Mike Covington mfcovington

I'm in the process of making a CMS for scientific research labs. Our lab does a lot of genome/transcriptome sequencing and bioinformatic analyses. Therefore, I've been creating apps that would be useful for a scientific lab in general as well as one with our focus. I chose to build these upon django CMS to give extra flexibility in the both site design and the way the lab members interact with/edit the content.

There are a few integral apps still in the pipeline, but below are the ones that are in a usable state (although they do vary in terms of completeness). Once I've made sufficient progress, I plan on writing up a manuscript to submit to a scientific journal, because I believe that this type of site could be very useful for many labs. The project that I have incorporated these apps into is djangocms-lab-site.

django CMS apps:
djangocms-lab-members (Live App - [GitHub](https://github.com/mfcovi

	function extract_sequences {
	GENE=$1
	EXON=$2

	CHR=$3

	BAM_START=$4
	BAM_END=$5

	EXON_START=$6

	sudo yum -y update
	sudo yum install -y gcc48-plugin-devel.x86_64

	sudo mkdir /installs
	cd /installs

	sudo wget https://github.com/samtools/samtools/releases/download/1.3.1/samtools-1.3.1.tar.bz2
	sudo tar -xjf samtools-1.3.1.tar.bz2
	cd samtools-1.3.1

	library(edgeR)
	library(ggplot2)

	setwd('/path/to/counts-directory')

	counts.files <- list.files(pattern="\\.counts$")
	sample.names <- c('H6 GFP #1', 'H6 GFP #2', 'HIF-2α #3', 'HIF-2α #4', 'HIF-1α #7', 'HIF-1α #8')
	counts.df <- readDGE(counts.files, labels=sample.names, group=c(rep('H6 GFP', 2), rep('HIF-2α', 2), rep('HIF-1α', 2)))

	# In this case, need to remove the ".1", etc. in order to be able to merge with annotation file

	#!/usr/bin/env sh
	# Count reads and validate FASTQ files

	FASTQ_DIR="$1"

	if [ -z ${FASTQ_DIR+x} ]; then
	echo "Usage: $0 /path/to/fastq/files/"
	exit 1
	fi

	################################
	# Auto-merge by sample and end #
	################################

	BASE_DIR=/Volumes/seagate/giriget

	for SAMPLE in {1..144}; do
	for END in R1 R2; do

	# Gather files to process

	[
	{
	sampleId: "CMMC001_33",
	lane: 2,
	barcode: "AACAGGCG",
	clusters: 3681934
	},
	{
	sampleId: "CMMC001_33",
	lane: 3,

	from openpyxl import load_workbook


	wb = load_workbook(filename = 'SubmissionForm.xlsx')
	sheet = wb.get_sheet_by_name(wb.sheetnames[0])
	header_row = sheet.rows[0]

	for row in sheet.rows[1:]:

	# Ignore empty rows

	REPOS_DIR=~/git.repos

	for DIR in find $REPOS_DIR/* -maxdepth 0 -type d; do
	cd $DIR
	NEEDS_PUSH=`git rev-list develop...origin/develop --count`
	if [ "$NEEDS_PUSH" -gt 0 ]; then
	echo $DIR >> ~/repos-that-need-pushed
	fi
	done

	cell culture
	purification