\begin{verbatim}
-% cd embassy
-
-% gunzip MSE-0.0.4.tar.gz
-% tar xf MSE-0.0.4.tar
-\end{verbatim}
-
-and so on for each EMBASSY package.
-
-Go back up one directory to the main \EMBOSS\ package directory and
-prepare to start compilation.
-
-\section{Graphics Requirements}
-
-Depending on your system you may need to explicitly configure the
-graphics. EMBOSS includes the plplot graphics library and will link to
-X11 and the recent (non-GIF) releases of the gd graphics library which
-also require libz and libpng (and possibly libjpeg). Please see the
-section 'Configuring \EMBOSS\ graphics' below.
-
-To get PLPLOT to produce PNG images you will need to have the
-\filename{z}\URL{http://www.info-zip.org/pub/infozip/zlib/},
-\filename{png}\URL{http://libpng.sourceforge.net/} and
-\filename{gd}\URL{http://www.boutell.com/gd/} libraries
-installed. \filename{gd} version $>=$ 1.8.4 is recommended. A recent
-release must be used as older versions support GIF which is NOT
-supported in later versions because of software patent problems. If
-for some reason you do not have the required libraries and your system
-support group will not update them for the system then install all
-three latest versions (\filename{z},\filename{gd},\filename{png}) to a
-new directory and then add this new directory to your configure line
-for \EMBOSS\ --- \verb+./configure --with-pngdriver=my_dir+ where the
-\filename{z}, \filename{png} and \filename{gd} libraries were each
-installed using \verb+./configure --prefix=my_dir+
-
-??? It may also be helpful to ensure that the \ilcomm{LD\_LIBRARY\_PATH}
-environment variable is set appropriately to include the libraries in
-the path. ???
-
- GD) http://www.boutell.com/gd/
- Z) http://www.mirror.ac.uk/sites/ftp.cdrom.com/pub/infozip/zlib/
- PNG) http://www.mirror.ac.uk/sites/ftp.libpng.org/pub/png/libpng.html
-
- These also list the various mirror sites for non UK people.
-
- Alternatively, using ftp :-
-
- GD) (boutell.com no longer allows FTP, no known mirror sites, use HTTP)
- Z) ftp://ftp.info-zip.org/pub/infozip/zlib/zlib-1.1.3.tar.gz
- PNG) ftp://swrinde.nde.swri.edu/pub/png/src/libpng.1.2.1.tar.gz
- You can unpack the tar.gz files in any directory, and install them in
- a common area.
-
- By default everything (including EMBOSS) installs
- in /usr/local but in the examples below we use /home/joe/local
-
- Note: gd does not use a ./configure script, and will fail at the
- "make install" stage if the installation directory does not have a
- /bin subdirectory. You can create this directory
- (e.g. /home/joe/local/bin) if it does not already exist.
-
-\subsection{zlib}
-
-Zlib is avilable from these sites:
-
-\filename{http://www.mirror.ac.uk/sites/ftp.cdrom.com/pub/infozip/zlib/}
-\URL{http://www.mirror.ac.uk/sites/ftp.cdrom.com/pub/infozip/zlib/}
-\filename{http://www.info-zip.org/pub/infozip/zlib/}
-\URL{http://www.info-zip.org/pub/infozip/zlib/}
-\filename{ftp://ftp.info-zip.org/pub/infozip/zlib/zlib-1.1.3.tar.gz}
-\URL{ftp://ftp.info-zip.org/pub/infozip/zlib/zlib-1.1.3.tar.gz}
-
-To install, pick up the sources and then:
-
-\begin{verbatim}
-% gunzip -c zlib-1_1_3_tar.gz | tar xf -
-% ln -s zlib-1.1.3 zlib
-% cd zlib
-% ./configure --prefix=/home/joe/local
-% make
-% make install
-% cd ..
-\end{verbatim}
-
-\subsection{libpng}
-
-Libpng is avilable from these sites:
-
-\URL{http://libpng.sourceforge.net/}
-\URL{http://www.mirror.ac.uk/sites/ftp.libpng.org/pub/png/libpng.html}
-\URL{ftp://swrinde.nde.swri.edu/pub/png/src/libpng.1.2.1.tar.gz}
-
-To install, pick up the sources and then:
-
-\begin{verbatim}
-% gunzip -c libpng-1_2_1_tar.gz | tar xf -
-% ln -s libpng-1.2.1 libpng
-% cd libpng
-% cp scripts/makefile.linux makefile
-\end{verbatim}
-
-Libpng has no configure script so you have to do some work by
-hand. Edit makefile, change prefix to be /home/joe/local and any
-other places - some files point to ../zlib others use
-/usr/local/lib and /usr/local/include. On HP-UX this is
-trickier. CFLAGS has to match the definition for zlib.
-
-Now build using the edited makefile:
-
-\begin{verbatim}
-% make
-% make install
-% cd ..
-\end{verbatim}
-
-
-\subsection{gd}
-
-Gd is available from these sites:
-
-\URL{http://www.boutell.com/gd/}
-
-There is no FTP server at this site.
-
-To install, pick up the sources, build zlib and libpng first, and then:
-
-\begin{verbatim}
-% gunzip -c gd-1.8.4.tar.gz | tar xf -
-% ln -s gd-1.8.4 gd
-% cd gd
-\end{verbatim}
-
-Now edit Makefile, change the definitions for INCLUDEDIRS, LIBDIRS,
-INSTALL\_LIB, INSTALL\_INCLUDE, INSTALL\_BIN, and change all
-\filename{/usr/local} to \filename{/home/joe/local}
-
-\begin{verbatim}
-% make
-% make install
-% cd ..
-\end{verbatim}
-
-If the gd "make install" fails with a warning about the "bin"
-directory, you need to create it by hand (see above).
-
-To compile with the local version your EMBOSS configure line should
-now read:
-
-\begin{verbatim}
-./configure --with-pngdriver=/home/joe/local
-\end{verbatim}
-
-This will look for the graphics libraries in your local installation
-under \filename{/home/joe/local} instead of a system-wide location
-
-configure keeps a copy of the previous settings. With earlier releases
-of EMBOSS, or as a developer with an earlier release of autoconf, you
-may need to delete files \filename{config.cache} and
-\filename{config.status} if configure has been run before.
-
-\section{Compilation}
-
-Building \EMBOSS\ is easy. It follows the usual GNU style of
-\ilcomm{./configure}, \ilcomm{make}, \ilcomm{make install}. We'll take
-these steps one at a time.
-
-\subsection{Configure}
-
-To accept the default configuration, just type \ilcomm{./configure}
-and let \EMBOSS\ get on with it. You may however want to make some
-changes to the configuration parameters according to your local
-policy. This section will not cover all the possibilities, just some
-of the more common. The configuration script will attempt to find the
-necessary components in your system to determine how to successfully
-build \EMBOSS. It typically expects the GNU C compiler (gcc) and
-several standard libraries that should already be part of your
-Unix/Linux system. \EMBOSS\ should configure, compile and run on most
-modern Linux distributions straight out of the box.
-
-
-\subsubsection{Installation directory}
-
-You need to have write permission on the directory in which you
-eventually wish to install \EMBOSS. You may also wish to put it
-somewhere else other than the standard location of
-\filename{/usr/local/emboss}.
-
-The installation directory is controlled by the \ilcomm{--prefix}
-argument. For example, you can have all third party applications owned
-by a non-privileged user and installed in a package specific directory
-under \filename{/site/prog}
-
-\begin{verbatim}
-% ./configure --prefix=/site/prog/emboss
-\end{verbatim}
-
-will install \EMBOSS\ under \filename{/site/prog/emboss}. The binaries
-will be installed in \filename{/site/prog/emboss/bin} with shared
-libraries installed in \filename{/site/prog/emboss/lib}. System wide
-data are installed in \filename{/site/prog/emboss/share/EMBOSS/data},
-and the configuration files (ACD files) for the applications will be
-installed in \filename{/site/prog/emboss/share/EMBOSS/acd} (or for
-EMBASSY in directories corresponding to the package name.)
-Documentation is installed in
-\filename{/site/prog/emboss/share/EMBOSS/doc}. The installation
-directory should be specified using a full path otherwise interesting
-failures may occur.
-
-The individual directories for installation can be modified with other
-configuration commands but this is usually not necessary. Run
-\ilcomm{./configure --help} to get more information on the directories
-that can be changed and other configuration options.
-
-Run \ilcomm{./configure} with the options you wish to use. This may
-take a short time as various messages scroll up the screen.
-
-All should be well with this and configure should exit with a message
-like this:
-
-\begin{verbatim}
-... much output skipped
-
-creating ./config.status
-creating plplot/Makefile
-creating plplot/lib/Makefile
-creating nucleus/Makefile
-creating ajax/Makefile
-creating emboss/Makefile
-creating emboss/acd/Makefile
-creating test/Makefile
-creating test/data/Makefile
-creating test/embl/Makefile
-creating test/pir/Makefile
-creating test/swiss/Makefile
-creating test/swnew/Makefile
-creating test/wormpep/Makefile
-creating emboss/data/Makefile
-creating emboss/data/AAINDEX/Makefile
-creating emboss/data/CODONS/Makefile
-creating emboss/data/REBASE/Makefile
-creating emboss/data/PRINTS/Makefile
-creating emboss/data/PROSITE/Makefile
-creating Makefile
-\end{verbatim}
-
-Configuration is now complete.
-
-\subsubsection{Reconfiguration}
-
-If at first you don't succeed, try, try and try again. It is not
-uncommon to make typos or other mistakes when running
-\ilcomm{./configure}. If you want to run configure again you should
-run \ilcomm{make clean} before running \ilcomm{./configure} with
-(hopefully) the correct options. With an earlier EMBOSS release, or as
-a developer with an earlier release of autoconf, you must first delete
-the file \filename{config.cache} but this is no longer produced.
-
-\subsubsection{Configuring \EMBOSS\ graphics}
-
-The PLPLOT library can produce output to many devices but requires
-certain libraries that are NOT distributed with \EMBOSS
-
-To get X-windows based output you must have X installed, or else PLplot
-will not build the required driver. You may need to specify the
-location of your X-windows library with the configuration options:
-\ilcomm{--x-includes=DIR} (X include files are in DIR)
-\ilcomm{--x-libraries=DIR} (X library files are in DIR)
-
-To explicitly configure PLPLOT without X-windows, use \ilcomm{--without-x}.
-
-You can explicitly tell \EMBOSS\ to not include PNG support with
-\ilcomm{--without-pngdriver}.
-
- You can tell if \ilcomm{./configure} has
-found a suitable PNG library by watching for something like the
-following when running \ilcomm{./configure}:
-
-\begin{verbatim}
-checking if png driver is wanted... yes
-checking for inflateEnd in -lz... (cached) yes
-checking for png_destroy_read_struct in -lpng... (cached) yes
-checking for gdImageCreateFromPng in -lgd... (cached) yes
-\end{verbatim}
-
-This means that the configuration script has located the PNG libraries
-on your system. If you see a message indicating that
-\ilcomm{./configure} could not find the libraries or that the version
-of \filename{gd} was too old then you should install the latest
-versions of the libraries yourself and rerun configure with the
-correct \ilcomm{--with-pngdriver} value.
-
-When you run an EMBOSS graphical application you can see the list of
-installed graph devices by giving '?' as the response to the 'Graph
-type' prompt.
-
-\subsection{Configuring for 64 bit systems}
-
-\EMBOSS\ configure looks for \progname{gcc} and uses this of
-preference when compiling \EMBOSS. This is not ideal for those who
-wish to have a compiled and linked 64bit version of \EMBOSS. The
-current version is NOT 64 bit clean (ie. it does not necessarily use
-64 bit representation internally) but will compile and run quite
-happily on 64 bit systems.
-
-Additional notes are appended below for the various operating systems
-we have information on.
