Niknafs

This list is outdated. This post has a list of bioinformatics/genomics/genetics workshops and training materials that I haven't updated since 2015.

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In-person courses

Note that many of the courses shown below also have course materials from past years publicly available online.

Cold Spring Harbor Courses:

Niknafs

Preparing for Installation

wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh

bash Miniconda3-latest-Linux-x86_64.sh

conda update conda

# install tensorflow in conda
conda install -c conda-forge tensorflow

Niknafs

qrsh
module load python/2.7.9
git clone https://github.com/NCI-GDC/gdc-client/
cd gdc-client
git checkout master
virtualenv venv
source venv/bin/activate
pip install --upgrade pip
pip install --upgrade setuptools argparse
pip install -r requirements.txt

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addGrp:
        java -Xmx${heap}m -Djava.io.tmpdir\=${temp_folder}/${patient}  \
         -jar ${picard}/AddOrReplaceReadGroups.jar \
          RGLB\=${sample}.fastq \
          RGPL\=Illumina \
          RGPU\=${sample} \
          RGSM\=${sample} \
          I\=${SCRATCH}/${sample}/${sample}.rmdup.bam \
          O\=${SCRATCH}/${sample}/${sample}.rmdup.grp.bam \
          SORT_ORDER\=coordinate \

Niknafs

Start a docker with correct working directory mounted

docker run -d --name expands -i -t -v xxx:xxx ubuntu:14.04 bash

Install the requirements in the container

docker attach expands
# apt-get update
# apt-get install emacs

Niknafs

Problem:

Often, after restarting my machine (OS X Yosemite, version 10.10.5) I encounter the following error the first time I run docker quick start terminal. The problem is discussed in great length here, but none of the proposed solutions seemed to fix it on my machine.

Specs

OS X Yosemite version 10.10.5
Docker version  1.9.1

Niknafs

1. Install the required linux library

apt-get install libxmu-dev

2. Install matlab component runtime

From the directory ([MCR dir]) with instal script run:

Niknafs

BAM files generated by Exome sequencing at several sequencing service centers do not comply with the required specs assumed by the GATK tools. Here are steps involved in processing these raw bam files to prepare them for analysis by other tools.

These steps are formatted as a sequence of bocks in a make file. Before getting started, make sure that you have specified the path to the following pre-requisites in the header of the make file.

Prerequisites:

# general workspace path definitions
SRC=/my/source/directory/with/installed/tools/
temp_folder=/mnt/hn07_disk001/my-project/tmp/
SCRATCH=/mnt/hn07_disk001/my-project/pipeline 

Niknafs

Overview

This document will cover the steps involved in installation of python-igraph package for python 2.7. For python 3.x, the steps will likely be similar, but possibly not identical.

The python-igraph package requires cairo library, and Pycairo python package, and igraph C core. cairo is a 2D graphics library with support for multiple output devices and Pycairo is a set of python bindings for cairo graphics library.

In this document, it is assumed that the user does not have root access and thus uses --prefix to indicate a local directory where /lib and /bin can be located, for which the user has write privilage.

Cairo

Niknafs

This document will cover the steps involved in installation of `python-igraph` package for python 2.7. For python 3.x, the steps will likely be similar, but possibly not identical.

The python-igraph package requires `cairo` library, and `py2cairo` python package. `cairo` is a