bsmith89

#!/usr/bin/env bash
remote='<PROJECT_PATH_HERE>'

for path in $@
do
    dirname=$(dirname $path)
    basename=$(basename $path)
    mkdir -p "$dirname"

    # Use rsync --partial for restartable transfers.

bsmith89

#!/usr/bin/env bash
# Remove pairs which hit the mouse reference.
#
# I haven't tested this script, but you should be able to use the commands in it
# to do your contaminant filtering.
# It would probably be best to feed in fully trimmed reads.  Otherwise you
# might want to use "local" mapping.
# See: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml#end-to-end-alignment-versus-local-alignment

# Adapter trim and quality trim your HiSeq reads

bsmith89

bsmith89

bsmith89

*.ipynb	filter=dropoutput_jupyter
*.[tc]sv	diff=daff-csv
*.[tc]sv	merge=daff-csv

bsmith89

bsmith89

# ====================
#  Project Makefile
# ====================
#  User Configuration {{{1
# ====================

# Major targets {{{2
.PHONY: figs res
figs:
# [Partially redacted]

bsmith89

#! /usr/bin/env python
"""From http://stackoverflow.com/a/20844506/1951857

To use::

    # Add the script to your path
    chmod +x path/to/this/ipynb_output_filter.py
    echo "*.ipynb    filter=dropoutput_ipynb" >> ~/.gitattributes
    git config --global core.attributesfile ~/.gitattributes
    git config --global filter.dropoutput_ipynb.clean ipynb_output_filter.py