moved all binaries and created symlinks instead

git-svn-id: http://biopieces.googlecode.com/svn/trunk@373 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/00README b/bp_bin/00README
index 49d4a8441783704286f1ae9759cd508f421ed09c..5991f9bd383a84cac3873d256d27e59d7720f263 100644 (file)
--- a/bp_bin/00README
+++ b/bp_bin/00README
@@ -1,4 +1,4 @@
-This directory should only contain biopiece executables.
+This directory should only contain symlinks to Biopiece executables.
 
 
 

diff --git a/bp_bin/add_ident b/bp_bin/add_ident
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/add_ident
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/add_ident b/bp_bin/add_ident
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..f5577548abf4ab72bd7d983e77b640f3a2323296
--- /dev/null
+++ b/bp_bin/add_ident
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/add_ident
\ No newline at end of file

diff --git a/bp_bin/align_seq b/bp_bin/align_seq
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/align_seq
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/align_seq b/bp_bin/align_seq
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..000079606e403290e6e879f9cfe55f6407fbeada
--- /dev/null
+++ b/bp_bin/align_seq
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/align_seq
\ No newline at end of file

diff --git a/bp_bin/analyze_bed b/bp_bin/analyze_bed
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/analyze_bed
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/analyze_bed b/bp_bin/analyze_bed
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..6f0d8ca46f3e459bad801350f607c2fc0cc43d56
--- /dev/null
+++ b/bp_bin/analyze_bed
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/analyze_bed
\ No newline at end of file

diff --git a/bp_bin/analyze_seq b/bp_bin/analyze_seq
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/analyze_seq
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/analyze_seq b/bp_bin/analyze_seq
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..ac17cf2fa4271400f3de43e8b3fc3a978af2d509
--- /dev/null
+++ b/bp_bin/analyze_seq
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/analyze_seq
\ No newline at end of file

diff --git a/bp_bin/analyze_tags b/bp_bin/analyze_tags
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/analyze_tags
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/analyze_tags b/bp_bin/analyze_tags
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..3cb9f03bd880aec76488e7147b14bb58a774e293
--- /dev/null
+++ b/bp_bin/analyze_tags
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/analyze_tags
\ No newline at end of file

diff --git a/bp_bin/analyze_vals b/bp_bin/analyze_vals
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/analyze_vals
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/analyze_vals b/bp_bin/analyze_vals
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..c25d2e8b9dd393bca05f4b4152ed693895250637
--- /dev/null
+++ b/bp_bin/analyze_vals
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/analyze_vals
\ No newline at end of file

diff --git a/bp_bin/assemble_tag_contigs b/bp_bin/assemble_tag_contigs
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/assemble_tag_contigs
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/assemble_tag_contigs b/bp_bin/assemble_tag_contigs
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..23527921556dbee9a7100336e3086523d965b795
--- /dev/null
+++ b/bp_bin/assemble_tag_contigs
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/assemble_tag_contigs
\ No newline at end of file

diff --git a/bp_bin/blast_seq b/bp_bin/blast_seq
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/blast_seq
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/blast_seq b/bp_bin/blast_seq
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..27d57adddbd80540d5a684d859de69a8d8a24c72
--- /dev/null
+++ b/bp_bin/blast_seq
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/blast_seq
\ No newline at end of file

diff --git a/bp_bin/blat_seq b/bp_bin/blat_seq
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/blat_seq
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/blat_seq b/bp_bin/blat_seq
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..eb77e305a4416e7b8c352bd9256603eb4381908f
--- /dev/null
+++ b/bp_bin/blat_seq
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/blat_seq
\ No newline at end of file

diff --git a/bp_bin/calc_bit_scores b/bp_bin/calc_bit_scores
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/calc_bit_scores
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/calc_bit_scores b/bp_bin/calc_bit_scores
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..7105a3a49afd127b66c971246469eb57ef1acf77
--- /dev/null
+++ b/bp_bin/calc_bit_scores
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/calc_bit_scores
\ No newline at end of file

diff --git a/bp_bin/calc_fixedstep b/bp_bin/calc_fixedstep
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/calc_fixedstep
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/calc_fixedstep b/bp_bin/calc_fixedstep
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..b177a7551695886fbc6c49f75d6c88a253db703d
--- /dev/null
+++ b/bp_bin/calc_fixedstep
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/calc_fixedstep
\ No newline at end of file

diff --git a/bp_bin/complement_seq b/bp_bin/complement_seq
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/complement_seq
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/complement_seq b/bp_bin/complement_seq
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..c45e684c093f49d9cb1159f392a58cb3453ea27c
--- /dev/null
+++ b/bp_bin/complement_seq
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/complement_seq
\ No newline at end of file

diff --git a/bp_bin/complexity_seq b/bp_bin/complexity_seq
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/complexity_seq
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/complexity_seq b/bp_bin/complexity_seq
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..e67a447f39e7bc265070671600c30873b61a60c0
--- /dev/null
+++ b/bp_bin/complexity_seq
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/complexity_seq
\ No newline at end of file

diff --git a/bp_bin/compute b/bp_bin/compute
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/compute
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/compute b/bp_bin/compute
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..073fa409b1a11c5e8ca31717e98bde8dedb6102c
--- /dev/null
+++ b/bp_bin/compute
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/compute
\ No newline at end of file

diff --git a/bp_bin/count_records b/bp_bin/count_records
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/count_records
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/count_records b/bp_bin/count_records
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..ba524a8524af546796476e1b5281964a83c1c82a
--- /dev/null
+++ b/bp_bin/count_records
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/count_records
\ No newline at end of file

