From f246d97ce9ddc906801ed22b4e79567dc8914c45 Mon Sep 17 00:00:00 2001 From: martinahansen Date: Thu, 26 Jun 2008 06:11:11 +0000 Subject: [PATCH] restructure git-svn-id: http://biopieces.googlecode.com/svn/trunk@23 74ccb610-7750-0410-82ae-013aeee3265d --- INSTALL | 7 +++ {bp_scripts => bp_bin}/add_ident | 0 {bp_scripts => bp_bin}/align_seq | 0 {bp_scripts => bp_bin}/analyze_bed | 0 {bp_scripts => bp_bin}/analyze_seq | 0 {bp_scripts => bp_bin}/analyze_tags | 0 {bp_scripts => bp_bin}/analyze_vals | 0 {bp_scripts => bp_bin}/blast_seq | 0 {bp_scripts => bp_bin}/blat_seq | 0 {bp_scripts => bp_bin}/calc_bit_scores | 0 {bp_scripts => bp_bin}/complement_seq | 0 {bp_scripts => bp_bin}/complexity_seq | 0 {bp_scripts => bp_bin}/compute | 0 {bp_scripts => bp_bin}/count_records | 0 {bp_scripts => bp_bin}/count_vals | 0 {bp_scripts => bp_bin}/create_blast_db | 0 {bp_scripts => bp_bin}/create_vmatch_index | 0 {bp_scripts => bp_bin}/create_weight_matrix | 0 {bp_scripts => bp_bin}/extract_seq | 0 {bp_scripts => bp_bin}/flip_tab | 0 {bp_scripts => bp_bin}/fold_seq | 0 {bp_scripts => bp_bin}/get_genome_align | 0 {bp_scripts => bp_bin}/get_genome_phastcons | 0 {bp_scripts => bp_bin}/get_genome_seq | 0 {bp_scripts => bp_bin}/grab | 0 {bp_scripts => bp_bin}/head_records | 0 {bp_scripts => bp_bin}/invert_align | 0 {bp_scripts => bp_bin}/length_seq | 0 {bp_scripts => bp_bin}/length_vals | 0 {bp_scripts => bp_bin}/list_biotools | 0 {bp_scripts => bp_bin}/match_seq | 0 {bp_scripts => bp_bin}/max_vals | 0 {bp_scripts => bp_bin}/mean_vals | 0 {bp_scripts => bp_bin}/median_vals | 0 {bp_scripts => bp_bin}/merge_vals | 0 {bp_scripts => bp_bin}/min_vals | 0 {bp_scripts => bp_bin}/oligo_freq | 0 {bp_scripts => bp_bin}/patscan_seq | 0 {bp_scripts => bp_bin}/plot_chrdist | 0 {bp_scripts => bp_bin}/plot_histogram | 0 {bp_scripts => bp_bin}/plot_karyogram | 0 {bp_scripts => bp_bin}/plot_lendist | 0 {bp_scripts => bp_bin}/plot_matches | 0 .../plot_phastcons_profiles | 0 {bp_scripts => bp_bin}/plot_seqlogo | 0 {bp_scripts => bp_bin}/print_usage | 0 {bp_scripts => bp_bin}/random_records | 0 {bp_scripts => bp_bin}/read_2bit | 0 {bp_scripts => bp_bin}/read_align | 0 {bp_scripts => bp_bin}/read_bed | 0 {bp_scripts => bp_bin}/read_blast_tab | 0 {bp_scripts => bp_bin}/read_embl | 0 {bp_scripts => bp_bin}/read_fasta | 0 {bp_scripts => bp_bin}/read_gff | 0 {bp_scripts => bp_bin}/read_mysql | 0 {bp_scripts => bp_bin}/read_phastcons | 0 {bp_scripts => bp_bin}/read_psl | 0 {bp_scripts => bp_bin}/read_soft | 0 {bp_scripts => bp_bin}/read_solexa | 0 {bp_scripts => bp_bin}/read_solid | 0 {bp_scripts => bp_bin}/read_stockholm | 0 {bp_scripts => bp_bin}/read_tab | 0 {bp_scripts => bp_bin}/remove_indels | 0 {bp_scripts => bp_bin}/remove_keys | 0 {bp_scripts => bp_bin}/rename_keys | 0 {bp_scripts => bp_bin}/reverse_seq | 0 {bp_scripts => bp_bin}/shuffle_seq | 0 {bp_scripts => bp_bin}/sort_records | 0 {bp_scripts => bp_bin}/split_bed | 0 {bp_scripts => bp_bin}/split_seq | 0 {bp_scripts => bp_bin}/sum_vals | 0 {bp_scripts => bp_bin}/tile_seq | 0 {bp_scripts => bp_bin}/translate_seq | 0 {bp_scripts => bp_bin}/transliterate_seq | 0 {bp_scripts => bp_bin}/transliterate_vals | 0 {bp_scripts => bp_bin}/uniq_vals | 0 {bp_scripts => bp_bin}/upload_to_ucsc | 0 {bp_scripts => bp_bin}/uppercase_seq | 0 {bp_scripts => bp_bin}/vmatch_seq | 0 {bp_scripts => bp_bin}/write_2bit | 0 {bp_scripts => bp_bin}/write_align | 0 {bp_scripts => bp_bin}/write_bed | 0 {bp_scripts => bp_bin}/write_blast | 0 {bp_scripts => bp_bin}/write_fasta | 0 {bp_scripts => bp_bin}/write_psl | 0 {bp_scripts => bp_bin}/write_solid | 0 {bp_scripts => bp_bin}/write_tab | 0 bp_conf/bashrc | 51 ++++++++++++++----- 88 files changed, 45 insertions(+), 13 deletions(-) rename {bp_scripts => bp_bin}/add_ident (100%) rename {bp_scripts => bp_bin}/align_seq (100%) rename {bp_scripts => bp_bin}/analyze_bed (100%) rename {bp_scripts => bp_bin}/analyze_seq (100%) rename {bp_scripts => bp_bin}/analyze_tags (100%) rename {bp_scripts => bp_bin}/analyze_vals (100%) rename {bp_scripts => bp_bin}/blast_seq (100%) rename {bp_scripts => bp_bin}/blat_seq (100%) rename {bp_scripts => bp_bin}/calc_bit_scores (100%) rename {bp_scripts => bp_bin}/complement_seq (100%) rename {bp_scripts => bp_bin}/complexity_seq (100%) rename {bp_scripts => bp_bin}/compute (100%) rename {bp_scripts => bp_bin}/count_records (100%) rename {bp_scripts => bp_bin}/count_vals (100%) rename {bp_scripts => bp_bin}/create_blast_db (100%) rename {bp_scripts => bp_bin}/create_vmatch_index (100%) rename {bp_scripts => bp_bin}/create_weight_matrix (100%) rename {bp_scripts => bp_bin}/extract_seq (100%) rename {bp_scripts => bp_bin}/flip_tab (100%) rename {bp_scripts => bp_bin}/fold_seq (100%) rename {bp_scripts => bp_bin}/get_genome_align (100%) rename {bp_scripts => bp_bin}/get_genome_phastcons (100%) rename {bp_scripts => bp_bin}/get_genome_seq (100%) rename {bp_scripts => bp_bin}/grab (100%) rename {bp_scripts => bp_bin}/head_records (100%) rename {bp_scripts => bp_bin}/invert_align (100%) rename {bp_scripts => bp_bin}/length_seq (100%) rename {bp_scripts => bp_bin}/length_vals (100%) rename {bp_scripts => bp_bin}/list_biotools (100%) rename {bp_scripts => bp_bin}/match_seq (100%) rename {bp_scripts => bp_bin}/max_vals (100%) rename {bp_scripts => bp_bin}/mean_vals (100%) rename {bp_scripts => bp_bin}/median_vals (100%) rename {bp_scripts => bp_bin}/merge_vals (100%) rename {bp_scripts => bp_bin}/min_vals (100%) rename {bp_scripts => bp_bin}/oligo_freq (100%) rename {bp_scripts => bp_bin}/patscan_seq (100%) rename {bp_scripts => bp_bin}/plot_chrdist (100%) rename {bp_scripts => bp_bin}/plot_histogram (100%) rename {bp_scripts => bp_bin}/plot_karyogram (100%) rename {bp_scripts => bp_bin}/plot_lendist (100%) rename {bp_scripts => bp_bin}/plot_matches (100%) rename {bp_scripts => bp_bin}/plot_phastcons_profiles (100%) rename {bp_scripts => bp_bin}/plot_seqlogo (100%) rename {bp_scripts => bp_bin}/print_usage (100%) rename {bp_scripts => bp_bin}/random_records (100%) rename {bp_scripts => bp_bin}/read_2bit (100%) rename {bp_scripts => bp_bin}/read_align (100%) rename {bp_scripts => bp_bin}/read_bed (100%) rename {bp_scripts => bp_bin}/read_blast_tab (100%) rename {bp_scripts => bp_bin}/read_embl (100%) rename {bp_scripts => bp_bin}/read_fasta (100%) rename {bp_scripts => bp_bin}/read_gff (100%) rename {bp_scripts => bp_bin}/read_mysql (100%) rename {bp_scripts => bp_bin}/read_phastcons (100%) rename {bp_scripts => bp_bin}/read_psl (100%) rename {bp_scripts => bp_bin}/read_soft (100%) rename {bp_scripts => bp_bin}/read_solexa (100%) rename {bp_scripts => bp_bin}/read_solid (100%) rename {bp_scripts => bp_bin}/read_stockholm (100%) rename {bp_scripts => bp_bin}/read_tab (100%) rename {bp_scripts => bp_bin}/remove_indels (100%) rename {bp_scripts => bp_bin}/remove_keys (100%) rename {bp_scripts => bp_bin}/rename_keys (100%) rename {bp_scripts => bp_bin}/reverse_seq (100%) rename {bp_scripts => bp_bin}/shuffle_seq (100%) rename {bp_scripts => bp_bin}/sort_records (100%) rename {bp_scripts => bp_bin}/split_bed (100%) rename {bp_scripts => bp_bin}/split_seq (100%) rename {bp_scripts => bp_bin}/sum_vals (100%) rename {bp_scripts => bp_bin}/tile_seq (100%) rename {bp_scripts => bp_bin}/translate_seq (100%) rename {bp_scripts => bp_bin}/transliterate_seq (100%) rename {bp_scripts => bp_bin}/transliterate_vals (100%) rename {bp_scripts => bp_bin}/uniq_vals (100%) rename {bp_scripts => bp_bin}/upload_to_ucsc (100%) rename {bp_scripts => bp_bin}/uppercase_seq (100%) rename {bp_scripts => bp_bin}/vmatch_seq (100%) rename {bp_scripts => bp_bin}/write_2bit (100%) rename {bp_scripts => bp_bin}/write_align (100%) rename {bp_scripts => bp_bin}/write_bed (100%) rename {bp_scripts => bp_bin}/write_blast (100%) rename {bp_scripts => bp_bin}/write_fasta (100%) rename {bp_scripts => bp_bin}/write_psl (100%) rename {bp_scripts => bp_bin}/write_solid (100%) rename {bp_scripts => bp_bin}/write_tab (100%) diff --git a/INSTALL b/INSTALL index e69de29..0c9e09a 100644 --- a/INSTALL +++ b/INSTALL @@ -0,0 +1,7 @@ +Find installation instructions online at: + +http://code.google.com/p/biopieces/wiki/Installation + + + +Martin A. Hansen, June 2008 diff --git a/bp_scripts/add_ident b/bp_bin/add_ident similarity index 100% rename from bp_scripts/add_ident rename to bp_bin/add_ident diff --git a/bp_scripts/align_seq b/bp_bin/align_seq similarity index 100% rename from bp_scripts/align_seq rename to bp_bin/align_seq diff --git a/bp_scripts/analyze_bed b/bp_bin/analyze_bed similarity index 100% rename from bp_scripts/analyze_bed rename to bp_bin/analyze_bed diff --git a/bp_scripts/analyze_seq b/bp_bin/analyze_seq similarity index 100% rename from bp_scripts/analyze_seq rename to bp_bin/analyze_seq diff --git a/bp_scripts/analyze_tags b/bp_bin/analyze_tags similarity index 100% rename from bp_scripts/analyze_tags rename to bp_bin/analyze_tags diff --git a/bp_scripts/analyze_vals b/bp_bin/analyze_vals similarity index 100% rename from bp_scripts/analyze_vals rename to bp_bin/analyze_vals diff --git a/bp_scripts/blast_seq b/bp_bin/blast_seq similarity index 100% rename from bp_scripts/blast_seq rename to bp_bin/blast_seq diff --git a/bp_scripts/blat_seq b/bp_bin/blat_seq similarity index 100% rename from bp_scripts/blat_seq rename to bp_bin/blat_seq diff --git a/bp_scripts/calc_bit_scores b/bp_bin/calc_bit_scores similarity index 100% rename from bp_scripts/calc_bit_scores rename to bp_bin/calc_bit_scores diff --git a/bp_scripts/complement_seq b/bp_bin/complement_seq similarity index 100% rename from bp_scripts/complement_seq rename to bp_bin/complement_seq diff --git a/bp_scripts/complexity_seq b/bp_bin/complexity_seq similarity index 100% rename from bp_scripts/complexity_seq rename to bp_bin/complexity_seq diff --git a/bp_scripts/compute b/bp_bin/compute similarity index 100% rename from bp_scripts/compute rename to bp_bin/compute diff --git a/bp_scripts/count_records b/bp_bin/count_records similarity index 100% rename from bp_scripts/count_records rename to bp_bin/count_records diff --git a/bp_scripts/count_vals b/bp_bin/count_vals similarity index 100% rename from bp_scripts/count_vals rename to bp_bin/count_vals diff --git a/bp_scripts/create_blast_db b/bp_bin/create_blast_db similarity index 100% rename from bp_scripts/create_blast_db rename to bp_bin/create_blast_db diff --git a/bp_scripts/create_vmatch_index