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# Create the directory fake/test and the file fake/test/sample.Mutect2.snpSift.vcf.gz
# Run on cluster, example:
# snakemake --cluster 'bash ' -j1 -p

rule all:
    input:
        expand(
            "fake/test/{t}.Mutect2.snpSift.hardfilter.vcf.gz",
            t=['sample']),

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#!/usr/bin/env python3

import requests
import hashlib
import getpass

password = getpass.getpass()
hash = hashlib.sha1(password.encode("utf8")).hexdigest().upper()
head, rest = hash[:5], hash[5:]
r = requests.get("https://api.pwnedpasswords.com/range/%s" % head)

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Download Google Drive files with WGET

Example Google Drive download link:

https://docs.google.com/open?id=[ID]
To download the file with WGET you need to use this link:

https://googledrive.com/host/[ID]

Example WGET command:

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Ensembl's VEP (Variant Effect Predictor) is popular for how it picks a single effect per gene as detailed here, its CLIA-compliant HGVS variant format, and Sequence Ontology nomenclature for variant effects.

To follow these instructions, we'll assume you have these packaged essentials installed:

## For Debian/Ubuntu system admins ##
sudo apt-get install -y build-essential git libncurses-dev

## For RHEL/CentOS system admins ##
sudo yum groupinstall -y 'Development Tools'
sudo yum install -y git ncurses-devel

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for file in *.vcf*; do
  for sample in `bcftools view -h $file | grep "^#CHROM" | cut -f10-`; do
    bcftools view -c1 -Oz -s $sample -o ${file/.vcf*/.$sample.vcf.gz} $file
  done
done

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Install Samtools, BCFTools and htslib on linux

Install some build dependencies

sudo apt-get install autoconf automake make gcc perl zlib1g-dev libbz2-dev liblzma-dev libcurl4-gnutls-dev libssl-dev libncurses5-dev

[samtools]

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Install dependecies

$ sudo apt-get install mysql-server mysql-client mysql-common libmysqlclient-dev
$ sudo apt-get install build-essential git-core cmake zlib1g-dev libncurses-dev patch
$ sudo apt-get install samtools

Create a new enviromnent to pvac-sec

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Create a conda environment to be used with caRpools

$ conda create -n carpools -y pip

Activate the new env

$ source activate carpools

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Download Miniconda

• Python 2.7

  # 32 bits
  $ wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86.sh
  # 64 bits
  $ wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh

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#!/bin/bash

NAME="hello_app"                                  # Name of the application
DJANGODIR=/webapps/hello_django/hello             # Django project directory
SOCKFILE=/webapps/hello_django/run/gunicorn.sock  # we will communicte using this unix socket
USER=hello                                        # the user to run as
GROUP=webapps                                     # the group to run as
NUM_WORKERS=3                                     # how many worker processes should Gunicorn spawn
DJANGO_SETTINGS_MODULE=hello.settings             # which settings file should Django use
DJANGO_WSGI_MODULE=hello.wsgi                     # WSGI module name