#!/usr/bin/env perl
use strict;
use warnings;
use Test::More tests => 10;
use IPC::Cmd qw(can_run);
SKIP: {
skip 'cat seemingly not available',1
unless defined(can_run('cat')) ;
ok( defined(can_run('cat')), 'cat available and executable');
}
SKIP: {
skip 'awk seemingly not available',1
unless defined(can_run('awk')) ;
ok( defined(can_run('awk')), 'awk available and executable');
}
SKIP: {
skip 'bedToBigBed seemingly not available',1
unless defined(can_run('bedToBigBed')) ;
ok( defined(can_run('bedToBigBed')), 'bedToBigBed available and executable');
}
SKIP: {
skip 'genomeCoverageBed seemingly not available',1
unless defined(can_run('genomeCoverageBed')) ;
ok( defined(can_run('genomeCoverageBed')), 'genomeCoverageBed available and executable');
}
SKIP: {
skip 'bedGraphToBigWig seemingly not available',1
unless defined(can_run('bedGraphToBigWig')) ;
ok( defined(can_run('bedGraphToBigWig')), 'bedGraphToBigWig available and executable');
}
SKIP: {
skip ('faToTwoBit seemingly is not available',1)
unless defined(can_run('faToTwoBit'));
ok( defined(can_run('faToTwoBit')), 'faToTwoBit available and executable') or
diag ("please install the 'faToTwoBit' utility");
}
SKIP: {
skip ('bedtools seemingly is not available',1)
unless defined(can_run('bedtools'));
ok( defined(can_run('bedtools')), 'bedtools available and executable');
}
SKIP: {
skip ('sortBed seemingly is not available',1)
unless defined(can_run('sortBed'));
ok( defined(can_run('sortBed')), 'sortBed available and executable');
}
SKIP: {
skip ('fetchChromSizes seemingly is not available',1)
unless defined(can_run('fetchChromSizes'));
ok( defined(can_run('fetchChromSizes')), 'fetchChromSizes available and executable');
}
SKIP: {
skip ('R seemingly is not available',1)
unless defined(can_run('R'));
ok( defined(can_run('R')), 'R available and executable');
}