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-### 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.
-### 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"
-### Alias allowing power scripting with biopieces.
+### Here we add the Biopieces Ruby libraries to RUBYLIB.
+
+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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