b/bp_bin/create_vmatch_index similarity index 100% rename from bp_scripts/create_vmatch_index rename to bp_bin/create_vmatch_index diff --git a/bp_scripts/create_weight_matrix b/bp_bin/create_weight_matrix similarity index 100% rename from bp_scripts/create_weight_matrix rename to bp_bin/create_weight_matrix diff --git a/bp_scripts/extract_seq b/bp_bin/extract_seq similarity index 100% rename from bp_scripts/extract_seq rename to bp_bin/extract_seq diff --git a/bp_scripts/flip_tab b/bp_bin/flip_tab similarity index 100% rename from bp_scripts/flip_tab rename to bp_bin/flip_tab diff --git a/bp_scripts/fold_seq b/bp_bin/fold_seq similarity index 100% rename from bp_scripts/fold_seq rename to bp_bin/fold_seq diff --git a/bp_scripts/get_genome_align b/bp_bin/get_genome_align similarity index 100% rename from bp_scripts/get_genome_align rename to bp_bin/get_genome_align diff --git a/bp_scripts/get_genome_phastcons b/bp_bin/get_genome_phastcons similarity index 100% rename from bp_scripts/get_genome_phastcons rename to bp_bin/get_genome_phastcons diff --git a/bp_scripts/get_genome_seq b/bp_bin/get_genome_seq similarity index 100% rename from bp_scripts/get_genome_seq rename to bp_bin/get_genome_seq diff --git a/bp_scripts/grab b/bp_bin/grab similarity index 100% rename from bp_scripts/grab rename to bp_bin/grab diff --git a/bp_scripts/head_records b/bp_bin/head_records similarity index 100% rename from bp_scripts/head_records rename to bp_bin/head_records diff --git a/bp_scripts/invert_align b/bp_bin/invert_align similarity index 100% rename from bp_scripts/invert_align rename to bp_bin/invert_align diff --git a/bp_scripts/length_seq b/bp_bin/length_seq similarity index 100% rename from bp_scripts/length_seq rename to bp_bin/length_seq diff --git a/bp_scripts/length_vals b/bp_bin/length_vals similarity index 100% rename from bp_scripts/length_vals rename to bp_bin/length_vals diff --git a/bp_scripts/list_biotools b/bp_bin/list_biotools similarity index 100% rename from bp_scripts/list_biotools rename to bp_bin/list_biotools diff --git a/bp_scripts/match_seq b/bp_bin/match_seq similarity index 100% rename from bp_scripts/match_seq rename to bp_bin/match_seq diff --git a/bp_scripts/max_vals b/bp_bin/max_vals similarity index 100% rename from bp_scripts/max_vals rename to bp_bin/max_vals diff --git a/bp_scripts/mean_vals b/bp_bin/mean_vals similarity index 100% rename from bp_scripts/mean_vals rename to bp_bin/mean_vals diff --git a/bp_scripts/median_vals b/bp_bin/median_vals similarity index 100% rename from bp_scripts/median_vals rename to bp_bin/median_vals diff --git a/bp_scripts/merge_vals b/bp_bin/merge_vals similarity index 100% rename from bp_scripts/merge_vals rename to bp_bin/merge_vals diff --git a/bp_scripts/min_vals b/bp_bin/min_vals similarity index 100% rename from bp_scripts/min_vals rename to bp_bin/min_vals diff --git a/bp_scripts/oligo_freq b/bp_bin/oligo_freq similarity index 100% rename from bp_scripts/oligo_freq rename to bp_bin/oligo_freq diff --git a/bp_scripts/patscan_seq b/bp_bin/patscan_seq similarity index 100% rename from bp_scripts/patscan_seq rename to bp_bin/patscan_seq diff --git a/bp_scripts/plot_chrdist b/bp_bin/plot_chrdist similarity index 100% rename from bp_scripts/plot_chrdist rename to bp_bin/plot_chrdist diff --git a/bp_scripts/plot_histogram b/bp_bin/plot_histogram similarity index 100% rename from bp_scripts/plot_histogram rename to bp_bin/plot_histogram diff --git