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3 ### Stuff that enables biopieces.
5 ### Initially we need to configure the directories where biopieces are installed
6 ### and where the data (genomes and indexes) that the biopieces work on are installed.
7 ### Allso, it is possible to change the temporary directory from the system's tmp.
9 export BP_DIR="/Users/m.hansen/biopieces" # Directory where biopieces are installed
10 export BP_DATA="/Users/m.hansen/BP_DATA" # Contains genomic data etc.
11 export BP_TMP="/tmp" # Required temporary directory.
14 ### The below bin directory should hold biopiece executables - regardsles of programming language.
16 export BP_BIN="$BP_DIR/bp_bin" # Directory with biopiece executables.
18 ### The following directories hold the biopiece libraries, modules, gems, etc - one per programming language.
20 export BP_PERL="$BP_DIR/code_perl" # Direcotry with Perl code.
21 export BP_C="$BP_DIR/code_c" # Direcotry with c code.
22 export BP_PYTHON="$BP_DIR/code_python" # Direcotry with Pyton code.
23 export BP_RUBY="$BP_DIR/code_ruby" # Direcotry with Ruby code.
26 ### Here we add the biopiece variable to the existing PATH and PERL5LIB variables.
28 export PATH="$PATH:$BP_BIN"
29 export PERL5LIB="$PERL5LIB:$BP_PERL"
31 ### Alias allowing power scripting with biopieces.
33 alias bioscript="perl -MMaasha::Biopieces=read_stream,get_record,put_record -e"
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39 ### Martin A. Hansen, June 2008