-
-\subsubsection{IRIX 6.5.10}
-
-In order to compile for 64 bit on IRIX you have to specify the native
-compiler in 64 bit mode (\ilcomm{cc -64}) and the linker in 64 bit
-mode (\ilcomm{/bin/ld -64}). The following notes were provided by Jose
-Ramon Valverde\footnote{jrvalverde\@@cnb.uam.es}.
-
-
-{\it We have succeeded in compiling EMBOSS for IRIX using 64 bit
-compilation.
-
-It required some tweaking, but works. The recipe for those willing to
-give it a try is: }
-
-\begin{itemize}
- \item remove '\filename{gcc}' from your path
- \item define \filename{COMPILER\_DEFAULTS\_PATH} appropriately
- (see \filename{pe\_environ}) to look for a
- \filename{compiler.defaults} file containing
- e.g. \ilcomm{:abi=64:isa=4:proc=r10k}
- \item \ilcomm{./configure} in \EMBOSS\ and all EMBASSY subdirs
- \item search in all files for '\ilcomm{CC = cc}' and
- substitute it for '\ilcomm{CC = cc -64}'
- \item same for '\ilcomm{LD = /bin/ld}' to '\ilcomm{LD = /bin/ld -64}'
- \item \ilcomm{make}
-\end{itemize}
-
-{\it The reason is that compiling depends on the Makefile and on libtool,
-as well as linking. We didn't spend much in looking at configure since
-the above steps where so straightforward. We know we should look into
-the configure script and add an option for 64-bit-irix-compile or some
-such, but that'll have to wait till we have time for it.
-
-Yes, we know, the search and substitute thing looks tedious, but it
-isn't, honest: create a 'chfile.sh' out of the EMBOSS source hierarchy
-containing: }
-
-\begin{verbatim}
-#/bin/sh
-cp \$1 \$1.orig
-mv \$1 tmpfile
-sed -e 's/CC="cc"/CC="cc -64"/g' tmpfile | \
-sed -e 's/CC = cc/CC = cc -64/g' | \
-sed -e 's/\/bin\/ld/\/bin\/ld -64/g' \$1
-rm tmpfile
-## if you are sure, uncomment this
-#rm \$1.orig
-\end{verbatim}
-
-{\it
-'\ilcomm{cd}' to the \filename{emboss} directory and run}
-
-\begin{verbatim}
- find . -type f -exec /path/to/chfile.sh {} \; -print
-\end{verbatim}
-
-{\it and you are done with the \progname{CC}
-changes. \progname{Libtool} requires special treatment since it uses
-quotes. }
-
-\subsection{Building \EMBOSS}
-
-Building \EMBOSS\ is a matter of typing '\ilcomm{make}' and going to
-find something else to do for the next ten minutes to half an hour
-depending on the speed of your system. \EMBOSS\ will first build the
-shared libraries (\filename{PL\_PLOT}, \filename{AJAX}, and
-\filename{NUCLEUS}) and then build the applications.
-
-You may see plenty of warnings (especially on SGI systems) complaining
-about libraries not being used to resolve any symbols. These can be
-safely ignored.
-
-If all goes according to plan you should have built \EMBOSS
-successfully. If not you will have to try to work out why the build
-failed. If you can't work it out yourself, send an email describing
-the problem to emboss-bug at emboss.open-bio.org preferably with a copy of the
-output from the installation.
-
-Assuming that compilation was successful, you can\footnote{You don't
-have to do this. You can leave \EMBOSS\ where it is and just add the
-path to the \filename{emboss} directory to your \ilcomm{PATH}} now
-type '\ilcomm{make install}'. After a few minutes and many pagefuls of
-messages, \EMBOSS\ should be installed where you specified in the
-\ilcomm{--prefix} option (or in the default location of
-\filename{/usr/local/emboss} if \ilcomm{--prefix} was not specified).
-
-\subsection{Post compilation setup}
-
-You will now need to make a few adjustments to your enviromnent to
-ensure that \EMBOSS\ runs smoothly. \EMBOSS\ looks for certain
-environment variables to determine where the libraries and data are
-found. These instructions assumed you installed \EMBOSS\ in
-\filename{/site/prog/emboss}. Adjust these instructions to suit your
-installation. Insert the following lines at the end of
-\filename{/etc/cshrc} (or \filename{~/.cshrc} for a personal
-installation)
-
-\begin{verbatim}
-setenv PLPLOT_LIB /site/prog/emboss/lib
-set path=( /site/prog/emboss/bin \${path} )
-\end{verbatim}
-
-Or for bash/ksh/sh users, insert the following at the end of
-\filename{/etc/profile} or \filename{~/.bashrc}
-
-\begin{verbatim}
-PLPLOT_LIB=/site/prog/emboss/lib
-PATH=/site/prog/emboss/bin:\$PATH
-export PLPLOT_LIB PATH
-\end{verbatim}
-
-\EMBOSS\ should now be ready for use.
-
-\subsection{\EMBOSS\ data files}
-
-\EMBOSS\ will by default install the data files (including those
-installed with \progname{Rebaseextract}, \progname{Prosextract}
-\progname{Printsextract} \progname{Aaindexextract} or
-\progname{Cutgsextract}) in the default directory
-\filename{share/EMBOSS/data} in the install prefix directory. If
-\EMBOSS\ is not installed (for example, your own personal
-installation) the data files are written to \filename{emboss/data} in
-the directory where emboss was built.
-
-If you want to place your data files elsewhere, or have a separate set
-of datafiles you wish to use, you can set the \ilcomm{EMBOSS\_DATA}
-variable in \filename{emboss.default} or, for personal use, in your \filename{.embossrc} file.
-
-\subsection{Testing your \EMBOSS\ installation}
-
-You can test your \EMBOSS\ installation by trying the program
-'\ilcomm{wossname}'
-
-\begin{verbatim}
-% wossname -auto |more
-\end{verbatim}
-
-This should give a long list of programs that are available. Press
-space to page down through the list. This is just the \EMBOSS
-programs and doesn't include any of the EMBASSY programs, but only
-because they are not yet installed. (Note: Although wossname does have
-a -noembassy option this does not work with installed programs because
-wossname can no longer find any difference between EMBOSS and EMBASSY)
-
-\section{Installing EMBASSY}
-
-As well as the base libraries and standard EMBOSS distribution,
-various extra packages (EMBASSY) are distributed with EMBOSS.
-
-To install an EMBASSY package, go to the relevant directory. For
-example to install PHYLIP (which was unpacked into
-\filename{/packages/EMBOSS-2.5.0/embassy/PHYLIP-3.573c} earlier) go to
-the relevant directory.
-
-\begin{verbatim}
-% cd /packages/EMBOSS-2.5.0/embassy/PHYLIP-3.573c
-% ./configure --prefix=/site/prog/emboss
-... output not shown
-% make
-... output not shown
-% make install
-... output not shown
-\end{verbatim}
-
-Note. You {\bf MUST} use the same arguments for \ilcomm{./configure}
-that you used for the installation of the main \EMBOSS\ package. It
-may be necessary to add other options as required by individual
-packages (see below).
-
-Repeat as necessary for the other EMBASSY packages. It should also be
-noted that certain EMBASSY packages may require additional libraries.
-
-You should now find that running \progname{wossname} as before lists
-the EMBASSY programs.
-
-\subsection{EMBASSY package specific notes}
-
-In most cases, EMBASSY packages should build with no problems. Known
-problems are described below.
-
-\subsubsection{Packages with no known problems}
-So far \progname{ESIM4}, \progname{HMMER}, \progname{MEME},
-\progname{MSE}, \progname{PHYLIP} and \progname{TOPO} appear to
-install without a problem using the same arguments to
-\ilcomm{configure}.
-
-\subsubsection{\progname{EMNU}}
-
-\progname{EMNU} requires the \filename{curses} or \filename{ncurses} libraries
-that come as standard on most Unix-like systems. In particular \progname{EMNU}
-requires two header files \filename{form.h} and \filename{menu.h} that are not
-distributed with all implementations.
-
-If your \filename{curses/ncurses}
-library is installed in a strange place then you may need to instruct
-\ilcomm{configure} with the option
-
-\begin{verbatim}
---with-curses=/path/to/curses
-\end{verbatim}
-
-
-\section{Installing \EMBOSS\ in package format}
-\label{sec:FreeBSD}
-\EMBOSS\ can be installed on almost all Unix/Linux operating systems
-using the instructions above, but the package format can be far more
-convenient. A package is a precompiled set of binaries with
-installation instructions that can be set up on your system with a
-minimum of work. In some cases the package will check for the correct
-libraries and install those as necessary.
-
-Brief instructions are given here for the packages of which we are
-aware. These are maintained separately from the main source tree and
-may also install some files in operating system standard locations
-instead of the locations used by the `raw' \EMBOSS
-distribution. Please read the more detailed instructions that
-accompany each package.
-
-\subsection{Installing \EMBOSS\ on FreeBSD}
-
-A FreeBSD \EMBOSS\ package has been created by Johann
-Visagie\URL{johann\@@egenetics.com} of Electric Genetics. This will be
-distributed on the installation CD's and through the normal
-distribution channels from FreeBSD version 4.2 onwards.
-
-For the FreeBSD user with an up-to-date ports tree\footnote{FreeBSD
-users can update their ports tree through a variety of
-mechanisms. Please see the FreeBSD specific guide produced by Johann
-for more information}, installing \EMBOSS\ reduces to two simple
-commands (as root):
-
-\begin{verbatim}
-# cd /usr/ports/biology/emboss
-# make install
-\end{verbatim}
-
-The FreeBSD specific parts of the port are that
-\filename{emboss.default} is included with the other configuration
-files under \filename{/usr/local/etc} as
-\filename{emboss.default.sample}, and the \EMBOSS\ documentation is
-installed in \filename{/usr/local/share/doc/EMBOSS} instead of the
-default location. For further information on installation under
-FreeBSD you are referred to the Resources chapter.
-
-
-\chapter{Configuration}
-
-\EMBOSS\ can be readily configured to match your requirements. In a
-standard installation of \EMBOSS\ the configuration directives are
-looked for in the following locations and in the following search
-order:
-\begin{enumerate}
-\item A file \filename{emboss.default} in the \filename{share/EMBOSS}
-subdirectory of your \EMBOSS\ installation.\footnote{This location may
-have been redefined in installations of \EMBOSS\ that have been
-packaged for specific operating systems. See section \ref{sec:FreeBSD}
-for further information on OS specific package
-installations.}\footnote{\EMBOSS\ will also look in the
-\filename{emboss} directory under the \EMBOSS\ source distribution for
-\filename{emboss.default.template} and install this as
-\filename{emboss.default} if no existing file is found under the
-installation directory}
-\item A file \filename{.embossrc} in the directory specified by the
-\ilcomm{EMBOSSRC} environment variable.
-\item A file \filename{.embossrc} in the users home directory.
-\end{enumerate}
-\filename{emboss.default} and \filename{.embossrc} are plain text
-files that can readily be edited to suit.\footnote{A sample
-\filename{emboss.default} is located in \filename{emboss/acd} under
-the source distribution.} Redefinitions of configuration parameters
-will override those previously defined. In the descriptions that
-follow only \filename{.embossrc} will be mentioned but all directives
-can be placed in \filename{emboss.default} for site wide
-configuration.
-
-Several aspects of \EMBOSS\ can be defined. These are:
-\begin{itemize}
-\item\EMBOSS\ environment variables
-\item\EMBOSS\ databases
-\item Default behaviour of \EMBOSS\ programs
-\end{itemize}
-Databases are by far the most complex of these.
-
-\EMBOSS\ will ignore blank lines in the \filename{emboss.default} and
-\filename{.embossrc} files. It will also ignore any lines beginning
-with \ilcomm{\#} or \ilcomm{!} allowing comments to illuminate the
-declarations in the file.
