jfear’s gists

jfear / run_rail_parallel.py

Created April 21, 2016 19:50

starting point for wrapping rail-rna

	#!/usr/bin/env python

	import os
	import sys
	import subprocess
	import time
	import logging
	import ipyparallel

	TEMPLATE="""#!/bin/sh

jfear / emr_simulator.patch

Created April 21, 2016 19:57

patch of rail-rna to avoid race condition

	1064,1068d1063
	< retries = 0
	< while not os.path.isfile(file_or_archive):
	< time.sleep(5)
	< if retries > 5: break
	< retries += 1
	1426,1430d1420
	< retries = 0
	< while not os.path.isfile(file_or_archive):
	< time.sleep(5)

jfear / profile-save.py

Last active April 26, 2016 14:50 — forked from jbwhit/profile-save.py

	c = get_config()
	### If you want to auto-save .html and .py versions of your notebook:
	# modified from: https://github.com/ipython/ipython/issues/8009
	import os
	from subprocess import check_call

	def post_save(model, os_path, contents_manager):
	"""post-save hook for converting notebooks to .py scripts"""
	if model['type'] != 'notebook':
	return # only do this for notebooks

jfear / download_sra_xsd.sh

Created June 23, 2016 21:32

Download SRA XSDs for use with biopython

	#!/bin/bash
	# Trying to get biopython to parse SRA xml output. I think I need these XSDs produced by SRA to do this.

	if [ ! -e ~/.biopython/Bio/Entrez/XSDs ]; then mkdir -p ~/.biopython/Bio/Entrez/XSDs; fi
	cd ~/.biopython/Bio/Entrez/XSDs

	wget -O SRA.common.xsd "http://www.ncbi.nlm.nih.gov/viewvc/v1/trunk/sra/doc/SRA_1-5/SRA.common.xsd?view=co"
	wget -O SRA.submission.xsd "http://www.ncbi.nlm.nih.gov/viewvc/v1/trunk/sra/doc/SRA_1-5/SRA.submission.xsd?view=co"
	wget -O SRA.study.xsd "http://www.ncbi.nlm.nih.gov/viewvc/v1/trunk/sra/doc/SRA_1-5/SRA.study.xsd?view=co"
	wget -O SRA.sample.xsd "http://www.ncbi.nlm.nih.gov/viewvc/v1/trunk/sra/doc/SRA_1-5/SRA.sample.xsd?view=co"

jfear / reference-markdown-metadata-from-jinja-template.py

Created July 27, 2016 21:02 — forked from glombard/reference-markdown-metadata-from-jinja-template.py

How to use Markdown as a filter in a Jinja2 template, and then extract the Markdown Meta property directly from the template. Assuming you want to use the Meta-data value before rendering the converted Markdown content (e.g. in the html head), the trick is to render the markdown first, save it to a variable (html_content in this example) using a…

	from pprint import pprint
	import jinja2
	import markdown

	HTML_TEMPLATE = """{% macro get_html() %}
	{{ content \| markdown }}
	{% endmacro %}
	{% set html_content = get_html() %}

	Title from Markdown meta-data: {{ get_title() }}

jfear / jupyterTunnel

Last active September 12, 2017 18:55

A helper script for creating an ssh tunnel between machines for running jupyter notebook.

	#!/bin/bash
	# This is a little bash script to create a tunnel for running jupyter
	# notebooks.
	#
	# You can run the script like so:
	#
	# $ jupyterTunnel start remote1
	#
	# This will create an ssh tunnel on port 7000 to remote 1, and create a control
	# socket 'jupyter-ctrl-socket' in the current working direcotry. To stop the

jfear / homebrew-install-gnu.sh

Last active August 11, 2017 14:51 — forked from xuhdev/homebrew-install-gnu.sh

Install GNU programs on OS X https://www.topbug.net/blog/2013/04/14/install-and-use-gnu-command-line-tools-in-mac-os-x/

	# see https://www.topbug.net/blog/2013/04/14/install-and-use-gnu-command-line-tools-in-mac-os-x/

	# core
	brew install coreutils

	# key commands
	brew install binutils
	brew install diffutils
	brew install ed --default-names
	brew install findutils --with-default-names

jfear / workflowy.css

Created January 26, 2017 22:36

workflowy dark simple

	@namespace url(http://www.w3.org/1999/xhtml);
	/* minimal page background */
	#pageContainer {
	margin-top: 24px;
	}
	.page {
	max-width: 100% !important;
	border: none !important;
	margin-bottom: 0 !important;
	/* fix for dynamic positioning of the .page div */

jfear / hisat.snake

Created February 9, 2017 16:30

	# vim: set ft=snakemake:
	shell.prefix("""set -euo pipefail;
	if [ -e /lscratch/$SLURM_JOBID ]; then
	export TMPDIR=/lscratch/$SLURM_JOBID
	else
	export TMPDIR=/tmp
	fi;
	""")
	workdir: '.'

jfear / test_minimal.snake

Last active February 21, 2017 22:44

Minimal test file for conda error

	#/usr/bin/env python
	import os

	from lcdblib.snakemake import helpers
	from lcdblib.utils import utils

	URI = '../lcdb-wrapper-tests'
	TMPDIR='/mnt/threeTB/centos_scratch'
	references = {
	'dmel': {

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