diff --git a/bp_bin/count_vals b/bp_bin/count_vals
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/count_vals
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/count_vals b/bp_bin/count_vals
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..25740945baa0246495d69221796921917bbdb262
--- /dev/null
+++ b/bp_bin/count_vals
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/count_vals
\ No newline at end of file

diff --git a/bp_bin/create_blast_db b/bp_bin/create_blast_db
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/create_blast_db
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/create_blast_db b/bp_bin/create_blast_db
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..f7b963758b0a280b229feca663c86af084048c2f
--- /dev/null
+++ b/bp_bin/create_blast_db
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/create_blast_db
\ No newline at end of file

diff --git a/bp_bin/create_vmatch_index b/bp_bin/create_vmatch_index
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/create_vmatch_index
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/create_vmatch_index b/bp_bin/create_vmatch_index
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..6590fad08cc8136b7d561b57ffd0f742856bae02
--- /dev/null
+++ b/bp_bin/create_vmatch_index
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/create_vmatch_index
\ No newline at end of file

diff --git a/bp_bin/create_weight_matrix b/bp_bin/create_weight_matrix
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/create_weight_matrix
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/create_weight_matrix b/bp_bin/create_weight_matrix
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..17345c64c197ef680131af5dea2b4016a6b969cf
--- /dev/null
+++ b/bp_bin/create_weight_matrix
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/create_weight_matrix
\ No newline at end of file

diff --git a/bp_bin/extract_seq b/bp_bin/extract_seq
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/extract_seq
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/extract_seq b/bp_bin/extract_seq
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..bd5293f8a57f124e5d2d495bab23d1ed1d75b6ee
--- /dev/null
+++ b/bp_bin/extract_seq
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/extract_seq
\ No newline at end of file

diff --git a/bp_bin/flip_tab b/bp_bin/flip_tab
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/flip_tab
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/flip_tab b/bp_bin/flip_tab
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..2703aa57efcb0ef0ac5bddceb484ce85909615a8
--- /dev/null
+++ b/bp_bin/flip_tab
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/flip_tab
\ No newline at end of file

diff --git a/bp_bin/fold_seq b/bp_bin/fold_seq
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/fold_seq
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/fold_seq b/bp_bin/fold_seq
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..c5f37283ab5c09e4801ef6249850dc5c322dc5da
--- /dev/null
+++ b/bp_bin/fold_seq
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/fold_seq
\ No newline at end of file

diff --git a/bp_bin/format_genome b/bp_bin/format_genome
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/format_genome
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/format_genome b/bp_bin/format_genome
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..c4b373b5d671a3c95dc8ba06639930e85fed0616
--- /dev/null
+++ b/bp_bin/format_genome
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/format_genome
\ No newline at end of file

diff --git a/bp_bin/get_genome_align b/bp_bin/get_genome_align
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/get_genome_align
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/get_genome_align b/bp_bin/get_genome_align
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..65d4851efdbe3d1406c4496693cf03193f3ed06e
--- /dev/null
+++ b/bp_bin/get_genome_align
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/get_genome_align
\ No newline at end of file

diff --git a/bp_bin/get_genome_phastcons b/bp_bin/get_genome_phastcons
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/get_genome_phastcons
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/get_genome_phastcons b/bp_bin/get_genome_phastcons
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..e725c697afbed5bd4bd0e89133973ace2f80cd47
--- /dev/null
+++ b/bp_bin/get_genome_phastcons
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/get_genome_phastcons
\ No newline at end of file

diff --git a/bp_bin/get_genome_seq b/bp_bin/get_genome_seq
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/get_genome_seq
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/get_genome_seq b/bp_bin/get_genome_seq
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..3f6c4cccaff44b51ad9ada59a2dc0c3bc894b17b
--- /dev/null
+++ b/bp_bin/get_genome_seq
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/get_genome_seq
\ No newline at end of file

diff --git a/bp_bin/grab b/bp_bin/grab
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/grab
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/grab b/bp_bin/grab
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..3319f75a03148f4eb947e2ed7784230c52f9473a
--- /dev/null
+++ b/bp_bin/grab
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/grab
\ No newline at end of file

diff --git a/bp_bin/head_records b/bp_bin/head_records
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/head_records
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/head_records b/bp_bin/head_records
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..db1b690636a2d6c4f670cd6facd82a737b95ee6a
--- /dev/null
+++ b/bp_bin/head_records
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/head_records
\ No newline at end of file

diff --git a/bp_bin/invert_align b/bp_bin/invert_align
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/invert_align
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/invert_align b/bp_bin/invert_align
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..40c0b388b5b9d1032477bc4bdb725e1e68d95de6
--- /dev/null
+++ b/bp_bin/invert_align
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/invert_align
\ No newline at end of file

diff --git a/bp_bin/length_seq b/bp_bin/length_seq
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/length_seq
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/length_seq b/bp_bin/length_seq
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..b3a16a722598c8067642e1d75bb3e3bbd7f56fa6
--- /dev/null
+++ b/bp_bin/length_seq
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/length_seq
\ No newline at end of file

diff --git a/bp_bin/length_vals b/bp_bin/length_vals
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/length_vals
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/length_vals b/bp_bin/length_vals
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..46515364fa0515e0e454a4b0c516aad365dff1d8
--- /dev/null
+++ b/bp_bin/length_vals
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/length_vals
\ No newline at end of file

