seandavi

FROM ubuntu:18.04

RUN apt-get update
RUN apt-get install -y wget 

# We do things this way to keep the docker image
# size down. See https://nickjanetakis.com/blog/docker-tip-3-chain-your-docker-run-instructions-to-shrink-your-images
RUN wget http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.9.2/sratoolkit.2.9.2-ubuntu64.tar.gz \
    && tar -xvzf sratoolkit.2.9.2-ubuntu64.tar.gz \
    && rm sratoolkit.2.9.2-ubuntu64.tar.gz

seandavi

from __future__ import print_function
import apache_beam as beam
from apache_beam.options.pipeline_options import PipelineOptions
from apache_beam.io.filesystems import FileSystems
import urllib
import json
import argparse
import logging
logging.basicConfig(level=logging.INFO)

seandavi

---
title: "fusion genes"
output: 
  html_document:
    self_contained: true
---


```{r include=FALSE}
library(knitr)

seandavi

# requires python 2.7
# pip install apache_beam
from __future__ import print_function
import apache_beam as beam
from apache_beam.options.pipeline_options import PipelineOptions
import json
import argparse
import logging
import urllib2
import urllib

seandavi

{
  "sra_experiment_joined2": {
    "mappings": {
      "doc": {
        "properties": {
          "library_name": {
            "fields": {
              "keyword": {
                "ignore_above": 256,
                "type": "keyword"

seandavi

Insert Workshop Title

Instructor(s) name(s) and contact information

Provide names and contact information for all instructors.

Workshop Description

Along with the topic of your workshop, include how students can expect to spend their time. For the description may also include information

seandavi

seandavi

# salmon wdl
#
# Assumes gencode here!!!!
#
#############################

task salmon_index {

  File transcript_file
  Int kmer 

seandavi

import groovy.json.JsonSlurper

def jsonSlurper = new JsonSlurper()

res = jsonSlurper.parse(new URL('https://api-omicidx.cancerdatasci.org/sra/1.0/search/run?q=experiment_accession:' + params.experiment + '&size=500'))

l = res.hits.hits.collect {
    [ it._source.experiment_accession, it._source.accession ]
}

seandavi