-
-
-\section{\EMBOSS\ environment variables}
-
-\EMBOSS\ environment variables are set with an '\ilcomm{env}' or a
-'\ilcomm{set}' declaration. '\ilcomm{env}' and '\ilcomm{set}' are
-interchangeable. The most important environment variable is the
-location of the \filename{.acd} files that describe each program.
-
-\begin{verbatim}
-set emboss_acdroot /site/prog/emboss/share/EMBOSS/acd
-\end{verbatim}
-
-Environment variables are useful for simplifying maintenance of your
-\filename{.embossrc}. For example you may want to specify the location
-of your databases as an environment variable. Then if you move the
-databases you only have to update one line in the configuration file.
-
-\begin{verbatim}
-set emboss_database_dir /data/databases/flatfiles
-\end{verbatim}
-
-This would then be referred to later in \filename{.embossrc} as
-
-\begin{verbatim}
-\$emboss_database_dir/embl
-\end{verbatim}
-
-for the directory \filename{/data/databases/flatfiles/embl}
-
-\subsection{Configuring \EMBOSS\ differently for different groups of users}
-It may be the case that you have users who need to share a specific
-setup. Maybe to have access to different sets of databases or need to
-use a different data directory.
-
-It can be time consuming and error prone to maintain a series of
-individual \filename{.embossrc} files or to cause users to have to
-work in the same directory or to copy an \filename{.embossrc} to each
-directory they wish to work in. The environment variable
-\ilcomm{EMBOSSRC} can be set to point to an arbitrary directory
-containing an \filename{.embossrc} which can then be used to give
-workgroup specific configuration. Each user then only needs to set
-\ilcomm{EMBOSSRC} in their \filename{.cshrc} (\progname{csh}) or
-\filename{.profile} (\progname{bash}) to get the workgroup specific
-setup.
-
-In our case we have several groups of researchers for whom we maintain
-biological sequence databases. These databases have been made
-available under restrictive licenses so that we cannot allow
-researchers outside the groups to access the databases. Using
-\ilcomm{\$EMBOSSRC} we can set up a common configuration for the
-members of each group by defining the databases in the
-\filename{\$EMBOSSRC/.embossrc} file.
-
-
-\section{Databases}
-
-\subsection{Database access modes}
-
-\EMBOSS\ offers three modes for accessing databases:
-\begin{description}
-
- \item[Single:]\EMBOSS\ retrieves a single sequence indexed by
- ID.
-
- \item[Query:]\EMBOSS\ retrieves a set of sequences
- corresponding to a query that can return more than one entry,
- including accession numbers or wildcard IDs.
-
- \item[All:]\EMBOSS\ returns all the sequences in the database
- in no particular order.
-
-\end{description}
-
-Each database definition can configure one or many of these modes for
-database access.
-
-Typically \EMBOSS\ uses variations on the \progname{emblcd} system of
-database indexing to provide rapid access in single and query modes to
-flat file databases. The \progname{emblcd} method is implemented in a
-variety of ways depending on the original format of your database.
-The \progname{emblcd} method assumes that you have one or both of ID
-and accession number in each record and that they are unique for the
-whole database index. \EMBOSS\ also provides methods for retrieving
-sequences via the WWW and three specific methods for interaction with
-SRS\URL{http://www.lionbioscience.com/solutions/srs} installed localy
-or through a remote public server. For other non flatfile databases
-or flat file databases in formats not currently supported by \EMBOSS
-you will have to configure an external application to retrieve
-sequences.
-
-\subsection{General database configuration.}
-
-Each database is configured using a DB declaration.
-
-The generalised form is
-
-\begin{verbatim}
-DB databasename [
-
-Configuration options
-
-]
-\end{verbatim}
-
-The configuration options are tag/value pairs and must contain at
-least a description of the access method (using \ilcomm{method:} or
-one or more of \ilcomm{methodsingle:}, \ilcomm{methodquery:} and
-\ilcomm{methodall:}) and a description of the original format of the
-sequences (using \ilcomm{format:}). In addition to these tags there
-will be other tags that are needed for particular methods and other
-tags that are optional.
-
-\subsubsection{Database access methods}
-
-The scope of each method is:
-
-\begin{description}
-
-\item[Single mode - \ilcomm{s}] Supports retrieval of a single
-sequence.
-
-\item[Query mode - \ilcomm{q}] Supports retrieval of a subset of the
-sequences in the database specified using a wild card query in the
-USA\footnote{Please see the \EMBOSS\ documentation for description of
-Uniform Sequence Address format}
-
-\item[All mode - \ilcomm{a}] Supports retrieval of all sequences in
-the database as a stream of data.
-
-\end{description}
-
-An example entry for each access method is shown.
-
-\paragraph{APP}\par\noindent
-Modes: \ilcomm{a q s}\par\noindent
-APP is the same as EXTERNAL.
-
-\paragraph{BLAST}\par\noindent
-Modes: \ilcomm{a q s} \par\noindent BLAST uses EMBLCD indices created
-with \progname{dbiblast} to access databases in BLAST format, created
-with NCBI's \ilcomm{formatdb} program.
-
-Note that the latest 'format version 4' is not yet documented by
-NCBI. \EMBOSS\ will only work with 'format version 3' databases, indexed
-with:
-
-\begin{verbatim}
-formatdb -A F
-\end{verbatim}
-
-We hope to support 'format version 4' databases in future. If you pick
-up a blast database from NCBI (or elsewhere) check the format. If it
-is in the new format, you will need to pick up the original FASTA
-format file, and either index it yourself with formatdb, or run
-\ilcomm{dbifasta} and use the FASTA file in \EMBOSS\ (see EMBLCD
-access method)
-
-The definition should use format: ncbi because this is what the blast
-formatdb databases store internally.
-
-\begin{verbatim}
-DB mydb [
-#required parameters
- method: "blast"
- format: "ncbi"
- type: "N"
- dir: "\$emboss_db_dir/blas"t
-#optional parameters
- fields: "sv des"
- release: "63.0"
- comment: "my comment"
- indexdir: "\$emboss_db_dir/blastindices"]
-\end{verbatim}
-
-The index files can be kept in the same directory as the database, but
-as each EMBLCD index needs its own directory (the filenames are fixed)
-the indexdir is usually defined.
-
-The EMBLCD index files include the filenames indexed by
-\ilcomm{dbiblast}. You can use the file: and exclude: attributes to
-create file-specific subsets from a single \ilcomm{dbiblast} generated
-index, but as blast index files are split only by the number of
-entries this is not generally useful.
-
-If the database was indexed with additional fields, they can be
-included in the definition as fields: to allow their use in USAs.
-
-\paragraph{DIRECT}\par\noindent
-Modes: \ilcomm{a}\par\noindent Direct accesses the flatfile
-directly. It returns all the database entries, one after the other. It
-assumes no indexing. Queries are still possible as \EMBOSS\ will read
-each entry and match it against the query, but are slow as the entire
-database must be read.
-
-\begin{verbatim}
-DB mydb [
-#required parameters
- method: "direct"
- format: "embl"
- type: "N"
- dir: "\$emboss_db_dir/mydb"
- file: "*.dat"
-#optional parameters
- fields: "sv des key org"
- release: "63.0"
- comment: "My own database with no indices"
- exclude: "est*.dat"
-]
-\end{verbatim}
-
-For most cases, it is simpler to use \ilcomm{dbiflat} for EMBL,
-Genbank or SwissProt format, or \ilcomm{dbifasta} to index FASTA or NCBI
-format files, and to use the EMBLCD access method.
-
-If the file format supports additional fields, they can be
-included in the definition as fields: to allow their use in USAs.
-
-\paragraph{EMBLCD}\par\noindent
-Modes: \ilcomm{a q s}\par\noindent EMBLCD uses EMBLCD indices created
-with \progname{dbiflat} or \progname{dbifasta} to access flatfile
-databases in the original format.
-
-\begin{verbatim}
-DB mydb [
-#required parameters
- method: "emblcd"
- format: "embl"
- type: "N"
- dir: "\$emboss_db_dir/emb"l
-#optional parameters
- fields: "sv des key org"
- file: "*.dat"
- release: "63.0"
- comment: "my comment"
- exclude: "est*.dat"
- indexdir: "\$emboss_db_dir/indice"s
-]
-\end{verbatim}
-
-The EMBLCD index files include the filenames indexed by
-\ilcomm{dbiflat} or \ilcomm{dbifasta}. You can use the file: and
-exclude: attributes to create file-specific subsets from a single
-index.
-
-This method can require careful setup. Please read the more specific
-descriptions below.
-
-If the database was indexed with additional fields, they can be
-included in the definition as fields: to allow their use in USAs.
-
-\paragraph{EXTERNAL}\par\noindent
-Modes: \ilcomm{a q s}\par\noindent EXTERNAL uses an external
-application to retrieve sequences. The ID is passed as an argument to
-the application, either replacing \%s in the command string (if
-present) or as an additional argument (if there is no \%s).
-
-EXTERNAL requires the application to return the sequence on STDOUT. If
-the application writes to somewhere else, simply wrap it in a script
-that copies the output to STDOUT.
-
-\begin{verbatim}
-DB mydb [
-#required parameters
- method: "app"
- format: "fasta"
- type: "P"
- app: "getfromdb"
-#optional parameters
- comment: "my own protein database with a custom retrieval program"
- app: "getfromdb mydatabase \%s"
-]
-\end{verbatim}
-
-The first app: definition will use the default call 'getfromdb mydb:id'
-
-The alternative app: definition will use the \%s format and call
-'getfromdb mydatabase id'
-
-Both will pass either the ID or accession from the query, so that USAs
-mydb-id:x13776 and mydb-acc:x13776 are equivalent.
-
-\paragraph{GCG}\par\noindent
-Modes: \ilcomm{a q s}\par\noindent GCG uses EMBLCD indices created
-with \progname{dbigcg} to access databases in GCG format. This method
-uses the \filename{.ref} and \filename{.seq} files created by the
-\progname{GCG} suite of programs.
-
-\begin{verbatim}
-DB mygcgdb [
-#required parameters
- method: "gcg"
- format: "embl"
- type: "N"
- dir: "\$emboss_db_dir/gcgembl"
-#optional parameters
- fields: "sv des key org"
- file: "*.seq"
- release: "63.0"
- comment: "my comment"
- exclude: "est*"
- indexdir: "\$emboss_db_dir/indices"
-]
-\end{verbatim}
-
-The EMBLCD index files include the filenames indexed by
-\ilcomm{dbigcg}. You can use the file: and exclude: attributes to
-create file-specific subsets from a single \ilcomm{dbigcg} generated
-index.
-
-\paragraph{SRS}\par\noindent
-Modes: \ilcomm{a q s}\par\noindent SRS returns entries from a local
-installation of SRS using the -e switch to getz to return entries in
-the original format.
-
-\begin{verbatim}
-DB mydb [
-#required parameters
- method: "srs"
- format: "embl"
- type: "N"
-#optional parameters
- dbalias: "embl"
- fields: "sv des key org"
- app: "getz"
- comment: "My srs indexed database"
- release: "63.0"
-]
-\end{verbatim}
-
-This access method builds an SRS commandline query to getz. If you
-have getz installed under another name, define this as app:
-
-The SRS query by default uses the EMBOSS database name. If the
-database has a different name in SRS, define dbalias: as the database
-name to pass to SRS.
-
-SRS will return the results using 'getz -e' so the format should match
-the format of the original data. For some formats this can be tricky
-(PIR for example), so consider using SRSFASTA although this will lose
-information that is not included in the FASTA format SRS output.
-
-To query using the additional fields SRS supports, add them as fields:
-
-\paragraph{SRSFASTA}\par\noindent
-Modes: \ilcomm{a q s}\par\noindent
-As SRS but returns the sequences in FASTA format. The definition must
-include format: fasta so that EMBOSS will read the results in FASTA
-format.
