mpkocher

[info] 2016-06-08  WARN [ForkJoinPool-2-worker-5] c.p.c.a.BaseApi$ServiceActor - Non-fatal exception: 500 - Internal Server Error - Cannot cast scala.util.Right to java.lang.String
[info] java.lang.ClassCastException: Cannot cast scala.util.Right to java.lang.String
[info] 	at java.lang.Class.cast(Class.java:3369)
[info] 	at scala.concurrent.Future$$anonfun$mapTo$1.apply(Future.scala:407)
[info] 	at scala.util.Success$$anonfun$map$1.apply(Try.scala:237)
[info] 	at scala.util.Try$.apply(Try.scala:192)
[info] 	at scala.util.Success.map(Try.scala:237)
[info] 	at scala.concurrent.Future$$anonfun$map$1.apply(Future.scala:237)
[info] 	at scala.concurrent.Future$$anonfun$map$1.apply(Future.scala:237)
[info] 	at scala.concurrent.impl.CallbackRunnable.run(Promise.scala:32)

mpkocher

PacBio Data Bundle Proposal

• minimal JSON format to encode paths and file types
• cross language model support for python, c++, and scala
• Testing: can be used in cram tests
• Extend model to download resources in next iteration

Example

mpkocher

Resequencing Condition Type

Has both the SubreadSet, ReferenceSet and final AlignmentSet output

{
  "_condition_doc": "Example of a 'Resequencing' Condition Type",
  "conditions": [
    {

mpkocher

tmp $> cd test-ve/
test-ve $> virtualenv ve
New python executable in /Users/mkocher/tmp/test-ve/ve/bin/python2.7
Also creating executable in /Users/mkocher/tmp/test-ve/ve/bin/python
Installing setuptools, pip, wheel...done.
test-ve $> git clone [email protected]:PacificBiosciences/pbsmrtpipe.git
Cloning into 'pbsmrtpipe'...
remote: Counting objects: 6672, done.
remote: Compressing objects: 100% (93/93), done.
remote: Total 6672 (delta 60), reused 0 (delta 0), pack-reused 6579

mpkocher

#!/bin/env bash

#set -o
# This is the new >= 4.1.0 config setup

source /mnt/software/Modules/current/init/bash
module load jq
module load jdk/1.8.0_71

# Sets up SMRT Link System ENV

mpkocher

import java.util.UUID

import spray.json._
import DefaultJsonProtocol._

/**
  * Run using
  *
  * amm -f predef.scala Example.scala
  *

mpkocher

ve/*
*.sh

mpkocher

<?xml version="1.0"?>
<pbmeta:OutputOptions>
  <!-- The Results Folder is now the RELATIVE PATH -->
  <pbmeta:ResultsFolder>r54001_20151222_200323/1_A01/43323838-9129-4c2e-b3bb-164c2d6804ef</pbmeta:ResultsFolder>
  <pbmeta:CollectionPathUri>/pbi/collections/xfer-test/r54001_20151222_200323/1_A01/43323838-9129-4c2e-b3bb-164c2d6804ef/</pbmeta:CollectionPathUri>
  <pbmeta:CopyFiles>
    <pbmeta:CollectionFileCopy>Fasta</pbmeta:CollectionFileCopy>
    <pbmeta:CollectionFileCopy>Bam</pbmeta:CollectionFileCopy>
    <pbmeta:CollectionFileCopy>DarkFrame</pbmeta:CollectionFileCopy>
  </pbmeta:CopyFiles>

mpkocher

#!/bin/bash

BZURL="https://bugzilla.nanofluidics.com/show_bug.cgi?id=$1"

if [ -z "$1" ]; then
    echo "No bug number provided"
else
    /usr/bin/open -a "/Applications/Google Chrome.app" "${BZURL}"
fi

mpkocher

(pbcommand_test)pbcommand $> pbservice get-jobs --max-items 10  2> err
[INFO] 2016-03-28 15:39:18,531 Starting tool version 0.2.0
[INFO] 2016-03-28 15:39:18,545 Starting new HTTP connection (1): smrtlink-beta
[INFO] 2016-03-28 15:39:18,565 Starting new HTTP connection (1): smrtlink-beta
----  ------------------------------------  ------------------------  ----------  ---------------------------------------------------------------------------------------------  ----------  --------------------------------
5823  84cbbad5-ec44-4909-97fe-207d5070f0b9  PEG_10kLib_BA010843       SUCCESSFUL  /pbi/dept/secondary/siv/smrtlink/smrtlink-beta/smrtsuite_166987/userdata/jobs_root/005/005823  pbsmrtpipe  2016-03-27 15:27:32.166000+00:00
5820  efee3169-c1e5-4054-b0c9-717334e7d979  54045_SAT_1Cell_20160326  SUCCESSFUL  /pbi/dept/secondary/siv/smrtlink/smrtlink-beta/smrtsuite_166987/userdata/jobs_root/005/005820  pbsmrtpipe  2016-03-27 00:20:34.946000+00:00
5818  0f3c51af-30bc-4356-abc2-ccc4a2940ce0  54042_SAT_1Cell_20160326