diff --git a/bp_bin/list_biopieces b/bp_bin/list_biopieces
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/list_biopieces
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/list_biopieces b/bp_bin/list_biopieces
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..cb718144dbeffac42bb57deca39f11b602860c2b
--- /dev/null
+++ b/bp_bin/list_biopieces
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/list_biopieces
\ No newline at end of file

diff --git a/bp_bin/list_genomes b/bp_bin/list_genomes
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/list_genomes
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/list_genomes b/bp_bin/list_genomes
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..2ad4d09f75e7372493bfb3462c667b4bba8eb4f7
--- /dev/null
+++ b/bp_bin/list_genomes
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/list_genomes
\ No newline at end of file

diff --git a/bp_bin/match_seq b/bp_bin/match_seq
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/match_seq
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/match_seq b/bp_bin/match_seq
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..2843de1ba6458a630d558d59241dd21e610b4093
--- /dev/null
+++ b/bp_bin/match_seq
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/match_seq
\ No newline at end of file

diff --git a/bp_bin/max_vals b/bp_bin/max_vals
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/max_vals
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/max_vals b/bp_bin/max_vals
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..0fd762016635ff321a9d411ea50ec1b1d13f1340
--- /dev/null
+++ b/bp_bin/max_vals
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/max_vals
\ No newline at end of file

diff --git a/bp_bin/mean_vals b/bp_bin/mean_vals
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/mean_vals
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/mean_vals b/bp_bin/mean_vals
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..9d6fae5ca516f2b4c4522c59745f7540678c6424
--- /dev/null
+++ b/bp_bin/mean_vals
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/mean_vals
\ No newline at end of file

diff --git a/bp_bin/median_vals b/bp_bin/median_vals
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/median_vals
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/median_vals b/bp_bin/median_vals
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..dfcd77522e1197f032c76795ac3ca6d1257be5cb
--- /dev/null
+++ b/bp_bin/median_vals
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/median_vals
\ No newline at end of file

diff --git a/bp_bin/merge_records b/bp_bin/merge_records
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/merge_records
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/merge_records b/bp_bin/merge_records
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..04dfe6c24a9c17d58b8ee6b911677f9d0f7d3e5e
--- /dev/null
+++ b/bp_bin/merge_records
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/merge_records
\ No newline at end of file

diff --git a/bp_bin/merge_vals b/bp_bin/merge_vals
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/merge_vals
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/merge_vals b/bp_bin/merge_vals
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..9da46f882df210e9cd53de0579bc8b7daa98d3a0
--- /dev/null
+++ b/bp_bin/merge_vals
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/merge_vals
\ No newline at end of file

diff --git a/bp_bin/min_vals b/bp_bin/min_vals
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/min_vals
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/min_vals b/bp_bin/min_vals
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..089e58b4af44e25538b213ba886c83d873cbd149
--- /dev/null
+++ b/bp_bin/min_vals
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/min_vals
\ No newline at end of file

diff --git a/bp_bin/oligo_freq b/bp_bin/oligo_freq
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/oligo_freq
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/oligo_freq b/bp_bin/oligo_freq
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..d2a9215767288de9068528781fabfd7f1d62b48b
--- /dev/null
+++ b/bp_bin/oligo_freq
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/oligo_freq
\ No newline at end of file

diff --git a/bp_bin/patscan_seq b/bp_bin/patscan_seq
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/patscan_seq
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/patscan_seq b/bp_bin/patscan_seq
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..45ff4a7a271f5ab357a13edf5391897f9b909bd2
--- /dev/null
+++ b/bp_bin/patscan_seq
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/patscan_seq
\ No newline at end of file

diff --git a/bp_bin/plot_chrdist b/bp_bin/plot_chrdist
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/plot_chrdist
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/plot_chrdist b/bp_bin/plot_chrdist
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..e88eb45f172f75d34fffe327cbedd98115ea7166
--- /dev/null
+++ b/bp_bin/plot_chrdist
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/plot_chrdist
\ No newline at end of file

diff --git a/bp_bin/plot_histogram b/bp_bin/plot_histogram
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/plot_histogram
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/plot_histogram b/bp_bin/plot_histogram
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..034da4efb2b55e85c1dedb7244912ad4a002b516
--- /dev/null
+++ b/bp_bin/plot_histogram
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/plot_histogram
\ No newline at end of file

diff --git a/bp_bin/plot_karyogram b/bp_bin/plot_karyogram
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/plot_karyogram
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/plot_karyogram b/bp_bin/plot_karyogram
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..99aeeba0bf99a234baf3827457305c79f780fc14
--- /dev/null
+++ b/bp_bin/plot_karyogram
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/plot_karyogram
\ No newline at end of file

diff --git a/bp_bin/plot_lendist b/bp_bin/plot_lendist
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/plot_lendist
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/plot_lendist b/bp_bin/plot_lendist
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..66ddb3c045ae3b21907d574b828dc1ed1b1e88c3
--- /dev/null
+++ b/bp_bin/plot_lendist
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/plot_lendist
\ No newline at end of file

diff --git a/bp_bin/plot_matches b/bp_bin/plot_matches
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/plot_matches
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/plot_matches b/bp_bin/plot_matches
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..4c310f965dbf249d5310edd57d2b61ebefb28534
--- /dev/null
+++ b/bp_bin/plot_matches
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/plot_matches
\ No newline at end of file

