hyeshik

SNU Bioinformatics and Practice 2 - Week 2

Contains the notebooks for the practice sessions.

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#!/usr/bin/env python3
#
# Copyright (c) 2018 Hyeshik Chang
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:

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hyeshik

hyeshik

{
 "metadata": {
  "name": "",
  "signature": "sha256:f99925a6f73a1e36bc91415d84266705e3bdf72304d8dba7bcfb6c94ca7b270a"
 },
 "nbformat": 3,
 "nbformat_minor": 0,
 "worksheets": [
  {
   "cells": [

hyeshik

{
 "metadata": {
  "name": "",
  "signature": "sha256:d1355cd3916fec7cb8d44c23a9217f3bbff36499b973ea66c47448aa35736365"
 },
 "nbformat": 3,
 "nbformat_minor": 0,
 "worksheets": [
  {
   "cells": [

hyeshik

#!/bin/sh
#rule: {job}
#input: {job.input}
#output: {job.output}
#threads: {job.threads}
{self.workflow.snakemakepath} --snakefile {self.workflow.snakefile} \
--force -j{self.cores} \
--directory {workdir} --nocolor --notemp --quiet --nolock {job.output} \
> /dev/null && touch "{jobfinished}" || touch "{jobfailed}"
exit 0

hyeshik

#!/bin/sh
#
# Adopts and submit a snakemake cluster job script to SGE queue
#
#  by Hyeshik Chang
#

JOBSCRIPT_SNAKEMAKE=$1
JOBSCRIPT_SGE="`dirname $1`/sge`basename $1`"