mpkocher

#!/usr/bin/env python
"""Tool for Scrapping Jobs and DataSets from a SMRT Link instance"""
import argparse
import base64
import datetime
import sys
import json
import os
import time
import functools

mpkocher

SMRT Link Dependencies

DOT Legend

Shape (and Color)	Description
RECT DOTTED	Third party dependency
OVAL GREEN	Build Output
RECT	BitBucket Repo

mpkocher

09:33 $ python /Users/mkocher/repos/pbcommand/extras/validation_argparse_option_example.py log
(pbsmrtpipe_test) ✔ ~/scratch_pad/verify-bugs/SL-1512 
09:33 $ python /Users/mkocher/repos/pbcommand/extras/validation_argparse_option_example.py dir-that-does-not-exist
ls: cannot access 'dir-that-does-not-exist': No such file or directory
Traceback (most recent call last):
  File "/Users/mkocher/repos/pbcommand/extras/validation_argparse_option_example.py", line 19, in <module>
    sys.exit(main(argv=sys.argv[1:]))
  File "/Users/mkocher/repos/pbcommand/extras/validation_argparse_option_example.py", line 14, in main
    p.parse_args(argv)
  File "/Users/mkocher/miniconda2/envs/pbsmrtpipe_test/lib/python2.7/argparse.py", line 1701, in parse_args

mpkocher

#!/bin/bash

declare -a packages=("devtools" "knitr" "ggplot2" "mplot" "googleVis" "data.table" "caret" "pRoc" "sqldf" "glmnet")
declare -a ghpackages=("ramnathv/rCharts")

for i in "${packages[$@]}"; do
  echo "Attempting to install '${i}'"
  R -e "install.packages('${i}', repos = 'http://cran.us.r-project.org')"
done

mpkocher

import hashlib
import hmac
import math
import datetime
import base64


def to_h(secret, method, segment, t=None):
    """
    Example:

mpkocher

library(lubridate)
library(dplyr)
library(readr)
library(ggplot2)

process_log <- function(csv_path, output_png, custom_title) {
  # CSV with a single column "request_time" with the UTC time of the request time stamp
  tdf <- read_csv(csv_path)
  rdf <- tdf %>% transmute(created_at = ymd_hms(request_time))
  # per day

mpkocher

mpkocher

from snakemake.core import SnakeMakeShellRule, SnakeMakePyRule, AllRule


class CollectReferences(SnakeMakeShellRule):
    ID = "collect_references"
    THREADS = 8
    DESCRIPTION = "Does some stuff"

    def inputs():
        return dict(alpha="f1.fasta")

mpkocher

SMRT Link System Architecture High Level Overview

The SMRT Link System is comprised of 6 core components:

• SMRT Link System Installer for general admin, configuring the system, and upgrading
• SMRT Link Tools Commandline tools written in python, c++ and scala from the SAT and SL team
• SMRT Link Analysis Services (SLA) Scala driven webservices using spray framework
• SMRT Link Tomcat WebServer For SMRT Link UI written in Javascript/Typescript using angular2
• SMRT View Visualization of SMRT Link Analysis Jobs
• Enterprise WSO2 API Manager for authentication and authorization

mpkocher

package com.pacbio.secondary.smrtserver.tools

import java.util.UUID


import akka.actor.ActorSystem
import com.pacbio.secondary.analysis.jobs.JobModels.EngineJob
import com.pacbio.secondary.analysis.reports.ReportModels.Report
import com.pacbio.secondary.smrtlink.models.{DataSetMetaDataSet, DataStoreReportFile}
import com.pacbio.secondary.smrtserver.client.AnalysisServiceAccessLayer