a/bp_scripts/plot_karyogram b/bp_bin/plot_karyogram similarity index 100% rename from bp_scripts/plot_karyogram rename to bp_bin/plot_karyogram diff --git a/bp_scripts/plot_lendist b/bp_bin/plot_lendist similarity index 100% rename from bp_scripts/plot_lendist rename to bp_bin/plot_lendist diff --git a/bp_scripts/plot_matches b/bp_bin/plot_matches similarity index 100% rename from bp_scripts/plot_matches rename to bp_bin/plot_matches diff --git a/bp_scripts/plot_phastcons_profiles b/bp_bin/plot_phastcons_profiles similarity index 100% rename from bp_scripts/plot_phastcons_profiles rename to bp_bin/plot_phastcons_profiles diff --git a/bp_scripts/plot_seqlogo b/bp_bin/plot_seqlogo similarity index 100% rename from bp_scripts/plot_seqlogo rename to bp_bin/plot_seqlogo diff --git a/bp_scripts/print_usage b/bp_bin/print_usage similarity index 100% rename from bp_scripts/print_usage rename to bp_bin/print_usage diff --git a/bp_scripts/random_records b/bp_bin/random_records similarity index 100% rename from bp_scripts/random_records rename to bp_bin/random_records diff --git a/bp_scripts/read_2bit b/bp_bin/read_2bit similarity index 100% rename from bp_scripts/read_2bit rename to bp_bin/read_2bit diff --git a/bp_scripts/read_align b/bp_bin/read_align similarity index 100% rename from bp_scripts/read_align rename to bp_bin/read_align diff --git a/bp_scripts/read_bed b/bp_bin/read_bed similarity index 100% rename from bp_scripts/read_bed rename to bp_bin/read_bed diff --git a/bp_scripts/read_blast_tab b/bp_bin/read_blast_tab similarity index 100% rename from bp_scripts/read_blast_tab rename to bp_bin/read_blast_tab diff --git a/bp_scripts/read_embl b/bp_bin/read_embl similarity index 100% rename from bp_scripts/read_embl rename to bp_bin/read_embl diff --git a/bp_scripts/read_fasta b/bp_bin/read_fasta similarity index 100% rename from bp_scripts/read_fasta rename to bp_bin/read_fasta diff --git a/bp_scripts/read_gff b/bp_bin/read_gff similarity index 100% rename from bp_scripts/read_gff rename to bp_bin/read_gff diff --git a/bp_scripts/read_mysql b/bp_bin/read_mysql similarity index 100% rename from bp_scripts/read_mysql rename to bp_bin/read_mysql diff --git a/bp_scripts/read_phastcons b/bp_bin/read_phastcons similarity index 100% rename from bp_scripts/read_phastcons rename to bp_bin/read_phastcons diff --git a/bp_scripts/read_psl b/bp_bin/read_psl similarity index 100% rename from bp_scripts/read_psl rename to bp_bin/read_psl diff --git a/bp_scripts/read_soft b/bp_bin/read_soft similarity index 100% rename from bp_scripts/read_soft rename to bp_bin/read_soft diff --git a/bp_scripts/read_solexa b/bp_bin/read_solexa similarity index 100% rename from bp_scripts/read_solexa rename to bp_bin/read_solexa diff --git a/bp_scripts/read_solid b/bp_bin/read_solid similarity index 100% rename from bp_scripts/read_solid rename to bp_bin/read_solid diff --git a/bp_scripts/read_stockholm b/bp_bin/read_stockholm similarity index 100% rename from bp_scripts/read_stockholm rename to bp_bin/read_stockholm diff --git a/bp_scripts/read_tab b/bp_bin/read_tab similarity index 100% rename from bp_scripts/read_tab rename to bp_bin/read_tab diff --git a/bp_scripts/remove_indels b/bp_bin/remove_indels similarity index 100% rename from bp_scripts/remove_indels rename to bp_bin/remove_indels diff --git a/bp_scripts/remove_keys b/bp_bin/remove_keys similarity index 100% rename from bp_scripts/remove_keys rename to bp_bin/remove_keys diff --git