From: martinahansen Date: Tue, 18 Nov 2008 04:01:34 +0000 (+0000) Subject: doc update X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;ds=sidebyside;h=7206222cb61a19d359faf21818557300e5ebc0e6;p=biopieces.git doc update git-svn-id: http://biopieces.googlecode.com/svn/trunk@317 74ccb610-7750-0410-82ae-013aeee3265d --- diff --git a/bp_conf/bashrc b/bp_conf/bashrc index 06563c6..473e0c5 100644 --- a/bp_conf/bashrc +++ b/bp_conf/bashrc @@ -1,6 +1,6 @@ ### >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< -### Stuff that enables biopieces. +### Stuff that enables Biopieces. ### BP_DIR, BP_DATA, BP_TMP, and BP_LOG should all be set in ~/.bashrc ### see http://code.google.com/p/biopieces/wiki/Installation @@ -16,11 +16,18 @@ export BP_C="$BP_DIR/code_c" # Direcotry with c code. export BP_PYTHON="$BP_DIR/code_python" # Direcotry with Pyton code. export BP_RUBY="$BP_DIR/code_ruby" # Direcotry with Ruby code. -### Here we add the biopiece variable to the existing PATH and PERL5LIB variables. +### Here we add the biopiece variable to the existing PATH. + +export PATH="$PATH:$BP_BIN" + +### Here we add the Biopieces Perl modules to PERL5LIB. -export PATH="$PATH:$BP_BIN" export PERL5LIB="$PERL5LIB:$BP_PERL" +### Here we add the Biopieces Ruby libraries to RUBYLIB. + +export RUBYLIB="$RUBYLIB:$BP_RUBY" + ### Alias allowing power scripting with biopieces. alias bioscript="perl -MMaasha::Biopieces=read_stream,get_record,put_record -e" diff --git a/bp_doc/dotplot.pdf b/bp_doc/dotplot.pdf index 377e3eb..ba921d5 100644 Binary files a/bp_doc/dotplot.pdf and b/bp_doc/dotplot.pdf differ diff --git a/bp_doc/dotplot.ps b/bp_doc/dotplot.ps index 7118d05..c77b14c 100644 --- a/bp_doc/dotplot.ps +++ b/bp_doc/dotplot.ps @@ -1,6 +1,6 @@ %!PS-Adobe-2.0 %%Creator: gnuplot 4.2 patchlevel 0 -%%CreationDate: Mon Sep 3 10:34:33 2007 +%%CreationDate: Thu Nov 13 17:03:30 2008 %%DocumentFonts: (atend) %%BoundingBox: 50 50 554 770 %%Orientation: Landscape @@ -49,7 +49,7 @@ SDict begin [ /Author (Martin Hansen) % /Producer (gnuplot) % /Keywords () - /CreationDate (Mon Sep 3 10:34:33 2007) + /CreationDate (Thu Nov 13 17:03:30 2008) /DOCINFO pdfmark end } ifelse @@ -743,12 +743,12 @@ Z stroke LCb setrgbcolor 140 2551 M currentpoint gsave translate 90 rotate 0 0 M -(gi|6626253|gb|AE000511.1|_Helicobacter_pylori_26695,_complete_genome) Cshow +(Helicobacter_pylori_26695) Cshow grestore LTb LCb setrgbcolor 4037 70 M -(gi|12057207|gb|AE001439.1|_Helicobacter_pylori_J99,_complete_genome ) Cshow +(Helicobacter_pylori_J99 ) Cshow LTb 4037 4830 M (plot_matches) Cshow diff --git a/bp_doc/seqlogo.svg b/bp_doc/seqlogo.svg index 4453a4c..9f2d94a 100644 --- a/bp_doc/seqlogo.svg +++ b/bp_doc/seqlogo.svg @@ -1,938 +1,334 @@ - - A - - - - . - - - - G - - - - U - - - - A - - - - C - - - - . - - - - G - - - - U - - - - . - - - - G - - - - C - - - - U - - - - A - - - - . - - - - U - - - - C - - - - A - - - - . - - - - G - - - - . - - - - G - - - - A - - - - A - - - - . - - - - G - - - - . - - - - G - - - - C - - - - A - - - - G - - - - < - - - - U - - - 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