fixed seq qual length check

[biopieces.git] / bp_conf / bashrc

diff --git a/bp_conf/bashrc b/bp_conf/bashrc
index 0a57f06eaea9e2646bafd443cbaf7b8d20cd9bac..ac5ace41d921a049878be187f38a775f27d383da 100644 (file)
--- a/bp_conf/bashrc
+++ b/bp_conf/bashrc
@@ -1,44 +1,43 @@
 ### >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
-### Stuff that enables biopieces.
+### DO NOT MAKE ANY CHANGES
 
-### Initially we need to configure the directories where biopieces are installed
-### and where the data (genomes and indexes) that the biopieces work on are installed.
-### Allso, it is possible to change the temporary directory from the system's tmp.
-
-export BP_DIR="/Users/m.hansen/biopieces"         # Directory where biopieces are installed
-export BP_DATA="/Users/m.hansen/bio_piece_data"   # Contains genomic data etc.
-export BP_TMP="/tmp"                              # Required temporary directory.
+### 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
 
 ### The below bin directory should hold biopiece executables - regardsles of programming language.
 
 export BP_BIN="$BP_DIR/bp_bin"              # Directory with biopiece executables.
 
-
 ### The following directories hold the biopiece libraries, modules, gems, etc - one per programming language.
 
-export BP_PERL="$BP_DIR/code_perl"          # Direcotry with Perl code.
-export BP_C="$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.
+export BP_PERL="$BP_DIR/code_perl"          # Direcotory with Perl code.
+export BP_C="$BP_DIR/code_c"                # Direcotory with C code.
+export BP_PYTHON="$BP_DIR/code_python"      # Direcotory with Pyton code.
+export BP_RUBY="$BP_DIR/code_ruby"          # Direcotory with Ruby code.
+
+### This is the directory with the document root fro the Biopieces Genome Browser:
 
+export BP_WWW="$BP_DIR/www"                 # Direcotory with Biopieces Genome Browser.
 
-### For the Perl modules they may be contributed by different developers, so we define a variable for each.
+### Here we add the biopiece variable to the existing PATH.
 
-export BP_PERL_LIBS="$BP_PERL/Maasha"                 # Perl modules from the developer Maasha.
-# export BP_PERL_LIBS="$BP_PERL_LIBS:$BP_PERL/<new>"  # Perl modules from a new developer.
+export PATH="$PATH:$BP_BIN"
 
+### Here we add the Biopieces Perl modules to PERL5LIB.
 
-### Here we add the biopiece variable to the existing PATH and PERL5LIB variables.
+export PERL5LIB="$PERL5LIB:$BP_PERL"
 
-export PATH="$PATH:$BP_BIN"  
-export PERL5LIB="$PERL5LIB:$BP_PERL_LIBS"
+### Here we add the Biopieces Ruby libraries to RUBYLIB.
 
-### Alias allowing power scripting with biopieces.
+export RUBYLIB="$RUBYLIB:$BP_RUBY/lib"
 
-alias bioscript="perl -MMaasha::Biopieces=read_stream,get_record,put_record -e"
+### Some useful aliases.
 
+alias bp_update="svn update $BP_DIR && svn update $BP_DIR/bp_usage"
+alias bp_test="$BP_DIR/bp_test/test_all"
 
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