dakl

pip install git+https://github.com/QuirkyCort/pgzhelper.git

dakl

I like super mario.

dakl

"""Simple example on how to log scalars and images to tensorboard without tensor ops.

License: Copyleft
"""
__author__ = "Michael Gygli"

import tensorflow as tf
from StringIO import StringIO
import matplotlib.pyplot as plt
import numpy as np

dakl

#/usr/bin/env bash

sudo apt install -y bzip2 git htop


######################################################
# FISH SHELL
sudo su -
echo 'deb http://download.opensuse.org/repositories/shells:/fish:/release:/2/Debian_9.0/ /' > /etc/apt/sources.list.d/fish.list
apt-get update -y

dakl

11540659 + 0 in total (QC-passed reads + QC-failed reads)
6365 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
11540643 + 0 mapped (100.00%:-nan%)
11534294 + 0 paired in sequencing
5767147 + 0 read1
5767147 + 0 read2
11518384 + 0 properly paired (99.86%:-nan%)
11534266 + 0 with itself and mate mapped

dakl

Sample	HS_LIBRARY_SIZE	HS_PENALTY_50X	PCT_TARGET_BASES_10X	OFF_BAIT_BASES	ON_BAIT_BASES	PCT_OFF_BAIT	ON_BAIT_VS_SELECTED	HS_PENALTY_30X	PCT_TARGET_BASES_30X	READ_GROUP
	HS_PENALTY_40X	TOTAL_READS	ON_TARGET_BASES	MEAN_TARGET_COVERAGE	ZERO_CVG_TARGETS_PCT	PCT_PF_UQ_READS	BAIT_TERRITORY	PCT_USABLE_BASES_ON_TARGET	PCT_PF_READS	LIBRARY	PF_READS	PCT_TARGET_BASES_2X	GC_DROPOUT	AT_DROPOUT	PCT_TARGET_BASES_50X	GENOME_SIZE	PCT_PF_UQ_READS_ALIGNED	FOLD_80_BASE_PENALTY	HS_PENALTY_10X	PCT_USABLE_BASES_ON_BAIT	HS_PENALTY_20X	PF_UNIQUE_READS	PCT_TARGET_BASES_20X	SAMPLE	NEAR_BAIT_BASES	TARGET_TERRITORY	FOLD_ENRICHMENT	PCT_TARGET_BASES_40X	PCT_TARGET_BASES_100X	BAIT_DESIGN_EFFICIENCY	BAIT_SET	HS_PENALTY_100X	PCT_SELECTED_BASES	MEAN_BAIT_COVERAGE	PF_UQ_BASES_ALIGNED	PF_UQ_READS_ALIGNED
P-00017852-N-03021179-TD2-CB1		0.0	0.0	899777371.0	524812.0	0.997626	0.245107	0.0	0.0	
	0.0	9609180.0	524812.0	0.899072	0.836774	1.0	1689097.0	0.000543	1.0		9609180.0	0.045124	2.779323	2.431879	0.0	3137454505.0	0.938492	?	0.0	0.000543	0.0	960918

dakl

COMMAND LINE:	skewer -z -t 2 --quiet -o trimmed test_1.fastq.gz test_2.fastq.gz
Input file:	test_1.fastq.gz
Paired file:	test_2.fastq.gz
trimmed:	trimmed-pair1.fastq.gz, trimmed-pair2.fastq.gz

Parameters used:
-- 3' end adapter sequence (-x):	AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
-- paired 3' end adapter sequence (-y):	AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA
-- maximum error ratio allowed (-r):	0.100
-- maximum indel error ratio allowed (-d):	0.030

dakl

## htsjdk.samtools.metrics.StringHeader
# picard.analysis.CollectOxoGMetrics INPUT=virtual-tumor.bam OUTPUT=oxog.txt REFERENCE_SEQUENCE=/proj/b2010040/private/nobackup/autoseqer-genome/genome/human_g1k_v37_decoy.fasta    MINIMUM_QUALITY_SCORE=20 MINIMUM_MAPPING_QUALITY=30 MINIMUM_INSERT_SIZE=60 MAXIMUM_INSERT_SIZE=600 USE_OQ=true CONTEXT_SIZE=1 STOP_AFTER=2147483647 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
## htsjdk.samtools.metrics.StringHeader
# Started on: Wed Feb 10 11:23:36 UTC 2016

## METRICS CLASS	picard.analysis.CollectOxoGMetrics$CpcgMetrics
SAMPLE_ALIAS	LIBRARY	CONTEXT	TOTAL_SITES	TOTAL_BASES	REF_NONOXO_BASES	REF_OXO_BASES	REF_TOTAL_BASES	ALT_NONOXO_BASES	ALT_OXO_BASES	OXIDATION_ERROR_RATE	OXIDATION_Q	C_REF_REF_BASES	G_REF_REF_BASES	C_REF_ALT_BASES	G_REF_ALT_BASES	C_REF_OXO_ERROR_RATE	C_REF_OXO_Q	G_REF_OXO_ERROR_RATE	G_REF_OXO_Q
virtual-tumor	virtual-tumor	ACT	27	388	238	150	388	0	0	0.002577	25.888

dakl

$ vagrant up
Bringing machine 'stackstorm-master' up with 'virtualbox' provider...
Bringing machine 'testarteria1' up with 'virtualbox' provider...
Bringing machine 'testuppmax' up with 'virtualbox' provider...
==> stackstorm-master: Importing base box 'ubuntu/trusty64'...
==> stackstorm-master: Matching MAC address for NAT networking...
==> stackstorm-master: Checking if box 'ubuntu/trusty64' is up to date...
==> stackstorm-master: Setting the name of the VM: arteria-provisioning_stackstorm-master_1445365324370_61846
==> stackstorm-master: Clearing any previously set forwarded ports...
==> stackstorm-master: Fixed port collision for 22 => 2222. Now on port 2201.

dakl

#Define the list of machines
machines = {
    :reportcreatormahcine => {
        :hostname => "reportcreatormahcine",
        :ipaddress => "10.10.10.99" #gretzky
    },
}

#--------------------------------------
# General provisioning inline script