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 06563c6d2d86ee4ff66323d8aec9f1cd2ad49dfa..473e0c5fc8e03023252c29371286bd877c74acd0 100644 (file)
--- 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 377e3eb4c795b691b4a4d60f8237ddafc628fdc3..ba921d5f123195f7dd3d480e5dfe1bf340d4d085 100644 (file)
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 7118d0548163d59598a58752b857f86627acec7e..c77b14c0d1c7f2381e66f0181f058119934f5b64 100644 (file)
--- 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 4453a4cbaa2e1d9b5abd4cbe140900841f8f6db4..9f2d94af13b0752d1fec31b8ea190d21d97fcc37 100644 (file)
--- a/bp_doc/seqlogo.svg
+++ b/bp_doc/seqlogo.svg
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