indraniel

#!/usr/bin/env csi -ss

;; An example file reading script with chicken scheme

(use extras)

(define (read-it file)
  (let ((fh (open-input-file file)))
     (let loop((c (read-line fh)))
        (if (eof-object? c)

indraniel

FROM ubuntu:16.04
MAINTAINER Pat Minx <pminx@wustl.edu>

# Volumes
VOLUME /build
VOLUME /release

# bootstrap build dependencies
RUN apt-get update -qq && \
    apt-get -y install apt-transport-https && \

indraniel

#!/usr/bin/env python

# Based on: https://github.com/piedar/pychromecast/blob/cast/cast.py
#           https://github.com/balloob/pychromecast/issues/8
#           https://github.com/balloob/pychromecast/issues/154
#           https://en.wikipedia.org/wiki/Multicast_DNS

# Copyright 2015 Benn Snyder <benn.snyder@gmail.com>
# Released under MIT license
#

indraniel

import sbt._

// project/Dependencies.scala

object Dependencies {
  lazy val scalaTest = "org.scalatest" %% "scalatest" % "3.0.1"
//  lazy val ammonite  = "com.lihaoyi" %% "ammonite" % "1.0.0" cross CrossVersion.full
//  lazy val scalaCompiler  = "org.scala-lang" % "scala-compiler" % scalaVersion.value
  lazy val scalaCompiler  = "org.scala-lang" % "scala-compiler" % "2.12.1"
  lazy val jline = "org.scala-lang.modules" % "scala-jline" % "2.12.1"

indraniel

#!/usr/bin/env csi -ss

;; An example file reading script with chicken scheme

(use extras)

(define (read-it file)
  (let ((fh (open-input-file file)))
     (let loop((c (read-line fh)))
        (if (eof-object? c)

indraniel

#!/gsc/bin/perl

# this was a test script created by thepler sometime on 2009-04-17

# test by running "bsub ./bstop_myself.pl" at a command prompt

use GSCApp;
App->init;

use Path::Class;

indraniel

#!/bin/bash 

# Example usage: bash get-passing-line-in-vcf.sh /gscmnt/gc2758/analysis/ccdg_gatk_callsets/eocad_aa_2017.05.18/post-vqsr/12-concat-vcfs

# programs
BCFTOOLS=/gscmnt/gc2802/halllab/idas/software/local/bin/bcftools1.4
TABIX=/gscmnt/gc2802/halllab/idas/software/local/bin/tabix
SORT=/gscmnt/gc2802/halllab/idas/software/local/bin/lh3-sort

# data

indraniel

#!/usr/bin/env python

from __future__ import print_function, division
import os, sys, re, subprocess, time, datetime, shutil

def log(msg):
    timestamp = datetime.datetime.now().strftime("%Y-%m-%d %T")
    print('[-- {} --] {}'.format(timestamp, msg), file=sys.stderr)

def touch(fname, times=None):

indraniel

#!/usr/bin/env python

from __future__ import print_function
import ftplib, datetime, sys

# ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr14.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz

def log(msg):
    timestamp = datetime.datetime.now().strftime("%Y-%m-%d %T")
    print('[-- {} --] {}'.format(timestamp, msg), file=sys.stderr)

indraniel

#!/bin/bash

# Usage:
#    bash b37-annotate-w-gnomAD.sh </path/to/input.vcf.gz> </path/to/output.vcf.gz>
#
# Note:
#    1. This script with create a "scratch" directory to hold intermediate file
#       states created during the annotation process.  The scratch directory will
#       be created next to the /path/to/outvcf.vcf.gz .  
#