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

mpkocher

(core)c2f558353ff0b4f63d542c94782fdf56 $> ipython -i semver_pad.py 
Python 2.7.10 (default, Jul 13 2015, 12:05:58) 
Type "copyright", "credits" or "license" for more information.

IPython 5.1.0 -- An enhanced Interactive Python.
?         -> Introduction and overview of IPython's features.
%quickref -> Quick reference.
help      -> Python's own help system.
object?   -> Details about 'object', use 'object??' for extra details.

mpkocher

package com.github.mpkocher.alarmpad

import java.nio.file.{Path, Paths}

import akka.actor._
import akka.util.Timeout
import com.typesafe.config.{Config, ConfigFactory}
import com.typesafe.scalalogging.LazyLogging

import scala.collection.mutable

mpkocher

/**
 * Created by mkocher on 1/21/17.
 */

interface IdAble {
    ix: string;
}

interface Primitive<T> {
    value: T;

mpkocher

PacBio Transfer Schemes Notes for 4.0.0

Supported Transfer Schemes:

• Rsync Server (aka "rsync")
• Rsync+SSH (aka "srs")

The new 4.0.0 data model (specifically relativePath) allows users to create Transfer Schemes for grouping of projects to manage under one root location. For example, user or group "alpha" can create Transfer Scheme "rsync-alpha" that writes to "/pbi/collections/groups/alpha". This Transfer Scheme can be completely separately managed from group "beta" that writes to "/pbi/collections/groups/beta".

mpkocher

import com.pacbio.secondary.analysis.datasets.io._ 
import java.nio.file.{Paths, Path}

import collection.JavaConversions._
import collection.JavaConverters._ 

import com.pacbio.secondary.analysis.datasets.io._ 
import com.pacificbiosciences.pacbiobasedatamodel.ExternalResources
import com.pacificbiosciences.pacbiobasedatamodel.ExternalResource