hkmoon

hkmoon

library(plotly)
library("RColorBrewer")

# display.brewer.all()
x <- c("Non-MT", "MT-8", "MT-16")
y <- c(61.88, 6.79, 2.38)
color <- brewer.pal(n = 3, name = "Dark2")

p <- plot_ly(
  x = ~x,

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export TRINITY="sudo singularity exec /home/vagrant/Trinity-v2.8.4.simg Trinity"

cd sample_data
$TRINITY --samples_file samples.PE.txt --seqType fq --max_memory 1G --output trinity_test_samples_PE

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export TRINITY_HOME="singularity exec /home/vagrant/Trinity-v2.8.4.simg Trinity"

mkdir trinityrnaseq
cd trinityrnaseq
git init
git remote add -f origin https://github.com/trinityrnaseq/trinityrnaseq.git
git config core.sparseCheckout true
echo "sample_data/test_Trinity_Assembly" >> .git/info/sparse-checkout
git pull origin master
mv sample_data/test_Trinity_Assembly/* .

hkmoon

# -*- mode: ruby -*-
# vi: set ft=ruby :

# All Vagrant configuration is done below. The "2" in Vagrant.configure
# configures the configuration version (we support older styles for
# backwards compatibility). Please don't change it unless you know what
# you're doing.
####################################################
# You can do this entire process while running on the filesystem you want to resize (yes, it's safe and fully supported). There is no need for rescue CDs or alternate operating systems.
#

hkmoon

#!/usr/bin/env bash
export DEBIAN_FRONTEND=noninteractive
apt-get update
apt-get install -y python-pip python3-pip
pip install numpy biopython
pip3 install numpy biopython

# create Trinity output, DATA, scripts folder
sudo -S -u vagrant mkdir -p /vagrant/output
sudo -S -u vagrant ln -s /vagrant/output output

hkmoon

Resize a Hard Disk for a Virtual Machine

Our Virtual Machines are provisioned using Vagrant from a Linux base box to run using VirutalBox. If the Hard Disk space runs out and you cannot remove files to free-up space, you can resize the Hard Disk using some VirtualBox and Linux commands.

Some assumptions

The following steps assume you've got a set-up like mine, where:

hkmoon

Byobu Commands
==============

        byobu                              Screen manager


Level 0 Commands (Quick Start)
------------------------------

        <F2>                               Create a new window

hkmoon

void process(File hdf5, SpimDataMinimal spimData, Interval roi) {
    AbstractSequenceDescription<?, ?, ?> sequenceDescription = spimData.getSequenceDescription();
    Hdf5ImageLoader hdf5Loader = new Hdf5ImageLoader(hdf5, /* hdf5 partitions */ null, sequenceDescription);
    for (TimePoint timepoint : sequenceDescription.getTimePoints().getTimePointsOrdered()) {
        for (BasicViewSetup setup : sequenceDescription.getViewSetupsOrdered()) {
            RandomAccessibleInterval<UnsignedShortType> img = hdf5Loader.getSetupImgLoader(setup.getId()).getImage(timepoint.getId(), 0); // full res
            RandomAccessibleInterval<UnsignedShortType> imgRoi = Views.interval(img, roi);
            // process imgRoi here, it will be lazily loaded when accessed
        }
    }

hkmoon

import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;

/**
 * Created by moon on 12/8/15.
 */
public class Check
{