-
-\begin{verbatim}
-DB mydb [
-#required parameters
- method: "srsfasta"
- format: "fasta"
- type: "N"
-#optional parameters
- dbalias: "embl"
- fields: "sv des key org"
- app: "getz"
- comment: "My srs indexed database"
- release: "63.0"
-]
-\end{verbatim}
-
-This access method builds an SRS commandline query to getz. If you
-have getz installed under another name, define this as app:
-
-The SRS query by default uses the EMBOSS database name. If the
-database has a different name in SRS, define dbalias: as the database
-name to pass to SRS.
-
-SRS will return the results using 'getz -f -sf fasta' so the format
-must be 'fasta'.
-
-To query using the additional fields SRS supports, add them as fields:
-
-\paragraph{SRSWWW}\par\noindent
-Modes: \ilcomm{a q s}\par\noindent
-As URL, but specific to an SRS web server. This method takes a base
-URL (up to wgetz) for an SRS server, and builds the rest of the URL as
-a valid SRS query.
-
-By building the URL, SRSWWW access can query both ID and accession
-number, and can query additional fields 'sv', 'des', 'key' and 'org'
-if they are allowed with a fields definition.
-
-\begin{verbatim}
-DB mydb [
-# required parameters
- method: "srswww"
- format: "genbank"
- type: "N"
- url: "http://www.infobiogen.fr/srs5bin/cgi-bin/wgetz?"
-#optional parameters
- dbalias: "genbank"
- fields: "sv des key org"
- comment: "Genbank by SRS from InfoBiogen"
- proxy: ":"
- httpversion: "1.0"
-]
-\end{verbatim}
-
-Because queries for such fields to a remote server can find a very
-large number of hits, and EMBOSS will load the entire output into
-memory to process the HTML, many EMBOSS administrators choose not to
-define these fields for an SRSWWW server.
-
-If there is sufficient demand, it should be possible to rewrite the
-HTML preprocessing to avoid buffering in memory.
-
-SRSWWW support the \ilcomm{proxy} and \ilcomm{httpversion} settings
-described under access method URL.
-
-\paragraph{URL}\par\noindent
-Modes: \ilcomm{s}\par\noindent URL uses a defined web server to
-retrieve a specific entry. EMBOSS may fail if the HTML causes
-complications with parsing of the entry.
-
-\begin{verbatim}
-DB mydb [
-# required parameters
- method: "url"
- format: "genbank"
- type: "N"
- url: "http://www.infobiogen.fr/srs5bin/cgi-bin/wgetz?-e+[genbank-id:%s]"
-#optional parameters
- comment: "Genbank by ID from InfoBiogen"
-]
-\end{verbatim}
-
-The \%s in the URL string indicates where \EMBOSS\ will insert the
-identifier portion of the USA.
-
-At many sites, remote HTTP access is controlled by a proxy
-server. EMBOSS uses a proxy server defined as EMBOSS\_PROXY with a
-value in the format \ilcomm{domain.address:port}, for example:
-
-\begin{verbatim}
-set emboss_httpversion 'proxy.mydomain.org:8080'
-\end{verbatim}
-
-This is a global definition. For selected databases (local web-based
-services, for example) you can turn off the proxy inside the database
-definition with:
-
-\begin{verbatim}
-DB [ ...
- proxy: ":"
-]
-\end{verbatim}
-
-HTTP access by default used HTTP protocol version 1.0. EMBOSS can also
-support version 1.1, which provides chunked HTML results to improve
-improve network performance. The HTTP version is controlled by a
-variable EMBOSS\_HTTPVERSION and by a DB attribute, for example:
-
-\begin{verbatim}
-set emboss_httpversion "1.1"
-\end{verbatim}
-
-or
-
-\begin{verbatim}
-DB [ ...
- httpversion: '1.1'
-]
-\end{verbatim}
-
-\subsection{Mixed access methods}
-
-For any given \ilcomm{method:} declaration, \EMBOSS\ will use that
-method for those access modes supported by the method.
-
-If you wish to specify which access mode (all, query or single) should
-be handled by which database retrieval method then the
-\ilcomm{methodsingle:}, \ilcomm{methodquery:} and \ilcomm{methodall:}
-declarations should be used instead of \ilcomm{method:}
-
-\begin{verbatim}
-DB mydb [
-methodsingle: app
-format: fasta
-app: "customapp myproteindb"
-methodall: direct
-dir: \$emboss_db_dir/myproteindb
-file: myproteindb.dat
-type: P
-comment: "single and all access for myproteindb"
-]
-\end{verbatim}
-
-You can mix these, for example, to use a script to query a file, and
-direct acces to read all entries,
-
-\begin{verbatim}
- methodall: 'direct'
- methodquery: 'external'
-\end{verbatim}
-
-\subsection{Indexing and configuring flatfile databases}
-
-Flatfile databases are plain text files in a defined format such as
-those released by EMBL, Swissprot and so on. The \EMBOSS\ program
-\progname{dbiflat} is used to generate EMBLCD indices that can be used
-for all types of database access. \progname{dbiflat} can process
-databases in EMBL, SWISSPROT and GENBANK format. Pseudo EMBL format
-databases which do not have unique ID and AC entries may cause
-\progname{dbiflat} to do mysterious things and should be avoided.
-
-\progname{dbiflat} (and the EMBLCD access method) requires the
-databases to be uncompressed. The examples given here will not probe
-the deeper secrets of \progname{dbiflat} (for which the reader is
-referred to the documentation, or failing that the source code) but
-will show a typical installation for a common database.
-
-We assume that \EMBOSS\ has been installed and works. This can be
-tested with the command \ilcomm{wossname -auto} which should list all
-the programs available.
-
-In this example we will index and configure the EMBL database for use
-with \EMBOSS.
-
-First download and unpack the EMBL database. This will require a
-considerable amount of disk space. If you do not have sufficient space
-available then just download a subset of the database.
-
-Use \ilcomm{cd} to move the directory in which you have unpacked
-EMBL. This should look something like this when you run \ilcomm{ls}:
-
-\begin{verbatim}
-% ls
-est_fun.dat
-est_hum1.dat
-est_hum10.dat
-.
-Output truncated
-.
-syn.dat
-unc.dat
-vrl.dat
-vrt.dat
-\end{verbatim}
-
-Run \progname{dbiflat} to create the EMBLCD indices.
-
-\begin{verbatim}
-% dbiflat
-
-Index a flat file database
- EMBL : EMBL
- SWISS : Swiss-Prot, SpTrEMBL, TrEMBLnew
- GB : Genbank, DDBJ
-Entry format [SWISS]: EMBL
-Database name: embl
-Database directory [.]:
-Wildcard database filename [*.dat]:
-Release number [0.0]: 63.0
-Index date [00/00/00]: 31/07/00
-\end{verbatim}
-
-\progname{dbiflat} should happily chug away for some considerable time
-(up to a few hours depending on the speed of your machine) and will
-generate (eventually) the following index files:
-
-\begin{verbatim}
-% ls
-acnum.hit
-acnum.trg
-division.lkp
-entrynam.idx
-\end{verbatim}
-
-Now we create an entry in the \EMBOSS\ configuration files to acces
-sthe database. It is probably a good idea to try new database
-definitions in your local configuration file first.
-
-Put the following entry in your \filename{.embossrc}
-
-\begin{verbatim}
-DB embl [
- type: N
- method: emblcd
- format: embl
- dir: \$emboss_db_dir/embl
- file: "*.dat"
- release: "63.0"
- comment: "EMBL release 63.0"
-]
-\end{verbatim}
-
-you will have needed to predefine \ilcomm{\$emboss\_db\_dir} using a
-directive such as
-
-\begin{verbatim}
-set emboss_db_dir /path_to_databases
-\end{verbatim}
-
-somewhere in your \filename{emboss.default} or \filename{.embossrc}.
-
-Save \filename{.embossrc} and try \progname{showdb}. You should see a
-line that looks like:
-
-\begin{verbatim}
-% showdb
-.. output deleted
-embl N OK OK OK EMBL release 63.0
-.. output deleted
-\end{verbatim}
-
-\subsection{Fine tuning the installation:}
-\label{sec:finetune}
-It is probably a good idea to set up subsections of the database so
-that end users can search just the regions they wish to search. This
-section applies to all access methods that use EMBLCD style indexes
-and probably to others as well.
-
-Files can be included with the declaration \ilcomm{file:} or excluded
-with the declaration \ilcomm{exclude:}. It is a good idea to put the
-wild card directory specifier (\filename{*/})in front of the filename
-to ensure that any path that may be included in
-\filename{division.lkp} will be matched. Please note especially the
-notes for \progname{GCG} formatted databases indexed with
-\progname{dbigcg}.
-
-In order to just take the EST files in our EMBL database try the following:
-
-\begin{verbatim}
-DB emblest [
- type: N
- method: emblcd
- format: embl
- dir: \$emboss_db_dir/embl
- file: "est*.dat"
- release: "63.0"
- comment: "EMBL release 63.0"
-]
-\end{verbatim}
-
-Files can also be given as a space separated list enclosed in
-quotes. For example to set up a database of all mamallian sequences
-(except genomes) try the following:
-
-\begin{verbatim}
-DB emblallmam [
- type: N
- method: emblcd
- format: embl
- dir: \$emboss_db_dir/embl
- file: "rod*.dat hum*.dat mam*.dat"
- release: "63.0"
- comment: "EMBL release 63.0"
-]
-\end{verbatim}
-
-As you can see from these two examples, the \ilcomm{file:} tag takes a
-space delimited list of filenames enclosed in quotes that can contain
-normal wildcard (\ilcomm{?*}) characters.
-
-It can be quite tedious to set up a long list of sequences to
-search. In many cases you can use the \ilcomm{exclude:} tag to make
-things easier.
-
-\begin{verbatim}
-DB emblnoest [
- type: N
- method: emblcd
- format: embl
- dir: \$emboss_db_dir/embl
- file: "*.dat"
- exclude: "est*.dat"
- release: "63.0"
- comment: "EMBL release 63.0"
-]
-\end{verbatim}
-
-This configures the \filename{emblnoest} database to contain all of
-EMBL except the EST's.
-
-\subsection{Indexing and configuring GCG format databases}
-
-\EMBOSS\ can access GCG formatted databases, thus avoiding having
-multiple copies of the same databases in different formats for those
-who still use GCG alongside the flatfiles. \EMBOSS\ creates EMBLCD
-like indices for the GCG format databases using the program
-\progname{dbigcg}. This runs in much the same way as
-\progname{dbiflat}. You will need the GCG format \filename{.seq} and
-\filename{.header} files in order to create an EMBLCD indexed
-database.
-
-Move to the GCG database directory containing your data and run
-\progname{dbigcg}
-
-\begin{verbatim}
-Index a GCG formatted database
- EMBL : EMBL
- SWISS : Swiss-Prot, SpTrEMBL, TrEMBLnew
- GB : Genbank, DDBJ
- PIR : NBRF
-Entry format [EMBL]:
-Database name: embl
-Database directory [.]:
-Wildcard database filename [*.seq]:
-Release number [0.0]: 63.0
-Index date [00/00/00]: 31/07/00
-\end{verbatim}
-
-The program will chug along for a while and will then generate the
-EMBLCD index files for the GCG format database.
-
-When \progname{dbigcg} prompts for the entry format (\ilcomm{Entry
-format [EMBL]:}) you should enter the original database format before
-you ran \progname{embltogcg} or similar to generate the \progname{GCG}
-databases.
-
-The following entry should be put in your \filename{.embossrc}
-
-\begin{verbatim}
-DB gcgembl [
- type: N
- method: gcg
- format: embl
- dir: \$emboss_db_dir/embl
- file: "*.dat"
- release: "63.0"
- comment: "EMBL release 63.0"
-]
-\end{verbatim}
-
-\progname{showdb} should show your newly configured database.