a/bp_scripts/rename_keys b/bp_bin/rename_keys similarity index 100% rename from bp_scripts/rename_keys rename to bp_bin/rename_keys diff --git a/bp_scripts/reverse_seq b/bp_bin/reverse_seq similarity index 100% rename from bp_scripts/reverse_seq rename to bp_bin/reverse_seq diff --git a/bp_scripts/shuffle_seq b/bp_bin/shuffle_seq similarity index 100% rename from bp_scripts/shuffle_seq rename to bp_bin/shuffle_seq diff --git a/bp_scripts/sort_records b/bp_bin/sort_records similarity index 100% rename from bp_scripts/sort_records rename to bp_bin/sort_records diff --git a/bp_scripts/split_bed b/bp_bin/split_bed similarity index 100% rename from bp_scripts/split_bed rename to bp_bin/split_bed diff --git a/bp_scripts/split_seq b/bp_bin/split_seq similarity index 100% rename from bp_scripts/split_seq rename to bp_bin/split_seq diff --git a/bp_scripts/sum_vals b/bp_bin/sum_vals similarity index 100% rename from bp_scripts/sum_vals rename to bp_bin/sum_vals diff --git a/bp_scripts/tile_seq b/bp_bin/tile_seq similarity index 100% rename from bp_scripts/tile_seq rename to bp_bin/tile_seq diff --git a/bp_scripts/translate_seq b/bp_bin/translate_seq similarity index 100% rename from bp_scripts/translate_seq rename to bp_bin/translate_seq diff --git a/bp_scripts/transliterate_seq b/bp_bin/transliterate_seq similarity index 100% rename from bp_scripts/transliterate_seq rename to bp_bin/transliterate_seq diff --git a/bp_scripts/transliterate_vals b/bp_bin/transliterate_vals similarity index 100% rename from bp_scripts/transliterate_vals rename to bp_bin/transliterate_vals diff --git a/bp_scripts/uniq_vals b/bp_bin/uniq_vals similarity index 100% rename from bp_scripts/uniq_vals rename to bp_bin/uniq_vals diff --git a/bp_scripts/upload_to_ucsc b/bp_bin/upload_to_ucsc similarity index 100% rename from bp_scripts/upload_to_ucsc rename to bp_bin/upload_to_ucsc diff --git a/bp_scripts/uppercase_seq b/bp_bin/uppercase_seq similarity index 100% rename from bp_scripts/uppercase_seq rename to bp_bin/uppercase_seq diff --git a/bp_scripts/vmatch_seq b/bp_bin/vmatch_seq similarity index 100% rename from bp_scripts/vmatch_seq rename to bp_bin/vmatch_seq diff --git a/bp_scripts/write_2bit b/bp_bin/write_2bit similarity index 100% rename from bp_scripts/write_2bit rename to bp_bin/write_2bit diff --git a/bp_scripts/write_align b/bp_bin/write_align similarity index 100% rename from bp_scripts/write_align rename to bp_bin/write_align diff --git a/bp_scripts/write_bed b/bp_bin/write_bed similarity index 100% rename from bp_scripts/write_bed rename to bp_bin/write_bed diff --git a/bp_scripts/write_blast b/bp_bin/write_blast similarity index 100% rename from bp_scripts/write_blast rename to bp_bin/write_blast diff --git a/bp_scripts/write_fasta b/bp_bin/write_fasta similarity index 100% rename from bp_scripts/write_fasta rename to bp_bin/write_fasta diff --git a/bp_scripts/write_psl b/bp_bin/write_psl similarity index 100% rename from bp_scripts/write_psl rename to bp_bin/write_psl diff --git a/bp_scripts/write_solid b/bp_bin/write_solid similarity index 100% rename from bp_scripts/write_solid rename to bp_bin/write_solid diff --git a/bp_scripts/write_tab b/bp_bin/write_tab similarity index 100% rename from bp_scripts/write_tab rename to bp_bin/write_tab diff --git a/bp_conf/bashrc b/bp_conf/bashrc index 60b0b78..0a57f06 100644 --- 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/" # 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 -- 2.39.5