sestaton

#!/bin/bash

## Location for local build of gmpy2 and deps
cd apps
mkdir gmpy2 && cd gmpy2

## Download and compile gmp
wget https://ftp.gnu.org/gnu/gmp/gmp-5.1.3.tar.bz2 && tar xjf gmp-5.1.3.tar.bz2
cd gmp-5.1.3
./configure --prefix=/home/jmblab/statonse/apps/gmpy2

sestaton

#!/usr/bin/env perl

use 5.010;
use strict;
use warnings;

my %hash = (
    id  => undef,
    id2 => 2,
    );

sestaton

#!/usr/bin/env perl

use strict;
use warnings;

my $usage = "blastn -outfmt 6 ... | $0 - > blast_msp_recon.txt\n-OR-\n".
    "$0 blasttable.bln > blast_msp_recon.txt\n";
die $usage if !@ARGV;

while (<>) {

sestaton

#!/usr/bin/env perl

use 5.010;
use strict;
use warnings;
use Bio::SeqIO;
use List::MoreUtils qw(any);

my @ids = (1, 5, 10); 
my $num = 0; 

sestaton

#!/usr/bin/env perl

use strict;
use warnings;
use File::Find;
use Bio::Tools::Run::Alignment::Clustalw;

my $dir = 'genes';
my @files;
find( sub {

sestaton

#!/bin/bash

## fetch the archive
wget ftp://ftp-trace.ncbi.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR156/SRR1561197/SRR1561197.sra

## extract the pairs
fastq-dump -F --split-files ./SRR1561197.sra

## trim
fastq_quality_filter -i SRR1561197_1.fastq -q 28 -p 100 -Q33 -o SRR1561197_1_filt.fastq

sestaton

#!/usr/bin/env perl

use 5.020;
use strict;
use warnings;
use Benchmark qw(:all);

my $seq = "ATCG" x 25e6; # 100Mb string
my $count = 10;

sestaton

package test::role;

use Moose::Role;
use Moose::Util::TypeConstraints;

subtype 'ModNum'
    => as 'Num'
    => where { /\_/ || /\d+/ };

coerce 'ModNum',

sestaton

#!/bin/bash

##NB: Follow these instructions for installing Transposome: http://sestaton.github.io/Transposome
##    What follows is to help users on really old Linux systems with a broken wget and no admin privileges. 

export PERLBREW_ROOT=$HOME/perl5/perlbrew
export PERLBREW_HOME=$HOME/.perlbrew

# install perlbrew and patchperl
echo "Downloading perlbrew..."

sestaton

#!/usr/bin/env perl

use 5.010;
use strict;
use warnings;

while (<DATA>) {
    chomp;
    my ($query, $subject, $percent_identity, $alignment_length, $mistmatches, 
        $gap_openings, $q_start, $q_end, $s_start, $s_end, $e_value, $bit_score) = split /\t/;