-
-You can configure subsets of the databases in the same way as for the
-original format databases, described in section \ref{sec:finetune}
-above. One difference to \progname{dbiflat} indexing is that both the
-\filename{.seq} and \filename{.header} files are listed in the
-\filename{division.lkp} file. \ilcomm{file:} and \ilcomm{exclude:}
-directives should therefore be of the form \ilcomm{exclude:
-*/em\_est*} instead of just \ilcomm{*/em\_est*.seq}.
-
-\subsection{Indexing and configuring BLAST databases}
-BLAST format databases are generated for efficient homology searching
-using the BLAST programs. It can be convenient to avoid redundant
-copies of databases so \EMBOSS\ provides a mechanism for accessing
-these databases.
-
-BLAST format databases are those generated using the tools distributed
-with NCBI-BLAST or with WU-BLAST.
-
-\begin{comment}At present \EMBOSS
-will only index BLAST databases created from FASTA format input files
-with one of the recognised header formats. More information on the
-relevant formats can be found in subsection \ref{subsec:fasta}
-below.
-\end{comment}
-
-For indexing of one BLAST database, move to the
-directory containing your BLAST format databases and run
-\progname{dbiblast}
-
-\begin{verbatim}
-Index a BLAST database
-Database name: blastsw
-Database directory [.]:
-database base filename [blastsw]:
-Release number [0.0]:
-Index date [00/00/00]:
- N : nucleic
- P : protein
- ? : unknown
-Sequence type [unknown]: p
- 1 : wublast and setdb/pressdb
- 2 : formatdb
- 0 : unknown
-Blast index version [unknown]: 2
-
-\end{verbatim}
-
-The program will chug along for a while and will then generate the
-EMBLCD index files for the BLAST format database.
-
-The following entry (or one like it that is more appropriate to your
-particular installation) should be put in your \filename{.embossrc}
-
-\begin{verbatim}
-DB blastsw [
- type: P
- method: blast
- format: ncbi
- dir: \$emboss_db_dir/blastsw
- file: "blastsw"
- release: "38.9"
- comment: "BLAST format Swissprot"
-]
-\end{verbatim}
-
-\progname{showdb} should show your newly configured database.
-
-Because of the way BLAST works, many sites may group their BLAST
-databases in the same directory. You can index these {\it in situ}
-with \progname{dbiblast} but this may require some extra steps if your
-databases are not of the same type as generation of subsequent index
-files will overwrite those that already exist. To avoid overwriting of
-index files you can index many databases with one set of index files,
-or you can use the \ilcomm{indexdir} options to place the indices in a
-different directory.
-
-There are two requirements for indexing several databases together in
-one index. The first is that the databases are the same type
-(protein/nucleic acid) and generated with the same tool (pressdb or
-formatdb); the second is that all the ID and accession numbers in the
-combined databases are unique.
-
-Run \progname{dbiblast} as before but specify all the databases you
-wish to be included when prompted for the database filename.
-
-\begin{verbatim}
-Index a BLAST database
-Database name: alldbs
-Database directory [.]:
-database base filename [alldbs]: dbone dbtwo dbthree dbfour
-Release number [0.0]:
-Index date [00/00/00]:
- N : nucleic
- P : protein
- ? : unknown
-Sequence type [unknown]: p
- 1 : wublast and setdb/pressdb
- 2 : formatdb
- 0 : unknown
-Blast index version [unknown]: 2
-
-\end{verbatim}
-
-These can then be configured as described in section
-\ref{sec:finetune} above by using the '\ilcomm{file:}' and
-'\ilcomm{exclude:}' tags as appropriate.\footnote{There is one
-difference to the standard EMBLCD access method in that the database
-indexes will not allow the generation of exclusive subsections of the
-combined database. If an ID or accession number is specified that is
-present in the index then the sequence will be returned irrespective
-of which database it is in.}
-
-When you have databases of different types, generated with different
-programs or where the ID/accession numbers are duplicated between
-databases the preferred strategy is probably to keep the source data
-for the individual databases in separate directories and index them
-there.\footnote{Keeping one directory with symbolic links for your
-BLAST installation will ensure that BLAST continues to function
-correctly if you set BLASTDB to point to the directory containing the
-symbolic links. The EMBOSS indices can be placed wherever you wish as
-long as you remember to run \progname{dbiblast} with the appropriate
-options and put an appropriate \ilcomm{indexdir} tag in the DB
-configuration in your ~/.embossrc}
-
-Alternatively you can place the index files in a separate
-directory. This requires that you run \progname{dbiblast} with the
-\ilcomm{-indexdirectory} option and set the \ilcomm{indexdir:} tag in
-the database configuration to point to the correct database. The
-example below illustrates database configuration using the
-\ilcomm{indexdir} options.
-
-\begin{verbatim}
-% dbiblast -indexdir=/databases/indices/mydb
-Index a BLAST database
-Database name: mydb
-Database directory [.]:
-database base filename [mydb]:
-Release number [0.0]:
-Index date [00/00/00]:
- N : nucleic
- P : protein
- ? : unknown
-Sequence type [unknown]: p
- 1 : wublast and setdb/pressdb
- 2 : formatdb
- 0 : unknown
-Blast index version [unknown]: 2
-
-\end{verbatim}
-
-The corresponding entry in \filename{~/.embossrc} (or
-\filename{emboss.default}) would look like:
-
-
-\begin{verbatim}
-DB mydb [
- type: P
- method: blast
- format: ncbi
- dir: \$emboss_db_dir/blastsw
- indexdir: /databases/indices/mydb
- file: mydb
- release: "1.0"
- comment: "My BLAST DB with an index in a different directory"
-]
-\end{verbatim}
-
-Again, multiple indices cannot coexist in the same directory so care
-should be taken when using the \ilcomm{indexdir} options that an
-existing database index is not overwritten.
-
-\begin{comment}
-\subsubsection{FASTA formats used with \progname{dbiblast}}
-\label{subsec:fasta}
-The following FASTA formats are recognised by \progname{dbiblast}:
-
-\begin{tabular}[t]{|l|l|}\hline \setlength{\baselineskip}{1.2\baselineskip}
-GENBANK/NCBI & \ilcomm{> \ldots |accno|id \ldots }\\
-\hline
-GCG & \ilcomm{>{\sl dbname}:accno id \ldots }\\
-\hline
-SIMPLE &\ilcomm{ >accno id \ldots} \\
-\hline
-ID & \ilcomm{>id}\\
-\hline
-\end{tabular}
-\ilcomm{...} refers to any text. Note that the ID must be the only
-item in the header for the ID format.
-
-\end{comment}
-\subsection{Indexing and configuring FASTA databases}
-
-The FASTA specifications just define the sequence file as a header
-line that begins with \ilcomm{>} and subsequent lines containing the
-sequence. The header line can be present in an almost infinite number
-of formats, several of which can be processed by \EMBOSS. \EMBOSS
-attempts to determine the accession number and/or ID for each
-sequence. For indexing purposes there is no semantic difference
-between an accession number and an ID. In the real world, acession
-numbers are immutable, ie. they do not change with subsequent releases
-of the dataabse, but ID's may change. In any case IDs and accession
-numbers are unique, and that is all that matters for database indexing
-\EMBOSS.
-
-The program used to process FASTA format databases is
-\progname{dbifasta}. It can recognise the following header line
-formats, specified on the command line:
-
-\begin{tabular}[t]{|l|l|}\hline\setlength{\baselineskip}{1.5\baselineskip}
-simple &%
-\ilcomm{>id ...}\\
-\hline
-idacc &%
-\ilcomm{>id accno ...}\\
-\hline
-gcgid &%
-\ilcomm{>db:id ...}\footnotemark[\value{footnote}]\\
-\hline
-gcgidacc &%
-\ilcomm{>db:id acc ...}\footnotemark[\value{footnote}]\\
-\hline
-dbid &%
-\ilcomm{>db id ...}\footnotemark\\
-\hline
-ncbi &%
-\ilcomm{>...[|accno]|id ...}\footnotemark\\
-\hline
-\end{tabular}
-\addtocounter{footnote}{-1} \footnotetext{{\em db} is one word}
-\addtocounter{footnote}{1} \footnotetext{The ID is always taken to be
-the characters after the last bar (\ilcomm{|}). The previous field is
-also indexed but ONLY if it looks like an accession number
-(e.g. AC00001).}
-
-
-Other header formats will not be recognised by \progname{dbifasta} and
-will cause indexing and/or database lookup to fail. If you have a
-different header format that \progname{dbifasta} cannot yet handle you
-have two options:
-\begin{enumerate}
-\item (The preferred option) Get a C programmer to modify the source
-code for \progname{dbifasta} and recompile. If you are a community
-spirited person you will also contribute these changes to the main
-\EMBOSS\ source tree. (email emboss-dev\@@emboss.open-bio.org for more
-information on contributing changes to the \EMBOSS\ source code and/or
-read the \EMBOSS\ developers documentation)
-\item (The quick hack) Write a custom script (using
-e.g. BioPerl\URL{http://www.bioperl.org}) to access your database and
-use \ilcomm{method: external} to configure it. This is less desirable
-as you may be limited in the access modes you can use.
-\end{enumerate}
-
-To index a FASTA format database, run \progname{dbifasta}.
-
-\begin{verbatim}
-% dbifasta
-Index a fasta database
- simple : >ID
- idacc : >ID ACC
- gcgid : >db:ID
- gcgidacc : >db:ID ACC
- ncbi : >blah|...[|ACC]|ID
-ID line format [idacc]:
-Database name: mydb
-Database directory [.]:
-Wildcard database filename [*.dat]: mydb.fasta
-Release number [0.0]:
-Index date [00/00/00]:
-\end{verbatim}
-
-\progname{dbifasta} will chug along for a little while and will
-produce the index files. You can use the same \ilcomm{indexdir}
-options as for \progname{dbiflat},\progname{dbigcg} and
-\progname{dbiblast} to place the indices in a different directory.
-
-Place the following entry in your \filename{.embossrc}
-
-\begin{verbatim}
-DB mydb [
- type: P
- method: emblcd
- format: fasta
- dir: \$emboss_db_dir/mydb
- file: mydb.fasta
- comment: "My database"
-]
-\end{verbatim}
-
-\ilcomm{format:} should be \ilcomm{dbid}, \ilcomm{ncbi} or
-\ilcomm{fasta} (for every format except \ilcomm{dbid} or
-\ilcomm{ncbi}. The same \ilcomm{file:} and \ilcomm{include:} tags can
-be used as for the other database indexing programs.
-
-
-\subsection{Configuring \EMBOSS\ to use SRS for database lookup.}
-
-\ilcomm{method: srs} is really a special case of \ilcomm{method:
-external} with some additional features.
-
-SRS is a powerful database querying system that can cross reference
-between different databases, launch applications and so on. SRS can be
-run either through a web interface (see the description of the URL
-method above for an example) or via the command line program
-\progname{getz}. Indexing and configuring databases for SRS is
-outside the scope of this document which will describe how to connect
-to preconfigured and indexed SRS databases.\footnote{For information
-on configuring and indexing SRS databases please look at the SRS
-administrators guide \filename{www/doc/srsadmin.pdf} in your SRS 6
-installation} If \progname{getz} is already in your \ilcomm{PATH}
-environment variable then insert the following (or similar) in your
-\filename{.embossrc}:
-
-\begin{verbatim}
- DB emblgetz [
- type: N
- method: srs
- release: "63"
- format: embl
- comment: 'EMBL using getz'
- dbalias: embl
- app: getz
-]
-\end{verbatim}
-
-This will provide access to the SRS database 'embl' as
-\ilcomm{emblgetz:acc}. If the SRS database has a different name to the
-\EMBOSS\ database (as is the case here) then the \ilcomm{dbalias:} tag
-should be used to access the correct SRS database.