diff --git a/bp_bin/plot_phastcons_profiles b/bp_bin/plot_phastcons_profiles
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/plot_phastcons_profiles
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/plot_phastcons_profiles b/bp_bin/plot_phastcons_profiles
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..70757b2654ed64447528f756b346a688f2c16ca6
--- /dev/null
+++ b/bp_bin/plot_phastcons_profiles
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/plot_phastcons_profiles
\ No newline at end of file

diff --git a/bp_bin/plot_seqlogo b/bp_bin/plot_seqlogo
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/plot_seqlogo
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/plot_seqlogo b/bp_bin/plot_seqlogo
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..236f33c79e1e120c8fdfdd12ce6f1ad8322a4f23
--- /dev/null
+++ b/bp_bin/plot_seqlogo
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/plot_seqlogo
\ No newline at end of file

diff --git a/bp_bin/print_usage b/bp_bin/print_usage
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/print_usage
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/print_usage b/bp_bin/print_usage
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..8b052952acee08176b13ee919d7dda50bfd0351c
--- /dev/null
+++ b/bp_bin/print_usage
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/print_usage
\ No newline at end of file

diff --git a/bp_bin/random_records b/bp_bin/random_records
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/random_records
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/random_records b/bp_bin/random_records
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..2640774d6fd67deb11875e1a08fdf43fbba946f0
--- /dev/null
+++ b/bp_bin/random_records
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/random_records
\ No newline at end of file

diff --git a/bp_bin/read_2bit b/bp_bin/read_2bit
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/read_2bit
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/read_2bit b/bp_bin/read_2bit
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..9ddf3625d17bd93d1e783c39fa3c570d1a1217ce
--- /dev/null
+++ b/bp_bin/read_2bit
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/read_2bit
\ No newline at end of file

diff --git a/bp_bin/read_bed b/bp_bin/read_bed
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/read_bed
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/read_bed b/bp_bin/read_bed
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..a0b3227ba95d4662a6ebfcf3a1e04039472f492f
--- /dev/null
+++ b/bp_bin/read_bed
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/read_bed
\ No newline at end of file

diff --git a/bp_bin/read_blast_tab b/bp_bin/read_blast_tab
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/read_blast_tab
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/read_blast_tab b/bp_bin/read_blast_tab
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..7041a55e26a33bfa94b09e25cb54252a36d2c99c
--- /dev/null
+++ b/bp_bin/read_blast_tab
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/read_blast_tab
\ No newline at end of file

diff --git a/bp_bin/read_embl b/bp_bin/read_embl
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/read_embl
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/read_embl b/bp_bin/read_embl
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..c7bf9e68691962b235da30c86ae3afac157d58b6
--- /dev/null
+++ b/bp_bin/read_embl
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/read_embl
\ No newline at end of file

diff --git a/bp_bin/read_fasta b/bp_bin/read_fasta
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/read_fasta
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/read_fasta b/bp_bin/read_fasta
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..11935a9266f5a322cede608ff970e4623b905a1f
--- /dev/null
+++ b/bp_bin/read_fasta
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/read_fasta
\ No newline at end of file

diff --git a/bp_bin/read_fixedstep b/bp_bin/read_fixedstep
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/read_fixedstep
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/read_fixedstep b/bp_bin/read_fixedstep
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..25baf02dcf9844544f16239c1ab3a641394a24e6
--- /dev/null
+++ b/bp_bin/read_fixedstep
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/read_fixedstep
\ No newline at end of file

diff --git a/bp_bin/read_gff b/bp_bin/read_gff
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/read_gff
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/read_gff b/bp_bin/read_gff
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..879dad921b35a2a412db5dbde8ed98fcc928e68c
--- /dev/null
+++ b/bp_bin/read_gff
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/read_gff
\ No newline at end of file

diff --git a/bp_bin/read_mysql b/bp_bin/read_mysql
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/read_mysql
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/read_mysql b/bp_bin/read_mysql
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..6f3bbd131c56ae1f8182df572fe9a109213ae8e3
--- /dev/null
+++ b/bp_bin/read_mysql
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/read_mysql
\ No newline at end of file

diff --git a/bp_bin/read_phastcons b/bp_bin/read_phastcons
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/read_phastcons
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/read_phastcons b/bp_bin/read_phastcons
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..ce7d6ffc1c1bab79f19311295375db49db07db3d
--- /dev/null
+++ b/bp_bin/read_phastcons
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/read_phastcons
\ No newline at end of file

diff --git a/bp_bin/read_psl b/bp_bin/read_psl
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/read_psl
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/read_psl b/bp_bin/read_psl
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..9ea2e706b93cdb4b3cf0c3e181f8f81099ddfb05
--- /dev/null
+++ b/bp_bin/read_psl
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/read_psl
\ No newline at end of file

diff --git a/bp_bin/read_soft b/bp_bin/read_soft
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/read_soft
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/read_soft b/bp_bin/read_soft
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..339b425f2248e446eaeb81465ac90061e2a99452
--- /dev/null
+++ b/bp_bin/read_soft
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/read_soft
\ No newline at end of file

diff --git a/bp_bin/read_solexa b/bp_bin/read_solexa
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/read_solexa
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/read_solexa b/bp_bin/read_solexa
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..a38e5d876333329642255557ba0fe5dce45afd9c
--- /dev/null
+++ b/bp_bin/read_solexa
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/read_solexa
\ No newline at end of file

