Instalation and setup

Download the source code

git clone https://github.com/vertical-space/ALISEQ

git clone https://github.com/secastel/allelecounter.git ALISEQ/allelecounter

export SRC_DIR=`pwd`

conda env create -f ALISEQ/envs/aliseq.yaml -p ${SRC_DIR}/ALISEQ

source activate aliseq

mkdir testdirectory   # or whatever you want to call your working directory

cd testdirectory

Test if it’s working

echo 'ERR2353209' > targets.txt

bash aliseq.sh

It can take quite a while to download all of the required third party software

Edit the file targets.txt

manually edit the file targets.txt, placing one accession number per line, e.g.

ERR2352620
ERR2352630
ERR2352640
ERR2352650
ERR2352660
ERR2352670

alternatively, if you have run the simulate reads pipeline, you can specify simulated data, e.g.

simulation_1_x1
simulation_1_x2

Making sure the names correspond to fastq files in the reads directory, e.g.

simulation_1_x1.fastq.gz
simulation_1_x2.fastq.gz

Then you can just relaunch the workflow with:

bash aliseq.sh

Other stuff

this is a demo of how to generate a document in sphinx

secondFunc(arg1)

not a real function!

import random

random.seed(42)

def randomGene(m=300,M=10000):
    """create a random ATCG string with length randomly chosen from within the range [m,M]
    """
    length = 0
    while not m < length < (M+1):
        length = int(np.random.normal(3392,2600)) # mu, sigm
    return ''.join([random.choice('ATCG') for i in range(length)])

randomGene()

Note

this is an example of a note. i’m not really sure what it does yet, so this is also a test of that.

this is paragraph 2 of my fancy note.

Warning

I’m pretty sure i know what this does!

class Request

this is one way to document a class

func1()

description of the func1 method

attr1

description of the attr1 attribute

running the simulation

this is an insect

This is the caption of the figure (a simple paragraph).

running the ASE workflow

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