ebelter

#!/bin/bash

format="%-12s %-5s %-11s %-10s %-11s %s\n"
printf "$format" host cpus phys_cores virt_cores total_cores lsf_cores
for host in $(lshosts -w | grep wustl | grep -v vm | awk -F. '{print $1}'); do
    cpus=$(ssh $host "grep 'physical id' /proc/cpuinfo | sort -u | wc -l")
    core_ids=$(ssh $host "grep 'core id' /proc/cpuinfo | sort -u | wc -l")
    physical_cores=$(expr $cpus \* $core_ids)
    total_cores=$(ssh $host "grep 'proc' /proc/cpuinfo | wc -l")
    virtual_cores=$(expr $total_cores \- $physical_cores)

ebelter

#!/usr/bin/env perl

use strict;
use warnings 'FATAL';

use IO::String;
use Text::CSV;

my $tcga_sample_type_csv = <<TCGA_SAMPLE_TYPE_CSV;
"Code","Definition","Short Letter Code"

ebelter

#!/usr/bin/env perl

use strict;
use warnings 'FATAL';
 
use IO::String;
use List::MoreUtils;
use Text::CSV;
 
my $io = IO::String->new;

ebelter

#!/usr/bin/env perl

use strict;
use warnings;

use List::MoreUtils 'firstidx';

my @months = map { qr/$_/ } (qw/ jan feb mar apr may jun jul aug sep oct nov dec /);
use Data::Dumper;
my %metrics = ( seen => 0, renamed => 0, );

ebelter

#!/usr/bin/env ruby

def filename_for_pkg(filename)
    filename.gsub!(/\//, '')
    filename.gsub!(/([^A-Z])([A-Z])/,'\1_\2')
    File.join('', %w{ gscuser ebelter dev genome genome etc genome spec }, 'lsf_resource_dv2_' + filename.downcase + '.yaml')
end

def cleanup_resource(resource)
    resource.chomp!

ebelter

language: perl
perl:
  - "5.12"
sudo: false
before_install:
  - git clone git://github.com/travis-perl/helpers ~/travis-perl-helpers
  - source ~/travis-perl-helpers/init
  - build-perl
  - perl -V
install:

ebelter

// Use Gists to store code you would like to remember later on
console.log(window); // log the "window" object to the console

ebelter

#!/usr/bin/env perl

use strict;
use warnings 'FATAL';

use Net::LDAP;
use YAML;

my $ldap = Net::LDAP->new('ipa1.gsc.wustl.edu', version => 3);
my $mesg = $ldap->start_tls(verify => 'none');

ebelter

#!/usr/bin/env ruby

file = ARGV[0]
if ! file or ! File.exists?(file) 
  raise "No file!"
end

things = Array.new
fh = File.open(file, 'r')
fh.each_line do |line|

ebelter

### INSTANCE SETUP
# create instance CLI - change the instance nmae and boot disk name as needed
$ NUM=1; export NUM # update for intance number
$ gcloud compute instances create supernova-${NUM} --zone=us-central1-c \
  --machine-type=custom-56-372736 --subnet=default --maintenance-policy=MIGRATE \
  --service-account=816609412860-compute@developer.gserviceaccount.com --scopes=https://www.googleapis.com/auth/cloud-platform \
  --min-cpu-platform=Intel\ Skylake --tags=mgi-accessible,supernova-ui --image=centos-7-v20180507 --image-project=centos-cloud \
  --boot-disk-size=200GB --boot-disk-type=pd-standard --boot-disk-device-name=supernova-${NUM}