-
-This configuration can be extremely slow for the all access mode. It
-is probably a better idea to set up the database as follows:
-
-\begin{verbatim}
- DB emblgetz [
- type: N
- methodquery: srs
- release: "63"
- format: embl
- comment: 'EMBL using getz'
- dbalias: embl
- app: getz
- methodall: direct
- file: "*.dat"
- dir: \$emboss_db_dir/embl
-]
-\end{verbatim}
-
-which will use \ilcomm{method: srs} for the \ilcomm{query} access mode
-but will use \ilcomm{method: direct} for the \ilcomm{all} access mode,
-thus speeding up reading of the whole database.
-
-The SRSFASTA access method is identical to the normal SRS method
-except that it returns the sequence in FASTA format and so does not
-need a \ilcomm{format:} tag.
-
-
-\subsection{Indexing and configuring other databases}
-
-Many institutions may have local databases set up in their own
-Laboratory Information Management System. \EMBOSS\ provides a simple
-mechanism for interfacing with such systems.
-
-As long as a program is available that can be called noninteractively
-and returns the specified sequence on standard output, \EMBOSS\ can
-interface with it. Use method: app or external (the two are
-equivalent) and app: "program command". The ID given in the USA will
-be appended to the command used to run the program. It is probably
-best to specify the methods available using the method subsets,
-methodall:, methodquery: and methodsingle: rather than using the
-generic method: tag.
-
-
-\section{Other data}
-
-\EMBOSS\ can be integrated with some common biological
-databases. These are described in this section.
-
-\subsection{REBASE}
-
-Rebase is the restriction enzyme database maintained by New
-England Biolabs. It is needed for programs such as remap and
-restrict.
-
-The latest version of Rebase can be obtained by anonymous
-FTP.\footnote{ftp://ftp.ebi.ac.uk/pub/databases/rebase} \EMBOSS\ needs
-the \filename{withrefm} file. The data is extracted for \EMBOSS\ with
-the program \progname{rebaseextract}.
-
-\begin{verbatim}
-% mkdir /site/prog/emboss/data/REBASE
-% rebaseextract
-Extract data from REBASE
-Full pathname of WITHREFM: /data/rebase/withrefm.208
-\end{verbatim}
-
-Rebase is now installed and ready to use.
-
-\subsection{TRANSFAC}
-
-Transfac is the transcription factor binding site database. It is
-available by anonymous
-FTP.\footnote{ftp://transfac.gbf.de/pub/transfac/ascii/} Unpacking the
-distribution reveals a file called site.dat. This is the one \EMBOSS
-needs.
-
-Run \progname{tfextract} to extract the data from TRANSFAC.
-
-\begin{verbatim}
-% tfextract
-Extract data from TRANSFAC
-Full pathname of transfac SITE.DAT: /databases/transfac/site.dat
-\end{verbatim}
-
-\progname{tfscan} can now access the TRANSFAC database.
-
-\subsection{PROSITE}
-
-Prosite is a database of regular expressions that match potentially
-diagnostic regions for structural/functional classification of
-proteins. \EMBOSS\ needs this database for the patmatmotifs program.
-
-PROSITE can be obtained via anonymous
-FTP.\footnote{ftp://ftp.ebi.ac.uk/pub/databases/prosite}
-
-You may need to create a PROSITE subdirectory under data in the
-\EMBOSS\ installation directory.
-
-Then run \progname{prosextract} to build the \EMBOSS\ Prosite database.
-
-\begin{verbatim}
-% prosextract
-Builds the PROSITE motif database for patmatmotifs to search
-Enter name of prosite directory: /data/prosite
-\end{verbatim}
-
-PROSITE is now integrated into your EMBOSS installation.
-
-\subsection{PRINTS}
-
-Prints is a database of diagnostic patterns of blocks of sequence
-homology in protein families. The PRINTS database can be searched
-using the \EMBOSS\ program \progname{pscan}.
-
-PRINTS can be obtained via anonymous
-FTP.\footnote{ftp://ftp.ebi.ac.uk/pub/databases/prints} The database
-is made available as compressed files which should be uncompressed
-using \progname{gzip} before integrating them into \EMBOSS
-
-PRINTS is integrated with \EMBOSS\ using the program \progname{printsextract}
-
-\begin{verbatim}
-% printsextract
-Extract data from PRINTS
-Input file: /data/prints/prints27_0.dat
-\end{verbatim}
-
-The PRINTS database is now integrated with \EMBOSS.
-
-\subsection{AAINDEX}
-
-An amino acid index is a set of 20 numerical values representing any
-of the different physicochemical and biological properties of amino
-acids. The AAindex1 section of the Amino Acid Index Database is a
-collection of published indices together with the result of cluster
-analysis using the correlation coefficient as the distance between two
-indices. This section currently contains 437 indices in release
-\filename{4.0} of the database.
-
-The \EMBOSS\ programs \progname{pepwindow} and {pepwindowall} plot
-hydrophobicity using the data from an Aaindex entry. If Aaindex is
-installed these programs can plot the other amino acid properties.
-
-Aaindex can be obtained via anonymous
-FTP.\footnote{ftp://ftp.genome.ad.jp/pub/db/genomenet/aaindex/aaindex1}
-
-Aaindex is integrated with \EMBOSS\ using the program \progname{aaindexextract}
-
-\begin{verbatim}
-% aaindexextract
-Extract data from AAINDEX
-Full pathname of file aaindex1: /data/aaindex/aaindex1
-\end{verbatim}
-
-The AAINDEX database is now integrated with \EMBOSS.
-
-\subsection{CUTG}
-
-The CUTG database contains a series of codon usage tables calculated
-from GenBank.
-
-CUTG can be obtained via anonymous
-FTP.\footnote{ftp://ftp.ebi.ac.uk/pub/databases/cutg/ or
-ftp://ftp.kazusa.or.jp/pub/codon/current/}
-
-CUTG is integrated with \EMBOSS\ using the program
-\progname{cutgextract} which writes files to the CODONS data
-directory.
-
-\begin{verbatim}
-% cutgextract
-Extract data from CUTG
-CUTG directory [.]: /data/cutg/
-\end{verbatim}
-
-The CUTG database is now integrated with \EMBOSS.
-
-\subsection{Miscellaneous data files}
-
-Other data files should be kept in the data directory under the main
-\EMBOSS\ installation. Individual users personal data files can be
-kept in the current working directory, a subdirectory
-\filename{.embossdata} of the current directory, their home directory
-or a subdirectory \filename{.embossdata} of their home
-directory. \EMBOSS\ will search these locations in this order and will
-stop as soon as it finds a matching file. If the personal directories
-do not contain the desired file, \EMBOSS\ will search the system wide
-data directory, \filename{/site/prog/emboss/data} in this example.
-
-Apparently inexplicable errors when running \EMBOSS\ programs may be
-caused by the system not using the data files one expects. The search
-path can be displayed in search order using the command
-\progname{embossdata}.
-
-\section{Default program settings}
-
-As with many other areas, the default behaviour of programs can be
-controlled by setting appropriate values in \filename{.embossrc}.
-
-All general qualifiers\footnote{See the \EMBOSS\ Quick Guide or the
-web documentation (or use \ilcomm{wossname -help -verbose}) for an
-overview of general qualifiers.} can be specified as
-
-\begin{verbatim}
-set emboss_QUALIFIER 1
-\end{verbatim}
-
-where \ilcomm{QUALIFIER} is one of the general qualifiers and the
-value can be \ilcomm{1} or \ilcomm{1} for true, or \ilcomm{0} or
-\ilcomm{N} for false.
-
-Setting the qualifier value to true has the effect of running every
-program with that qualifier set.\footnote{You can specifically unset
-it by using the \ilcomm{-noQUALIFIER} command line option} Qualifiers
-can be set and will work in the same way as if you set them when
-running the program. For example you can \ilcomm{set emboss\_verbose
-Y} and the program will run normally, but when the program is run with
-the \ilcomm{-help} qualifier, the output will be in verbose form.
-
-There is no point in globally setting options that are there for
-producing help output.
-
-Qualifiers that can be set:
-
-\begin{description}
-
-\item[VERBOSE] Causes \ilcomm{-help} to print verbose text.
-
-\item[STDOUT] Causes all output to go to \filename{STDOUT} as
-default. Programs will usually build a default output file name form
-the input sequence and the program name.
-
-\item[DEBUG] Writes debugging output to a file. Useful for finding
-bugs as a command line option.
-
-\item[OPTIONS] Enable prompting for optional parameters.
-
-\item[FILTER] Take input from \filename{STDIN} and send it to
-\filename{STDOUT}, and turn on \ilcomm{-auto}
-
-\item[AUTO] Do not prompt for any options but accept the defaults if
-no values are given.
-
-\item[WARNING] Print warning messages to \filename{STDERR} (default is true)
-
-\item[ERROR] Print error messages to \filename{STDERR} (default is true)
-
-\item[FATAL] Print fatal messages to \filename{STDERR} (default is true)
-
-\item[DIE] Print crash messages to \filename{STDERR}
-
-\end{description}
-
-These general qualifiers are typically used by advanced users
-(\ilcomm{-options}, \ilcomm{-verbose}) or by developers
-(\ilcomm{-debug -acdlog}).
-
-
-Other program options that can be set are \ilcomm{emboss\_format},
-\ilcomm{emboss\_acdroot}, and \ilcomm{emboss\_data}. The value of
-\ilcomm{emboss\_format} determines which default sequence format to
-use for output. for example, if you are running \EMBOSS\ alongside
-\progname{GCG} you may wish to have the following entry in your
-\progname{.embossrc}
-
-\begin{verbatim}
-set emboss_FORMAT gcg
-set emboss_OUTFORMAT gcg
-\end{verbatim}
-
-which has the effect of using \progname{GCG} format by
-default.\footnote{This can of course be overridden using the
-\ilcomm{-sformat} and \ilcomm{-osformat} associated qualifiers. See
-the \EMBOSS\ ACD Syntax documentation or the \EMBOSS\ Quick Guide for
-more information.}
-
-\ilcomm{emboss\_acdroot} \filename{/path/to/acd} can be set if you
-wish to use a different directory for the ACD files, and
-\ilcomm{emboss\_data} \filename{/path/to/data} if you wish to use a
-separate data directory.
-
-
-\section{Logging}
-
-Many system administrators may wish to make use of the logging
-facilities of \EMBOSS. Setting the variable \ilcomm{emboss\_logfile}
-in \filename{emboss.default} or \filename{.embossrc} allows the system
-to keep a log of which programs are used when and by whom.
-
-\begin{verbatim}
-set emboss_logfile /site/log/emboss.log
-\end{verbatim}
-
-The log file structure is very simple. Three tab separated fields are
-stored, program name, user name, and the date and time.
-
-\begin{verbatim}
-prettyplot joeuser Wed Aug 02 14:29:13 2000
-\end{verbatim}
-
-The file defined in emboss\_logfile should be world writable. The
-following command ensures logging can occur.
-
-\begin{verbatim}
-chmod +w /site/log/emboss.log
-\end{verbatim}
-
-All settings can be overridden in a users \filename{.embossrc} files
-by redefining the relevant variables. So to prevent our system usage
-being logged we can redefine emboss\_logfile by putting the following
-entry in our \filename{.embossrc} file.
-
-\begin{verbatim}
-set emboss_logfile /dev/null
-\end{verbatim}
-
-This behaviour may change in the future to prevent users redefining
-some system settings.
-
-\chapter{Graphical interfaces to EMBOSS}
-
-This chapter needs to be written. It will be written when the
-available GUIs are stable enough to document.
-
-\chapter{Resources}
-\section{Web sites}
-\subsection{Programs}
-\begin{description}
-\item[\EMBOSS\ source code]ftp://emboss.open-bio.org/pub/EMBOSS
-\item[\EMBOSS\ Documentation]http://emboss.sf.net/
-\item[BLAST tools]Tools for generating BLAST format databases are
-contained in the NCBI toolkit which can be obtained from NCBI at:
-\begin{quote}
-http://www.ncbi.nlm.nih.gov/
-\end{quote}
-\item[SRS software]The SRS software can be obtained from Lion
-Bioscience.\URL{http://www.lionbioscience.com/solutions/srs} This is a
-commercial package but at the time of writing is available free of
-charge to academic institutions.