diff --git a/bp_bin/read_solid b/bp_bin/read_solid
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/read_solid
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/read_solid b/bp_bin/read_solid
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..cf25cc4fe55e5942f09ef568e12a6bbf9c08cae2
--- /dev/null
+++ b/bp_bin/read_solid
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/read_solid
\ No newline at end of file

diff --git a/bp_bin/read_stockholm b/bp_bin/read_stockholm
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/read_stockholm
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/read_stockholm b/bp_bin/read_stockholm
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..e203eb45c84d1e72c749f61ca0a085af034acd27
--- /dev/null
+++ b/bp_bin/read_stockholm
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/read_stockholm
\ No newline at end of file

diff --git a/bp_bin/read_tab b/bp_bin/read_tab
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/read_tab
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/read_tab b/bp_bin/read_tab
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..05c6209b9e525553b0d296106cc4fe1cfbf75598
--- /dev/null
+++ b/bp_bin/read_tab
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/read_tab
\ No newline at end of file

diff --git a/bp_bin/read_ucsc_config b/bp_bin/read_ucsc_config
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/read_ucsc_config
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/read_ucsc_config b/bp_bin/read_ucsc_config
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..5247bd75fa3c7a72280c148b4ddb16f9f98da61b
--- /dev/null
+++ b/bp_bin/read_ucsc_config
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/read_ucsc_config
\ No newline at end of file

diff --git a/bp_bin/remove_adaptor b/bp_bin/remove_adaptor
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/remove_adaptor
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/remove_adaptor b/bp_bin/remove_adaptor
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..639285c60237d5eef0889c71c579307d7babf8a3
--- /dev/null
+++ b/bp_bin/remove_adaptor
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/remove_adaptor
\ No newline at end of file

diff --git a/bp_bin/remove_indels b/bp_bin/remove_indels
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/remove_indels
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/remove_indels b/bp_bin/remove_indels
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..52c84d9f329b945536c4c6f7a325677547fbbf33
--- /dev/null
+++ b/bp_bin/remove_indels
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/remove_indels
\ No newline at end of file

diff --git a/bp_bin/remove_keys b/bp_bin/remove_keys
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/remove_keys
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/remove_keys b/bp_bin/remove_keys
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..afb4076eedfa5dfbea3cd8cca960d84bad74d314
--- /dev/null
+++ b/bp_bin/remove_keys
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/remove_keys
\ No newline at end of file

diff --git a/bp_bin/remove_mysql_tables b/bp_bin/remove_mysql_tables
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/remove_mysql_tables
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/remove_mysql_tables b/bp_bin/remove_mysql_tables
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..39a2428abb6f0ea325a73b69ff2084fe904fb137
--- /dev/null
+++ b/bp_bin/remove_mysql_tables
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/remove_mysql_tables
\ No newline at end of file

diff --git a/bp_bin/remove_ucsc_tracks b/bp_bin/remove_ucsc_tracks
deleted file mode 100644 (file)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/remove_ucsc_tracks
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/remove_ucsc_tracks b/bp_bin/remove_ucsc_tracks
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..fa1f7ca31d2ccb1b15acd60ea1ec18e17ef7a356
--- /dev/null
+++ b/bp_bin/remove_ucsc_tracks
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/remove_ucsc_tracks
\ No newline at end of file

diff --git a/bp_bin/rename_keys b/bp_bin/rename_keys
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/rename_keys
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/rename_keys b/bp_bin/rename_keys
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..78541e180885c73ffd9a5bad6405d0cd9ce8ba3a
--- /dev/null
+++ b/bp_bin/rename_keys
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/rename_keys
\ No newline at end of file

diff --git a/bp_bin/reverse_seq b/bp_bin/reverse_seq
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/reverse_seq
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/reverse_seq b/bp_bin/reverse_seq
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..2ae422647d3803d87ec9c7aee94c488e12aa6ba5
--- /dev/null
+++ b/bp_bin/reverse_seq
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/reverse_seq
\ No newline at end of file

diff --git a/bp_bin/shuffle_seq b/bp_bin/shuffle_seq
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/shuffle_seq
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/shuffle_seq b/bp_bin/shuffle_seq
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..e9f42f1a33bcf4d8d1c6059e44586e07b4cbd5d2
--- /dev/null
+++ b/bp_bin/shuffle_seq
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/shuffle_seq
\ No newline at end of file

diff --git a/bp_bin/soap_seq b/bp_bin/soap_seq
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/soap_seq
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/soap_seq b/bp_bin/soap_seq
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..7920fbc085c9cae8238d4045873396e3a3362143
--- /dev/null
+++ b/bp_bin/soap_seq
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/soap_seq
\ No newline at end of file

diff --git a/bp_bin/sort_records b/bp_bin/sort_records
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/sort_records
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/sort_records b/bp_bin/sort_records
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..6ff6dd32591bc2fda5df7a29bfef9da98dbf8754
--- /dev/null
+++ b/bp_bin/sort_records
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/sort_records
\ No newline at end of file

diff --git a/bp_bin/split_bed b/bp_bin/split_bed
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/split_bed
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/split_bed b/bp_bin/split_bed
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..89c57253da25b05ce1722b3a6e049cab715af5d6
--- /dev/null
+++ b/bp_bin/split_bed
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/split_bed
\ No newline at end of file

diff --git a/bp_bin/split_seq b/bp_bin/split_seq
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/split_seq
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/split_seq b/bp_bin/split_seq
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..a428a1e7f6f67c8326e1b646b44eda091e98381d
--- /dev/null
+++ b/bp_bin/split_seq
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/split_seq
\ No newline at end of file

