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#!/bin/bash
#SBATCH -t 24:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --array 1-97

cd /home/mcdonadt/agp_demux_barcode_assessment-8.4.21
source activate qiime2-2020.11
export TMPDIR=/panfs/dtmcdonald/
python processor.py demux.details $SLURM_ARRAY_TASK_ID

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import qiime2
import pandas as pd
import glob
from collections import defaultdict
import sys
import time, os

details = [l.strip() for l in open(sys.argv[1])]
f = details[int(sys.argv[2]) - 1]

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#!/bin/bash
set -e
set -x

envname=q2deblur_mvp_test
executiondir=mvp
redeploy=$1

source deactivate

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# python 2
# conda install biom-format -c bioconda
# conda install matplotlib  # pysurvey setup.py is incomplete
# pip install -e "hg+https://bitbucket.org/yonatanf/pysurvey#egg=pysurvey"
# note: the pysurvey build in pypi does not work. unsure why. 

import click

# this little gem is because pysurvey depends on an older version of scipy
# and attempts to import nanmedian from scipy.stats. This is a dirty hack.

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import numpy as np
import bp
import biom
import skbio
import sys
import joblib
import h5py

class biom_counts_wrapper(object):
    def __init__(self, table_f):

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{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []