restructure

[biopieces.git] / bp_conf / bashrc

diff --git a/bp_conf/bashrc b/bp_conf/bashrc
index 60b0b789f2f6e7b6ebbb43a29cc88725f7a4fe1c..0a57f06eaea9e2646bafd443cbaf7b8d20cd9bac 100644 (file)
--- a/bp_conf/bashrc
+++ b/bp_conf/bashrc
@@ -1,21 +1,46 @@
-# >>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<
+### >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
+### Stuff that enables biopieces.
 
-# Stuff that enables biotools.
+### 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 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
+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.
 
-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"
 
-# Alias allowing power scripting with biotools
+### The below bin directory should hold biopiece executables - regardsles of programming language.
 
-alias bioscript="perl -MMaasha::Biotools=read_stream,get_record,put_record -e"
+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.
+
+
+### For the Perl modules they may be contributed by different developers, so we define a variable for each.
+
+export BP_PERL_LIBS="$BP_PERL/Maasha"                 # Perl modules from the developer Maasha.
+# export BP_PERL_LIBS="$BP_PERL_LIBS:$BP_PERL/<new>"  # Perl modules from a new developer.
+
+
+### Here we add the biopiece variable to the existing PATH and PERL5LIB variables.
+
+export PATH="$PATH:$BP_BIN"  
+export PERL5LIB="$PERL5LIB:$BP_PERL_LIBS"
+
+### Alias allowing power scripting with biopieces.
+
+alias bioscript="perl -MMaasha::Biopieces=read_stream,get_record,put_record -e"
+
+
+### >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+### Martin A. Hansen, June 2008