Ryan Dale daler

On an m4.10xlarge:

sudo apt-get install imagemagick xorg libx11-dev libglu1-mesa-dev htop

Then fire up R as root, and run the following (note that biocLite nowadays will install from CRAN which is pretty nice!)

Shiny app for exploring Fisher's exact tests.

Run locally with the following command in this directory:

Rscript -e "shiny::runApp()"

Setup

Using bioconda, you can install everything you need for this example with

conda install --channel bioconda pybedtools bedtools htslib matplotlib

	#!/usr/bin/env python

	"""
	Expand orthogroups from an orthoXML file into TSV, and then only select the
	easy cases where there is exactly one gene from each species. The full TSV is
	output as well.

	Currently assumes pairwise files.

	Output will have suffixes _full.tsv and _pair.tsv, with full and only genes in

	"""
	Requirements:

	- access to an external, publicly-accessible server. The user
	authentication will redirect here. You can tail the logs on that server to
	see the response.

	- Access Key ID (akid) from LabArchives support. This requires a ticket and
	approval from whoever is running the LabArchives instance. It is expected
	that this is passed as an env var, LA_AKID.

	from __future__ import print_function
	import pybedtools

	import subprocess as sp
	print('pbt:', pybedtools.__version__)
	pybedtools.debug_mode(True)
	print(
	sp.check_output(['which', 'bedtools'], universal_newlines=True).strip(),
	'(',
	sp.check_output(['bedtools', '--version'], universal_newlines=True).strip(),

	recipe check info already_in_bioconda bat_file exists_in_channels fix missing_hash missing_home missing_license missing_summary no_tests parse_error uses_git_url
	recipes/multiqc-bcbio missing_hash "{'fix': 'add md5, sha1, or sha256 hash to ""source"" section', 'missing_hash': True}" "add md5, sha1, or sha256 hash to ""source"" section" True
	recipes/multiqc-bcbio uses_git_url {'fix': 'use tarballs whenever possible', 'uses_git_url': True} use tarballs whenever possible True
	recipes/moreutils missing_hash "{'fix': 'add md5, sha1, or sha256 hash to ""source"" section', 'missing_hash': True}" "add md5, sha1, or sha256 hash to ""source"" section" True
	recipes/vt missing_hash "{'fix': 'add md5, sha1, or sha256 hash to ""source"" section', 'missing_hash': True}" "add md5, sha1, or sha256 hash to ""source"" section" True
	recipes/bcdoc in_other_channels {'exists_in_channels': {'conda-forge'}, 'fix': 'consider deprecating'} {'conda-forge'} consider deprecating
	recipes/bcdoc

	"""
	Run the script to see example output.

	Modify the features in a, b, and c to see how they affect the output

	pybedtools.contrib.plotting.BinaryHeatmap uses the "cluster" method,
	but unclustered and naive merge versions are shown as well.
	"""

	import numpy as np

	#!/usr/bin/env python

	# Install into new environment and activate it before running this script:
	#
	# conda create -n biostars-212519 python=3 requests numpy pandas
	# source activate biostars-212519
	# python identify_encode_controls.py

	import pandas
	import numpy as np

	# Example for https://www.biostars.org/p/193145

	import pybedtools
	import pysam

	# Use an example BAM file included with pybedtools
	fn = pybedtools.example_filename('x.bam')
	bam = pysam.Samfile(fn, 'r')

	# Filter reads using pysam. Since all aspects of the SAM-format read