diff --git a/bp_bin/sum_vals b/bp_bin/sum_vals
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/sum_vals
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/sum_vals b/bp_bin/sum_vals
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..4193a498fd428fe099c78abbafcd2a42e4a9ce62
--- /dev/null
+++ b/bp_bin/sum_vals
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/sum_vals
\ No newline at end of file

diff --git a/bp_bin/tile_seq b/bp_bin/tile_seq
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/tile_seq
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/tile_seq b/bp_bin/tile_seq
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..f026dddccf7d72acac9baf7461befab60087b73e
--- /dev/null
+++ b/bp_bin/tile_seq
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/tile_seq
\ No newline at end of file

diff --git a/bp_bin/translate_seq b/bp_bin/translate_seq
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/translate_seq
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/translate_seq b/bp_bin/translate_seq
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..3e8ae5ef485f2bf839df393a79858452fbbfb952
--- /dev/null
+++ b/bp_bin/translate_seq
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/translate_seq
\ No newline at end of file

diff --git a/bp_bin/transliterate_seq b/bp_bin/transliterate_seq
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/transliterate_seq
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/transliterate_seq b/bp_bin/transliterate_seq
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..ce6ea54070788acd22e14d1d3f60a47e176ffc77
--- /dev/null
+++ b/bp_bin/transliterate_seq
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/transliterate_seq
\ No newline at end of file

diff --git a/bp_bin/transliterate_vals b/bp_bin/transliterate_vals
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/transliterate_vals
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/transliterate_vals b/bp_bin/transliterate_vals
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..bf8d8e2f048dc26b793be0b79e25d97150a3cfc8
--- /dev/null
+++ b/bp_bin/transliterate_vals
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/transliterate_vals
\ No newline at end of file

diff --git a/bp_bin/uniq_vals b/bp_bin/uniq_vals
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/uniq_vals
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/uniq_vals b/bp_bin/uniq_vals
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..fb3bafc441a4fb77dc01c9f3729c24cf475179ee
--- /dev/null
+++ b/bp_bin/uniq_vals
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/uniq_vals
\ No newline at end of file

diff --git a/bp_bin/upload_to_ucsc b/bp_bin/upload_to_ucsc
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/upload_to_ucsc
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/upload_to_ucsc b/bp_bin/upload_to_ucsc
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..e97a1ebc764799f1a3b0e49a79fc885ce01ad787
--- /dev/null
+++ b/bp_bin/upload_to_ucsc
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/upload_to_ucsc
\ No newline at end of file

diff --git a/bp_bin/uppercase_seq b/bp_bin/uppercase_seq
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/uppercase_seq
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/uppercase_seq b/bp_bin/uppercase_seq
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..d149da27c4aef34a3f2f31d34832bbaa35ff2c7c
--- /dev/null
+++ b/bp_bin/uppercase_seq
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/uppercase_seq
\ No newline at end of file

diff --git a/bp_bin/vmatch_seq b/bp_bin/vmatch_seq
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/vmatch_seq
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/vmatch_seq b/bp_bin/vmatch_seq
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..f98275cff4e50b928795f6c0276d51b43c01ef82
--- /dev/null
+++ b/bp_bin/vmatch_seq
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/vmatch_seq
\ No newline at end of file

diff --git a/bp_bin/write_2bit b/bp_bin/write_2bit
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/write_2bit
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/write_2bit b/bp_bin/write_2bit
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..3b58b3136be07b4edfea59ea5d562f243424f455
--- /dev/null
+++ b/bp_bin/write_2bit
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/write_2bit
\ No newline at end of file

diff --git a/bp_bin/write_align b/bp_bin/write_align
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/write_align
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/write_align b/bp_bin/write_align
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..15fd96a9e0cb36dc8bcc4bd49b9ff85e47d88155
--- /dev/null
+++ b/bp_bin/write_align
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/write_align
\ No newline at end of file

diff --git a/bp_bin/write_bed b/bp_bin/write_bed
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/write_bed
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/write_bed b/bp_bin/write_bed
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..38a4411baa257e66bc45169141f6d9d976ae0b21
--- /dev/null
+++ b/bp_bin/write_bed
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/write_bed
\ No newline at end of file

diff --git a/bp_bin/write_blast b/bp_bin/write_blast
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/write_blast
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/write_blast b/bp_bin/write_blast
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..e84bd5cc9f8f6da0a56613f44efa53e4297d2d59
--- /dev/null
+++ b/bp_bin/write_blast
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/write_blast
\ No newline at end of file

diff --git a/bp_bin/write_fasta b/bp_bin/write_fasta
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/write_fasta
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/write_fasta b/bp_bin/write_fasta
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..d7afcfb5a0da5d9352c52444c86ed63d6047acbb
--- /dev/null
+++ b/bp_bin/write_fasta
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/write_fasta
\ No newline at end of file

diff --git a/bp_bin/write_fixedstep b/bp_bin/write_fixedstep
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/write_fixedstep
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/write_fixedstep b/bp_bin/write_fixedstep
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..67f50bb15a9bef8a51d2bc0f997093d4c72d2a45
--- /dev/null
+++ b/bp_bin/write_fixedstep
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/write_fixedstep
\ No newline at end of file

diff --git a/bp_bin/write_psl b/bp_bin/write_psl
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/write_psl
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/write_psl b/bp_bin/write_psl
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..edf73ff61311f40843dc133c56b57a1361a75003
--- /dev/null
+++ b/bp_bin/write_psl
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/write_psl
\ No newline at end of file