-\item[\progname{wget}]Various useful utilities including the
-\progname{wget} program are available from the Free Software
-Foundation.\URL{http://www.gnu.org}
-\end{description}
-\subsection{Databases}
-
-Most of the databases mentioned in the text along with many others can
-be obtained via anonymous ftp from the European Bioinformatics
-Institute (EBI) at:
-\begin{quote}
-ftp://ftp.ebi.ac.uk/pub/databases
-\end{quote}
-Please use a mirror site where possible to avoid overloading of the
-EBI's resources.
-
-Other databases can be obtained from NCBI (Genbank,UniGene etc.)
-
-\subsection{Other Documentation}
-Please review the \EMBOSS\ documentation available on the WWW at the
-URL above.
-
-\begin{description}
-\item[The \EMBOSS\ Quick guide]A pocket reference guide to using
-\EMBOSS\URL{ftp://ftp.no.embnet.org/pub/EMBOSS-extra/emboss-qg.ps}.
-\item[The \EMBOSS\ Tutorial]A tutorial to give an introduction to
-using \EMBOSS\ for bioinformatics
-users.\URL{http://www.hgmp.mrc.ac.uk/Registered/Option/emboss.html}
-\item[The updated ABC guide]This is a series of bioinformatics
-practicals based predominantly on
-\EMBOSS.\URL{ftp://ftp.no.embnet.org/pub/ABC}
-\item[EMBOSS-FreeBSD-HOWTO]Detailed documentation on installation of
-\EMBOSS\ on
-FreeBSD.\URL{ftp://ftp.no.embnet.org/pub/EMBOSS-extra/EMBOSS-FreeBSD-HOWTO}
-\end{description}
-
-\section{Maintainance of your \EMBOSS\ installation}
-
-\EMBOSS\ is a rapidly evolving software packages. It is constantly
-being improved, new features added and `issues' resolved. In addition
-there are new applications added and you probably want to make use of
-these.
-
-\subsection{Automated installation of \EMBOSS\ and EMBASSY}
-
-Once you have installed \EMBOSS\ and got it to work you have solved
-the hardest part of the struggle. Updating \EMBOSS\ as new releases
-appear\footnote{\EMBOSS\ is rebuilt nightly from CVS, tested, and,
-assuming it passes the compilation tests, the latest version is posted
-to the \EMBOSS\ FTP server. } can be quite tedious. UNIX is designed
-for the lazy, so here is our lazy man's guide to always having an up to
-the minute \EMBOSS\ installation.
-
-The following script can be run manually (it should probably be
-`\ilcomm{source}d' rather than executed directly) or can be fired off
-with cron (in the early hours of the morning is a good time). It
-assumes you are installing \EMBOSS\ outside the source directory and
-have write permissions to do so.
-
-\EMBOSS\ will update \EMBOSS\ distributed files but will not alter or
-overwrite your own datafiles\footnote{Assuming of course that you
-haven't overwritten \EMBOSS\ datafiles with your own to begin with.}
-or your \filename{emboss.default}.
-
-\begin{verbatim}
-
-# This script should be sourced, not run.
-# EMBOSS UPDATE.
-# it assumes \$packages_dir/EMBOSS is a symbolic link to
-# \$mirror_dir/emboss.open-bio.org/pub/EMBOSS
-#
-
-#site specific variables: season according to taste..
-
-set mirror_dir=('/ftp/mirrors')
-set packages_dir=('/site/newprog')
-set emboss_config_options=\
-('--prefix=/site/prog/emboss --with-pngdriver=/site/lib')
-
-# Now the script proper
-
-set oldpwd=`pwd`
-
-cd \$mirror_dir
-echo 'updating EMBOSS'
-if ( `wget -m 'ftp://emboss.open-bio.org/pub/EMBOSS' |& \
- tail -1 | awk '/^Downloaded:/{print \$5}'` != "0" ) then
-
- cd \${packages_dir}/EMBOSS
- echo 'new EMBOSS programs found .. installing'
- set latest_emboss=`ls -t EMBOSS*|head -1`
-
- cd \$packages_dir
- rm -Rf EMBOSS-*
- tar zxf EMBOSS/\$latest_emboss
- set emboss_dir=`ls -dt EMBOSS-*[^z]|head -1`
-
-#the next line is necessary on our system but may not be for yours.
- setenv LD_LIBRARYN32_PATH /site/lib
-
- cd \$emboss_dir
-
-# If you have any site specific changes to the source code
-# that you want to include, copy them in here
-
- ./configure \$emboss_config_options &&\
- make && \
- make install
-
-#Now unpack and build EMBASSY
-
- mkdir embassy
- cd embassy
-
-#Unpack and build each package one at a time
-
- foreach embassadir ( `ls ../../EMBOSS/*gz |grep -v E
-MBOSS-` )
-
- tar zxf \$embassadir
- set embassadir_arch=\$embassadir:t
- set embassadir_root=\$embassadir_arch:r
-
- cd \$embassadir_root:r
- ./configure \$emboss_config_options &&\
- make && \
- make install
-
- cd ..
- end
-else
- echo 'No new version of EMBOSS available'
-endif
-
-cd \$oldpwd
-\end{verbatim}
-
-\subsection{Automated database updating}
-
-In the same way, scripts can be written to automatically update the
-biological databases. An example is given here for REBASE. As all the
-parameters for \EMBOSS\ programs can be specified on the command line
-it is a trivial matter to include index generation in your nightly
-update scripts. The management of a bioinformatic resource is beyond
-the scope of this document, though \EMBOSS\ goes a long way towards
-easing the burden of management.
-
-\subsubsection{Automated update of REBASE}
-
-This script will look for a new version of REBASE and install it in
-\EMBOSS\ using \progname{rebaseextract}.
-
-\begin{verbatim}
-# This script should be sourced, not run.
-# REBASE UPDATE. Should be run just after the beginning of the month.
-set mirrors_dir=('/ftp/mirrors')
-set oldpwd=`pwd`
-
-cd \$mirrors_dir
-
-if ( ` wget -m 'ftp://ftp.ebi.ac.uk/pub/databases/rebase/*' |& \
- tail -1 | awk '/^Downloaded:/{print \$5}'` != "0" ) then
- cd ftp.ebi.ac.uk/pub/databases/rebase
- cp `ls -t withrefm.*.Z|head -1` withrefm.Z
- uncompress withrefm.Z
- rebaseextract \
- \${mirrors_dir}/ftp.ebi.ac.uk/pub/databases/rebase/withrefm
- rm withrefm
-endif
-
-cd \$oldpwd
-\end{verbatim}
-
-We make no guarantees that these scripts will work correctly on your
-system. If it deletes all your files, spams your associates, scratches
-your CD's and initiates a nuclear strike on a small unpopulated
-pacific island it is NOT OUR FAULT. It just happens to work for us.
-
-\chapter{GNU Free Documentation License}
-
-\begin{verbatim}
- GNU Free Documentation License
- Version 1.1, March 2000
-
- Copyright (C) 2000 Free Software Foundation, Inc.
- 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
- Everyone is permitted to copy and distribute verbatim copies
- of this license document, but changing it is not allowed.
-
-
-0. PREAMBLE
-
-The purpose of this License is to make a manual, textbook, or other
-written document "free" in the sense of freedom: to assure everyone
-the effective freedom to copy and redistribute it, with or without
-modifying it, either commercially or noncommercially. Secondarily,
-this License preserves for the author and publisher a way to get
-credit for their work, while not being considered responsible for
-modifications made by others.
-
-This License is a kind of "copyleft", which means that derivative
-works of the document must themselves be free in the same sense. It
-complements the GNU General Public License, which is a copyleft
-license designed for free software.
-
-We have designed this License in order to use it for manuals for free
-software, because free software needs free documentation: a free
-program should come with manuals providing the same freedoms that the
-software does. But this License is not limited to software manuals;
-it can be used for any textual work, regardless of subject matter or
-whether it is published as a printed book. We recommend this License
-principally for works whose purpose is instruction or reference.
-
-
-1. APPLICABILITY AND DEFINITIONS
-
-This License applies to any manual or other work that contains a
-notice placed by the copyright holder saying it can be distributed
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-
-The "Invariant Sections" are certain Secondary Sections whose titles
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-The "Cover Texts" are certain short passages of text that are listed,
-as Front-Cover Texts or Back-Cover Texts, in the notice that says that
-the Document is released under this License.
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-plus such following pages as are needed to hold, legibly, the material
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-formats which do not have any title page as such, "Title Page" means
-the text near the most prominent appearance of the work's title,
-preceding the beginning of the body of the text.
-
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-2. VERBATIM COPYING
-
-You may copy and distribute the Document in any medium, either
-commercially or noncommercially, provided that this License, the
-copyright notices, and the license notice saying this License applies
-to the Document are reproduced in all copies, and that you add no other
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-technical measures to obstruct or control the reading or further
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-number of copies you must also follow the conditions in section 3.
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-You may also lend copies, under the same conditions stated above, and
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-3. COPYING IN QUANTITY
-
-If you publish printed copies of the Document numbering more than 100,
-and the Document's license notice requires Cover Texts, you must enclose
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-It is requested, but not required, that you contact the authors of the
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-
-4. MODIFICATIONS
-
-You may copy and distribute a Modified Version of the Document under
-the conditions of sections 2 and 3 above, provided that you release
-the Modified Version under precisely this License, with the Modified
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-E. Add an appropriate copyright notice for your modifications
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- terms of this License, in the form shown in the Addendum below.
-G. Preserve in that license notice the full lists of Invariant Sections
- and required Cover Texts given in the Document's license notice.
-H. Include an unaltered copy of this License.
-I. Preserve the section entitled "History", and its title, and add to
- it an item stating at least the title, year, new authors, and
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- there is no section entitled "History" in the Document, create one
- stating the title, year, authors, and publisher of the Document as
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-J. Preserve the network location, if any, given in the Document for
- public access to a Transparent copy of the Document, and likewise
- the network locations given in the Document for previous versions
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- You may omit a network location for a work that was published at
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- publisher of the version it refers to gives permission.
-K. In any section entitled "Acknowledgements" or "Dedications",
- preserve the section's title, and preserve in the section all the
- substance and tone of each of the contributor acknowledgements
- and/or dedications given therein.
-L. Preserve all the Invariant Sections of the Document,
- unaltered in their text and in their titles. Section numbers
- or the equivalent are not considered part of the section titles.
-M. Delete any section entitled "Endorsements". Such a section
- may not be included in the Modified Version.
-N. Do not retitle any existing section as "Endorsements"
- or to conflict in title with any Invariant Section.
-
-If the Modified Version includes new front-matter sections or
-appendices that qualify as Secondary Sections and contain no material
-copied from the Document, you may at your option designate some or all
-of these sections as invariant. To do this, add their titles to the
-list of Invariant Sections in the Modified Version's license notice.
-These titles must be distinct from any other section titles.
-
-You may add a section entitled "Endorsements", provided it contains
-nothing but endorsements of your Modified Version by various
-parties--for example, statements of peer review or that the text has
-been approved by an organization as the authoritative definition of a
-standard.
-
-You may add a passage of up to five words as a Front-Cover Text, and a
-passage of up to 25 words as a Back-Cover Text, to the end of the list
-of Cover Texts in the Modified Version. Only one passage of
-Front-Cover Text and one of Back-Cover Text may be added by (or
-through arrangements made by) any one entity. If the Document already
-includes a cover text for the same cover, previously added by you or
-by arrangement made by the same entity you are acting on behalf of,
-you may not add another; but you may replace the old one, on explicit
-permission from the previous publisher that added the old one.
