fixed seq qual length check

[biopieces.git] / bp_conf / bashrc

diff --git a/bp_conf/bashrc b/bp_conf/bashrc
index 60b0b789f2f6e7b6ebbb43a29cc88725f7a4fe1c..ac5ace41d921a049878be187f38a775f27d383da 100644 (file)
--- a/bp_conf/bashrc
+++ b/bp_conf/bashrc
@@ -1,21 +1,45 @@
-# >>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<
+### >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
+### DO NOT MAKE ANY CHANGES
 
-# Stuff that enables biotools.
+### Stuff that enables Biopieces.
 
-export TOOLS_DIR="/Users/m.hansen/tools"      # Contains binaries for BLAST and Vmatch.
-export  INST_DIR="/Users/m.hansen/maasha"     # Contains scripts and modules.
-export  DATA_DIR="/Users/m.hansen/DATA"       # Contains genomic data etc.
-export   TMP_DIR="/Users/m.hansen/maasha/tmp" # Required temporary directory.
-export   LOG_DIR="/Users/m.hansen/maasha/log" # Log directory
+### BP_DIR, BP_DATA, BP_TMP, and BP_LOG should all be set in ~/.bashrc
+### see http://code.google.com/p/biopieces/wiki/Installation
 
-export     PATH="$PATH:$TOOLS_DIR/blast-2.2.17/bin:$TOOLS_DIR/vmatch.distribution"
-export     PATH="$INST_DIR/bin/:$INST_DIR/perl/bin:$INST_DIR/perl_scripts/:$INST_DIR/biotools:$PATH"  
-export PERL5LIB="$PERL5LIB:$INST_DIR/perl_modules"
+### The below bin directory should hold biopiece executables - regardsles of programming language.
 
-# Alias allowing power scripting with biotools
+export BP_BIN="$BP_DIR/bp_bin"              # Directory with biopiece executables.
 
-alias bioscript="perl -MMaasha::Biotools=read_stream,get_record,put_record -e"
+### The following directories hold the biopiece libraries, modules, gems, etc - one per programming language.
 
+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="$BP_DIR/www"                 # Direcotory with Biopieces Genome Browser.
+
+### Here we add the biopiece variable to the existing PATH.
+
+export PATH="$PATH:$BP_BIN"
+
+### Here we add the Biopieces Perl modules to PERL5LIB.
+
+export PERL5LIB="$PERL5LIB:$BP_PERL"
+
+### Here we add the Biopieces Ruby libraries to RUBYLIB.
+
+export RUBYLIB="$RUBYLIB:$BP_RUBY/lib"
+
+### 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"
+
+### >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+### Martin A. Hansen, June 2008