seandavi

rule defuse:
    input:  source2fastq,'/usr/local/apps/defuse/current/scripts/config_hg19.txt'
    output: ["bam/{source}/RNA/defuse/"+fname for fname in ['results.classify.tsv','results.filtered.tsv','results.tsv']]
    params:  batch="-q ccr -l nodes=1:gpfs",
             outdir="bam/{source}/RNA/defuse",
             scratchdir = '/scratch'
    priority: 10
    threads: 16
    version: "0.6.1"
    log: "bam/{source}/RNA/defuse/defuse_rule.log"

seandavi

#!/usr/bin/env python
import argparse
import shutil
import subprocess
import os

parser = argparse.ArgumentParser()
parser.add_argument('tumorbam',help='full path to the Tumor BAM file')
parser.add_argument('normalbam',help='full path to the Normal BAM file')
parser.add_argument('twobitfile',help='full path to 2bit file for reference genome')

seandavi

#!/usr/bin/Rscript
# chmod +x runner.sh
# runner.sh "PACKAGENAME:path/to/script" <args to pass to script>
# Example (fake): 
#   runner.sh "GEOquery:scripts/abc.sh" arg1 arg2 arg3
#
args = commandArgs(trailingOnly=TRUE)
arg1 = strsplit(args[1],':')[[1]]
if(length(arg1)!=2) {
    stop("The first argument must be of the form 'PACKAGENAME:path/to/script.sh'")

seandavi

Serpentine

To get started, you need to create a virtual environment for snakemake. The following code will do this for you.

module load python/3.4.2
pyvenv snakemake
source snakemake/bin/activate
pip install snakemake

seandavi

---
title: "Clinomics"
author: "Sean Davis"
date: February 12, 2015
output: html_document
---

```{r style, echo = FALSE, results = 'asis',cache=FALSE}
suppressPackageStartupMessages(library(GenomicRanges))
BiocStyle::markdown()

seandavi

# Run this in R
# Supply any SRA accessions that you like.
# The .sra files will be downloaded.
# The actual sequence will need to be extracted
#   with the SRA SDK (for example fastq-dump)
source('http://bioconductor.org/biocLite.R')
biocLite('SRAdb')
library(SRAdb)
sradb = getSRAdbFile()
con = dbConnect(SQLite(),sradb)

seandavi

.require <-
    function(pkg)
{
    withCallingHandlers({
        suppressPackageStartupMessages({
            require(pkg, character.only=TRUE, quietly=TRUE)
        })
    }, warning=function(w) {
        invokeRestart("muffleWarning")
    }) || {

seandavi

#!/bin/bash
aws ec2 describe-instances | \
  jq -r '.Reservations[].Instances[].PublicDnsName//empty'| \
  parallel -j 8 -I {} ssh -X -o StrictHostKeyChecking=no -i ~/.ssh/MYKEY.pem USEANAME@{} 'sudo apt-get install zip'

seandavi

---
author: Sean Davis
date: 8/12/2015
title: "XML play"
output: html_document
---

Load the XML library and set the filename. You can loop over filenames if you like.

```{r}

seandavi

#  Copyright 2010 University Of Southern California
#
#  Licensed under the Apache License, Version 2.0 (the "License");
#  you may not use this file except in compliance with the License.
#  You may obtain a copy of the License at
#
#  http://www.apache.org/licenses/LICENSE-2.0
#
#  Unless required by applicable law or agreed to in writing,
#  software distributed under the License is distributed on an "AS IS" BASIS,