-
-The author(s) and publisher(s) of the Document do not by this License
-give permission to use their names for publicity for or to assert or
-imply endorsement of any Modified Version.
-
-
-5. COMBINING DOCUMENTS
-
-You may combine the Document with other documents released under this
-License, under the terms defined in section 4 above for modified
-versions, provided that you include in the combination all of the
-Invariant Sections of all of the original documents, unmodified, and
-list them all as Invariant Sections of your combined work in its
-license notice.
-
-The combined work need only contain one copy of this License, and
-multiple identical Invariant Sections may be replaced with a single
-copy. If there are multiple Invariant Sections with the same name but
-different contents, make the title of each such section unique by
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-author or publisher of that section if known, or else a unique number.
-Make the same adjustment to the section titles in the list of
-Invariant Sections in the license notice of the combined work.
-
-In the combination, you must combine any sections entitled "History"
-in the various original documents, forming one section entitled
-"History"; likewise combine any sections entitled "Acknowledgements",
-and any sections entitled "Dedications". You must delete all sections
-entitled "Endorsements."
-
-
-6. COLLECTIONS OF DOCUMENTS
-
-You may make a collection consisting of the Document and other documents
-released under this License, and replace the individual copies of this
-License in the various documents with a single copy that is included in
-the collection, provided that you follow the rules of this License for
-verbatim copying of each of the documents in all other respects.
-
-You may extract a single document from such a collection, and distribute
-it individually under this License, provided you insert a copy of this
-License into the extracted document, and follow this License in all
-other respects regarding verbatim copying of that document.
-
-
-7. AGGREGATION WITH INDEPENDENT WORKS
-
-A compilation of the Document or its derivatives with other separate
-and independent documents or works, in or on a volume of a storage or
-distribution medium, does not as a whole count as a Modified Version
-of the Document, provided no compilation copyright is claimed for the
-compilation. Such a compilation is called an "aggregate", and this
-License does not apply to the other self-contained works thus compiled
-with the Document, on account of their being thus compiled, if they
-are not themselves derivative works of the Document.
-
-If the Cover Text requirement of section 3 is applicable to these
-copies of the Document, then if the Document is less than one quarter
-of the entire aggregate, the Document's Cover Texts may be placed on
-covers that surround only the Document within the aggregate.
-Otherwise they must appear on covers around the whole aggregate.
-
-
-8. TRANSLATION
-
-Translation is considered a kind of modification, so you may
-distribute translations of the Document under the terms of section 4.
-Replacing Invariant Sections with translations requires special
-permission from their copyright holders, but you may include
-translations of some or all Invariant Sections in addition to the
-original versions of these Invariant Sections. You may include a
-translation of this License provided that you also include the
-original English version of this License. In case of a disagreement
-between the translation and the original English version of this
-License, the original English version will prevail.
-
-
-9. TERMINATION
-
-You may not copy, modify, sublicense, or distribute the Document except
-as expressly provided for under this License. Any other attempt to
-copy, modify, sublicense or distribute the Document is void, and will
-automatically terminate your rights under this License. However,
-parties who have received copies, or rights, from you under this
-License will not have their licenses terminated so long as such
-parties remain in full compliance.
-
-
-10. FUTURE REVISIONS OF THIS LICENSE
-
-The Free Software Foundation may publish new, revised versions
-of the GNU Free Documentation License from time to time. Such new
-versions will be similar in spirit to the present version, but may
-differ in detail to address new problems or concerns. See
-http://www.gnu.org/copyleft/.
-
-Each version of the License is given a distinguishing version number.
-If the Document specifies that a particular numbered version of this
-License "or any later version" applies to it, you have the option of
-following the terms and conditions either of that specified version or
-of any later version that has been published (not as a draft) by the
-Free Software Foundation. If the Document does not specify a version
-number of this License, you may choose any version ever published (not
-as a draft) by the Free Software Foundation.
-
-
-ADDENDUM: How to use this License for your documents
-
-To use this License in a document you have written, include a copy of
-the License in the document and put the following copyright and
-license notices just after the title page:
-
- Copyright (c) YEAR YOUR NAME.
- Permission is granted to copy, distribute and/or modify this document
- under the terms of the GNU Free Documentation License, Version 1.1
- or any later version published by the Free Software Foundation;
- with the Invariant Sections being LIST THEIR TITLES, with the
- Front-Cover Texts being LIST, and with the Back-Cover Texts being LIST.
- A copy of the license is included in the section entitled "GNU
- Free Documentation License".
-
-If you have no Invariant Sections, write "with no Invariant Sections"
-instead of saying which ones are invariant. If you have no
-Front-Cover Texts, write "no Front-Cover Texts" instead of
-"Front-Cover Texts being LIST"; likewise for Back-Cover Texts.
-
-If your document contains nontrivial examples of program code, we
-recommend releasing these examples in parallel under your choice of
-free software license, such as the GNU General Public License,
-to permit their use in free software.
-\end{verbatim}
-
-\chapter{Acknowledgements}
-
-The acknowledgements and credits are found at the front of this guide
-because no one ever reads them if they are at the back.
-
-\end{document}
-
-
-
diff --git a/doc/manuals/admin.toc b/doc/manuals/admin.toc
deleted file mode 100644
index 8367f55..0000000
--- a/doc/manuals/admin.toc
+++ /dev/null
@@ -1,79 +0,0 @@
-\contentsline {chapter}{\numberline {1}Introduction}{4}
-\contentsline {section}{\numberline {1.1}About this document}{4}
-\contentsline {subsection}{\numberline {1.1.1}Credits}{4}
-\contentsline {subsection}{\numberline {1.1.2}Reproduction}{4}
-\contentsline {section}{\numberline {1.2}What is {\sf \bfseries EMBOSS}?}{4}
-\contentsline {subsection}{\numberline {1.2.1}Where to get it?}{4}
-\contentsline {chapter}{\numberline {2}Installation}{6}
-\contentsline {section}{\numberline {2.1}Retrieving {\sf \bfseries EMBOSS}\ by anonymous ftp}{6}
-\contentsline {subsection}{\numberline {2.1.1}Interactive FTP}{6}
-\contentsline {subsection}{\numberline {2.1.2}FTP using {\sc wget}}{7}
-\contentsline {section}{\numberline {2.2}Unpacking}{7}
-\contentsline {section}{\numberline {2.3}Graphics Requirements}{8}
-\contentsline {subsection}{\numberline {2.3.1}zlib}{9}
-\contentsline {subsection}{\numberline {2.3.2}libpng}{9}
-\contentsline {subsection}{\numberline {2.3.3}gd}{10}
-\contentsline {section}{\numberline {2.4}Compilation}{10}
-\contentsline {subsection}{\numberline {2.4.1}Configure}{10}
-\contentsline {subsubsection}{Installation directory}{10}
-\contentsline {subsubsection}{Reconfiguration}{11}
-\contentsline {subsubsection}{Configuring {\sf \bfseries EMBOSS}\ graphics}{11}
-\contentsline {subsection}{\numberline {2.4.2}Configuring for 64 bit systems}{12}
-\contentsline {subsubsection}{IRIX 6.5.10}{12}
-\contentsline {subsection}{\numberline {2.4.3}Building {\sf \bfseries EMBOSS}}{13}
-\contentsline {subsection}{\numberline {2.4.4}Post compilation setup}{13}
-\contentsline {subsection}{\numberline {2.4.5}{\sf \bfseries EMBOSS}\ data files}{14}
-\contentsline {subsection}{\numberline {2.4.6}Testing your {\sf \bfseries EMBOSS}\ installation}{14}
-\contentsline {section}{\numberline {2.5}Installing EMBASSY}{14}
-\contentsline {subsection}{\numberline {2.5.1}EMBASSY package specific notes}{14}
-\contentsline {subsubsection}{Packages with no known problems}{14}
-\contentsline {subsubsection}{{\sc EMNU}}{15}
-\contentsline {section}{\numberline {2.6}Installing {\sf \bfseries EMBOSS}\ in package format}{15}
-\contentsline {subsection}{\numberline {2.6.1}Installing {\sf \bfseries EMBOSS}\ on FreeBSD}{15}
-\contentsline {chapter}{\numberline {3}Configuration}{16}
-\contentsline {section}{\numberline {3.1}{\sf \bfseries EMBOSS}\ environment variables}{16}
-\contentsline {subsection}{\numberline {3.1.1}Configuring {\sf \bfseries EMBOSS}\ differently for different groups of users}{17}
-\contentsline {section}{\numberline {3.2}Databases}{17}
-\contentsline {subsection}{\numberline {3.2.1}Database access modes}{17}
-\contentsline {subsection}{\numberline {3.2.2}General database configuration.}{17}
-\contentsline {subsubsection}{Database access methods}{18}
-\contentsline {paragraph}{APP}{18}
-\contentsline {paragraph}{BLAST}{18}
-\contentsline {paragraph}{DIRECT}{19}
-\contentsline {paragraph}{EMBLCD}{19}
-\contentsline {paragraph}{EXTERNAL}{19}
-\contentsline {paragraph}{GCG}{20}
-\contentsline {paragraph}{SRS}{20}
-\contentsline {paragraph}{SRSFASTA}{21}
-\contentsline {paragraph}{SRSWWW}{21}
-\contentsline {paragraph}{URL}{22}
-\contentsline {subsection}{\numberline {3.2.3}Mixed access methods}{22}
-\contentsline {subsection}{\numberline {3.2.4}Indexing and configuring flatfile databases}{23}
-\contentsline {subsection}{\numberline {3.2.5}Fine tuning the installation:}{24}
-\contentsline {subsection}{\numberline {3.2.6}Indexing and configuring GCG format databases}{25}
-\contentsline {subsection}{\numberline {3.2.7}Indexing and configuring BLAST databases}{26}
-\contentsline {subsection}{\numberline {3.2.8}Indexing and configuring FASTA databases}{28}
-\contentsline {subsection}{\numberline {3.2.9}Configuring {\sf \bfseries EMBOSS}\ to use SRS for database lookup.}{29}
-\contentsline {subsection}{\numberline {3.2.10}Indexing and configuring other databases}{30}
-\contentsline {section}{\numberline {3.3}Other data}{30}
-\contentsline {subsection}{\numberline {3.3.1}REBASE}{30}
-\contentsline {subsection}{\numberline {3.3.2}TRANSFAC}{31}
-\contentsline {subsection}{\numberline {3.3.3}PROSITE}{31}
-\contentsline {subsection}{\numberline {3.3.4}PRINTS}{31}
-\contentsline {subsection}{\numberline {3.3.5}AAINDEX}{32}
-\contentsline {subsection}{\numberline {3.3.6}CUTG}{32}
-\contentsline {subsection}{\numberline {3.3.7}Miscellaneous data files}{32}
-\contentsline {section}{\numberline {3.4}Default program settings}{32}
-\contentsline {section}{\numberline {3.5}Logging}{33}
-\contentsline {chapter}{\numberline {4}Graphical interfaces to EMBOSS}{35}
-\contentsline {chapter}{\numberline {5}Resources}{36}
-\contentsline {section}{\numberline {5.1}Web sites}{36}
-\contentsline {subsection}{\numberline {5.1.1}Programs}{36}
-\contentsline {subsection}{\numberline {5.1.2}Databases}{36}
-\contentsline {subsection}{\numberline {5.1.3}Other Documentation}{36}
-\contentsline {section}{\numberline {5.2}Maintainance of your {\sf \bfseries EMBOSS}\ installation}{37}
-\contentsline {subsection}{\numberline {5.2.1}Automated installation of {\sf \bfseries EMBOSS}\ and EMBASSY}{37}
-\contentsline {subsection}{\numberline {5.2.2}Automated database updating}{38}
-\contentsline {subsubsection}{Automated update of REBASE}{38}
-\contentsline {chapter}{\numberline {6}GNU Free Documentation License}{40}
-\contentsline {chapter}{\numberline {7}Acknowledgements}{47}
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