diff --git a/bp_bin/write_solid b/bp_bin/write_solid
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/write_solid
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/write_solid b/bp_bin/write_solid
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..48c24a49be90f7adca9a609ece15c88a38668d9d
--- /dev/null
+++ b/bp_bin/write_solid
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/write_solid
\ No newline at end of file

diff --git a/bp_bin/write_tab b/bp_bin/write_tab
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/write_tab
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/write_tab b/bp_bin/write_tab
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..1a45ade761ac8ad49f27b865214caad4df37afb3
--- /dev/null
+++ b/bp_bin/write_tab
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/write_tab
\ No newline at end of file

diff --git a/bp_bin/write_ucsc_config b/bp_bin/write_ucsc_config
deleted file mode 100755 (executable)
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..0000000000000000000000000000000000000000
--- a/bp_bin/write_ucsc_config
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::BioRun;

diff --git a/bp_bin/write_ucsc_config b/bp_bin/write_ucsc_config
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..d25e9972f6d0f1f9c1b387df8e27d582438440f3
--- /dev/null
+++ b/bp_bin/write_ucsc_config
@@ -0,0 +1 @@
+../code_perl/Maasha/bin/write_ucsc_config
\ No newline at end of file

diff --git a/code_perl/Maasha/bin/add_ident b/code_perl/Maasha/bin/add_ident
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/add_ident
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/align_seq b/code_perl/Maasha/bin/align_seq
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/align_seq
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/analyze_bed b/code_perl/Maasha/bin/analyze_bed
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/analyze_bed
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/analyze_seq b/code_perl/Maasha/bin/analyze_seq
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/analyze_seq
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/analyze_tags b/code_perl/Maasha/bin/analyze_tags
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/analyze_tags
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/analyze_vals b/code_perl/Maasha/bin/analyze_vals
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/analyze_vals
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/assemble_tag_contigs b/code_perl/Maasha/bin/assemble_tag_contigs
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/assemble_tag_contigs
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/blast_seq b/code_perl/Maasha/bin/blast_seq
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/blast_seq
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/blat_seq b/code_perl/Maasha/bin/blat_seq
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/blat_seq
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/calc_bit_scores b/code_perl/Maasha/bin/calc_bit_scores
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/calc_bit_scores
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/calc_fixedstep b/code_perl/Maasha/bin/calc_fixedstep
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/calc_fixedstep
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/complement_seq b/code_perl/Maasha/bin/complement_seq
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/complement_seq
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/complexity_seq b/code_perl/Maasha/bin/complexity_seq
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/complexity_seq
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/compute b/code_perl/Maasha/bin/compute
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/compute
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/count_records b/code_perl/Maasha/bin/count_records
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/count_records
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/count_vals b/code_perl/Maasha/bin/count_vals
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/count_vals
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/create_blast_db b/code_perl/Maasha/bin/create_blast_db
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/create_blast_db
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/create_vmatch_index b/code_perl/Maasha/bin/create_vmatch_index
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/create_vmatch_index
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/create_weight_matrix b/code_perl/Maasha/bin/create_weight_matrix
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/create_weight_matrix
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/extract_seq b/code_perl/Maasha/bin/extract_seq
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/extract_seq
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/flip_tab b/code_perl/Maasha/bin/flip_tab
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/flip_tab
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/fold_seq b/code_perl/Maasha/bin/fold_seq
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/fold_seq
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/format_genome b/code_perl/Maasha/bin/format_genome
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/format_genome
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/get_genome_align b/code_perl/Maasha/bin/get_genome_align
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/get_genome_align
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/get_genome_phastcons b/code_perl/Maasha/bin/get_genome_phastcons
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/get_genome_phastcons
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/get_genome_seq b/code_perl/Maasha/bin/get_genome_seq
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/get_genome_seq
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/grab b/code_perl/Maasha/bin/grab
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/grab
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/head_records b/code_perl/Maasha/bin/head_records
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/head_records
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/invert_align b/code_perl/Maasha/bin/invert_align
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/invert_align
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/length_seq b/code_perl/Maasha/bin/length_seq
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/length_seq
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/length_vals b/code_perl/Maasha/bin/length_vals
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/length_vals
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/list_biopieces b/code_perl/Maasha/bin/list_biopieces
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/list_biopieces
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/list_genomes b/code_perl/Maasha/bin/list_genomes
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/list_genomes
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/match_seq b/code_perl/Maasha/bin/match_seq
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/match_seq
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/max_vals b/code_perl/Maasha/bin/max_vals
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/max_vals
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/mean_vals b/code_perl/Maasha/bin/mean_vals
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/mean_vals
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/median_vals b/code_perl/Maasha/bin/median_vals
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/median_vals
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/merge_records b/code_perl/Maasha/bin/merge_records
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/merge_records
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/merge_vals b/code_perl/Maasha/bin/merge_vals
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/merge_vals
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/min_vals b/code_perl/Maasha/bin/min_vals
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/min_vals
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/oligo_freq b/code_perl/Maasha/bin/oligo_freq
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/oligo_freq
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/patscan_seq b/code_perl/Maasha/bin/patscan_seq
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/patscan_seq
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/plot_chrdist b/code_perl/Maasha/bin/plot_chrdist
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/plot_chrdist
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/plot_histogram b/code_perl/Maasha/bin/plot_histogram
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/plot_histogram
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/plot_karyogram b/code_perl/Maasha/bin/plot_karyogram
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/plot_karyogram
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/plot_lendist b/code_perl/Maasha/bin/plot_lendist
