emconfig/emwrap.bashrc at main · 3dem/emconfig · GitHub

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#!/bin/bash

# Get the directory of the current script
export ROOT="$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )"

# Load the required Python environment, either a conda or virtualenv
. ${ROOT}/../bashrc
export SCRIPTS=$ROOT/scripts

# emwrap config
export EMCONFIG_FOLDER=$ROOT

# Motioncor
export MOTIONCOR_PATH=$SCRIPTS/motioncor3.sh
export MOTIONCOR_VERSION=3

# Ctffind
export CTFFIND_PATH=/usr/local/em/ctffind-5.0/bin/ctffind
export CTFFIND_VERSION=5

# AreTomo
export ARETOMO_PATH=$SCRIPTS/aretomo3.sh
export ARETOMO_VERSION=3

export ARETOMO2=$SCRIPTS/aretomo2.sh

# CryoCare
#export CRYOCARE_PATH=$ROOT/cryocare.sh
export CRYOCARE_TRAIN=$SCRIPTS/cryocare_train.sh
export CRYOCARE_DENOISE=$SCRIPTS/cryocare_denoise.sh

# WarpTools
export WARP_LAUNCHER=$SCRIPTS/warp_launcher.sh

# PyTOM
export PYTOM_LAUNCHER=$SCRIPTS/pytom_launcher.sh

# Relion
export RELION_LAUNCHER=$SCRIPTS/relion_launcher.sh

# Shortcut to PurifiedApoF benchmark
alias bench='python -m emwrap.tests.benchmark_apof_purified'

alias emw-relion='python -m emwrap.relion'
alias emw-otf='python -m emwrap.mix.otf'
alias emw-pytom='python -m emwrap.pytom.pytom_pipeline'
alias emw-warp='python -m emwrap.warp'