run_yass.sh

#!/bin/bash

## Import functions for workflow management. 
## Get the path to this function: 
execpath="$0"
echo execpath
scriptpath="$(dirname "$execpath")/ncap_utils"

source "$scriptpath/workflow.sh"
## Import functions for data transfer 
source "$scriptpath/transfer.sh"

## Set up error logging. 
errorlog

## Declare variables: bucketname,inputpath,groupdir,resultdir,dataname,configname given standard arguments to bin script.
#parseargsstd "$1" "$2" "$3" "$4"

#errorrep
## Custom setup for this workflow.
source .dlamirc

export PATH="/home/ubuntu/anaconda3/bin:$PATH"

source activate yass

## Declare local storage locations: 
userhome="/home/ubuntu"
datastore="ncapdata/localdata/"
configstore="ncapdata/localconfig/"
outstore="ncapdata/localdata/tmp"
## Make local storage locations
accessdir "$userhome/$datastore" "$userhome/$configstore" "$userhome/$outstore"

## Stereotyped download script for data. The only reason this comes after something custom is because we depend upon the AWS CLI and installed credentials. 
download "$inputpath" "$bucketname" "$datastore"

## Stereotyped download script for config: 
download "$configpath" "$bucketname" "$configstore"

###############################################################################################
## Custom bulk processing. 
## Bring in other files!
yassconfigpath=$(jq ".config" "$userhome/$configstore/$configname" | sed 's/"//g')
yassgeompath=$(jq ".geom" "$userhome/$configstore/$configname" | sed 's/"//g')

echo $yassconfigpath
echo $yassgeompath
echo $configpath
echo paths
## download the 
## download the yass config file and the geom storate to the same storage area as the data.  
download "$yassconfigpath" "$bucketname" "$datastore"

download "$yassgeompath" "$bucketname" "$datastore"

cd "$userhome/$datastore"

source activate yass

yass sort config.yaml
#export CAIMAN_DATA="/home/ubuntu/caiman_data"
### For efficiency: 
#export MKL_NUM_THREADS=1
#export OPENBLAS_NUM_THREADS=1
#CAIMAN_DATA="$userhome/caiman_data"
#python parse_config.py "$bucketname" "$userhome/$configstore/$configname" "$userhome/$configstore"
#python process.py "$userhome/$configstore/final_pickled" "$userhome/$datastore/$dataname" "$userhome/$outstore"
cd $userhome
###############################################################################################
## Stereotyped upload script for the data
upload "$outstore" "$bucketname" "$groupdir" "$resultdir" "mp4"
#
#cleanup "$datastore" "$outstore"