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/plot_lendist
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/plot_matches b/code_perl/Maasha/bin/plot_matches
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/plot_matches
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/plot_phastcons_profiles b/code_perl/Maasha/bin/plot_phastcons_profiles
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/plot_phastcons_profiles
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/plot_seqlogo b/code_perl/Maasha/bin/plot_seqlogo
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/plot_seqlogo
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/print_usage b/code_perl/Maasha/bin/print_usage
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/print_usage
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/random_records b/code_perl/Maasha/bin/random_records
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/random_records
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/read_2bit b/code_perl/Maasha/bin/read_2bit
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/read_2bit
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/read_bed b/code_perl/Maasha/bin/read_bed
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/read_bed
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/read_blast_tab b/code_perl/Maasha/bin/read_blast_tab
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/read_blast_tab
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/read_embl b/code_perl/Maasha/bin/read_embl
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/read_embl
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/read_fasta b/code_perl/Maasha/bin/read_fasta
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/read_fasta
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/read_fixedstep b/code_perl/Maasha/bin/read_fixedstep
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/read_fixedstep
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/read_gff b/code_perl/Maasha/bin/read_gff
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/read_gff
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/read_mysql b/code_perl/Maasha/bin/read_mysql
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/read_mysql
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/read_phastcons b/code_perl/Maasha/bin/read_phastcons
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/read_phastcons
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/read_psl b/code_perl/Maasha/bin/read_psl
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/read_psl
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/read_soft b/code_perl/Maasha/bin/read_soft
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/read_soft
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/read_solexa b/code_perl/Maasha/bin/read_solexa
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/read_solexa
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/read_solid b/code_perl/Maasha/bin/read_solid
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/read_solid
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/read_stockholm b/code_perl/Maasha/bin/read_stockholm
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/read_stockholm
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/read_tab b/code_perl/Maasha/bin/read_tab
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/read_tab
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/read_ucsc_config b/code_perl/Maasha/bin/read_ucsc_config
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/read_ucsc_config
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/remove_adaptor b/code_perl/Maasha/bin/remove_adaptor
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/remove_adaptor
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/remove_indels b/code_perl/Maasha/bin/remove_indels
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/remove_indels
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/remove_keys b/code_perl/Maasha/bin/remove_keys
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/remove_keys
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/remove_mysql_tables b/code_perl/Maasha/bin/remove_mysql_tables
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/remove_mysql_tables
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/remove_ucsc_tracks b/code_perl/Maasha/bin/remove_ucsc_tracks
new file mode 100644 (file)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/remove_ucsc_tracks
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/rename_keys b/code_perl/Maasha/bin/rename_keys
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/rename_keys
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/reverse_seq b/code_perl/Maasha/bin/reverse_seq
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/reverse_seq
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/shuffle_seq b/code_perl/Maasha/bin/shuffle_seq
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/shuffle_seq
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/soap_seq b/code_perl/Maasha/bin/soap_seq
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/soap_seq
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/sort_records b/code_perl/Maasha/bin/sort_records
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/sort_records
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/split_bed b/code_perl/Maasha/bin/split_bed
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/split_bed
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/split_seq b/code_perl/Maasha/bin/split_seq
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/split_seq
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/sum_vals b/code_perl/Maasha/bin/sum_vals
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/sum_vals
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/tile_seq b/code_perl/Maasha/bin/tile_seq
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/tile_seq
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/translate_seq b/code_perl/Maasha/bin/translate_seq
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/translate_seq
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/transliterate_seq b/code_perl/Maasha/bin/transliterate_seq
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/transliterate_seq
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/transliterate_vals b/code_perl/Maasha/bin/transliterate_vals
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/transliterate_vals
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/uniq_vals b/code_perl/Maasha/bin/uniq_vals
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/uniq_vals
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/upload_to_ucsc b/code_perl/Maasha/bin/upload_to_ucsc
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/upload_to_ucsc
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/uppercase_seq b/code_perl/Maasha/bin/uppercase_seq
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/uppercase_seq
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/vmatch_seq b/code_perl/Maasha/bin/vmatch_seq
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/vmatch_seq
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/write_2bit b/code_perl/Maasha/bin/write_2bit
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/write_2bit
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/write_align b/code_perl/Maasha/bin/write_align
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/write_align
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/write_bed b/code_perl/Maasha/bin/write_bed
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/write_bed
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/write_blast b/code_perl/Maasha/bin/write_blast
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/write_blast
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/write_fasta b/code_perl/Maasha/bin/write_fasta
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/write_fasta
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/write_fixedstep b/code_perl/Maasha/bin/write_fixedstep
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/write_fixedstep
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/write_psl b/code_perl/Maasha/bin/write_psl
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/write_psl
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/write_solid b/code_perl/Maasha/bin/write_solid
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/write_solid
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/write_tab b/code_perl/Maasha/bin/write_tab
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/write_tab
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_perl/Maasha/bin/write_ucsc_config b/code_perl/Maasha/bin/write_ucsc_config
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/code_perl/Maasha/bin/write_ucsc_config
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/code_python/Cjung/Args.pyc b/code_python/Cjung/Args.pyc
index 8b121787fa51f401453d056b37e17c49ecd4e740..4e8e789b3798ad76e1306bcf450f0d152744ab37 100644 (file)
Binary files a/code_python/Cjung/Args.pyc and b/code_python/Cjung/Args.pyc differ