From 5d15e037ece9cd1846724d1587f440737fbd11c6 Mon Sep 17 00:00:00 2001
From: Lael Barlow <lael@ualberta.ca>
Date: Wed, 5 Jan 2022 14:46:22 -0700
Subject: [PATCH] Remove unnecessary Makefile and associated scripts.

---
 Makefile                                   |  49 ------
 scripts/activate_python_env.sh             |   7 -
 scripts/archive_workflow.sh                |  14 --
 scripts/clean_virtualenvs.sh               |  25 ---
 scripts/deactivate_python_env.sh           |  11 --
 scripts/determine_snakemake_env_options.sh |  17 --
 scripts/determine_snakemake_profile.sh     |  24 ---
 scripts/dry_run.sh                         |  29 ----
 scripts/install.sh                         | 179 ---------------------
 scripts/quantify_test_coverage.py          |  42 -----
 scripts/run_data_setup.sh                  |  22 ---
 scripts/run_fwd_only.sh                    |  22 ---
 scripts/run_workflow.sh                    |  23 ---
 scripts/uninstall.sh                       |  19 ---
 scripts/unlock_workflow.sh                 |  10 --
 scripts/workflow_python_env_definition.sh  | 131 ---------------
 16 files changed, 624 deletions(-)
 delete mode 100644 Makefile
 delete mode 100644 scripts/activate_python_env.sh
 delete mode 100644 scripts/archive_workflow.sh
 delete mode 100644 scripts/clean_virtualenvs.sh
 delete mode 100644 scripts/deactivate_python_env.sh
 delete mode 100644 scripts/determine_snakemake_env_options.sh
 delete mode 100644 scripts/determine_snakemake_profile.sh
 delete mode 100644 scripts/dry_run.sh
 delete mode 100644 scripts/install.sh
 delete mode 100644 scripts/quantify_test_coverage.py
 delete mode 100644 scripts/run_data_setup.sh
 delete mode 100644 scripts/run_fwd_only.sh
 delete mode 100644 scripts/run_workflow.sh
 delete mode 100644 scripts/uninstall.sh
 delete mode 100644 scripts/unlock_workflow.sh
 delete mode 100644 scripts/workflow_python_env_definition.sh

diff --git a/Makefile b/Makefile
deleted file mode 100644
index 7da5462..0000000
--- a/Makefile
+++ /dev/null
@@ -1,49 +0,0 @@
-# Makefile for the AMOEBAE Example Workflow repository.
-
-SHELL=/bin/bash
-
-install:
-	bash scripts/install.sh
-
-dry_run:
-	bash scripts/dry_run.sh
-
-run_data_setup:
-	nohup bash scripts/run_data_setup.sh & echo $$! > pid_nohup.txt
-
-run_fwd_only:
-	nohup bash scripts/run_fwd_only.sh & echo $$! > pid_nohup.txt
-
-run:
-	nohup bash scripts/run_workflow.sh & echo $$! > pid_nohup.txt
-
-archive:
-	nohup bash scripts/archive_workflow.sh & echo $$! > pid_nohup.txt
-
-killall:
-	kill -9 `cat pid_nohup.txt`
-	rm pid_nohup.txt
-	killall -TERM snakemake
-	echo Jobs may still be running on the cluster. Cancel those manually, if necessary.
-
-clean:
-	-rm nohup.out
-	-rm pid_nohup.txt
-
-clean_results:
-	rm -rf results/*
-
-clean_virtualenvs:
-	bash scripts/clean_virtualenvs.sh
-
-unlock:
-	bash scripts/unlock_workflow.sh
-
-uninstall:
-	bash scripts/uninstall.sh
-	
-.PHONY: list
-list:
-	@$(MAKE) -pRrq -f $(lastword $(MAKEFILE_LIST)) : 2>/dev/null | awk -v RS= -F: '/^# File/,/^# Finished Make data base/ {if ($$1 !~ "^[#.]") {print $$1}}' | sort | egrep -v -e '^[^[:alnum:]]' -e '^$@$$'
-
-
diff --git a/scripts/activate_python_env.sh b/scripts/activate_python_env.sh
deleted file mode 100644
index caea597..0000000
--- a/scripts/activate_python_env.sh
+++ /dev/null
@@ -1,7 +0,0 @@
-#!/usr/bin/env bash
-
-printf "\nActivating Python environment. Enter 'deactivate' when finished.\n\n"
-
-# Activate python virtual environment.
-source scripts/workflow_python_env_definition.sh
-
diff --git a/scripts/archive_workflow.sh b/scripts/archive_workflow.sh
deleted file mode 100644
index e705538..0000000
--- a/scripts/archive_workflow.sh
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/usr/bin/env bash
-
-# Activate python virtual environment.
-source scripts/workflow_python_env_definition.sh
-
-# Define a timestamp for the archive file.
-TIMESTAMP=`date +%Y-%m-%d_%H-%M-%S`
-
-# Run snakemake in python virtual environment.
-snakemake --archive amoebae_workflow_$TIMESTAMP.tar.gz --cores 1
-
-# Deactivate python virtual environment.
-source scripts/deactivate_python_env.sh
-
diff --git a/scripts/clean_virtualenvs.sh b/scripts/clean_virtualenvs.sh
deleted file mode 100644
index f1931c4..0000000
--- a/scripts/clean_virtualenvs.sh
+++ /dev/null
@@ -1,25 +0,0 @@
-#!/usr/bin/env bash
-# Script for removing all files associated with amoebae_example_workflow
-# virtual environments. This is so that they can be re-generated when the code
-# is modified.
-
-# Define a function to confirm with the user before deleting files.
-confirm() {
-    echo -n "Do you want to run $*? [N/y] "
-    read -N 1 REPLY
-    echo
-    if test "$REPLY" = "y" -o "$REPLY" = "Y"; then
-        "$@"
-    else
-        echo "Cancelled by user"
-    fi
-}
-
-# Remove files associated with virtual environments.
-if test "$(command -v conda)"; then
-    confirm conda env remove --name conda_env_amoebae_snakemake_workflow
-else
-    confirm rm -rf ~/env_amoebae_snakemake_workflow
-fi
-
-
diff --git a/scripts/deactivate_python_env.sh b/scripts/deactivate_python_env.sh
deleted file mode 100644
index 2874691..0000000
--- a/scripts/deactivate_python_env.sh
+++ /dev/null
@@ -1,11 +0,0 @@
-#!/usr/bin/env bash
-
-# Deactivate python virtual environment.
-if test "$(command -v conda)"; then
-  # Deactivate Conda environment.
-  conda deactivate
-else
-  # Assume a Python venv environment was used instead of Conda.
-  deactivate
-fi
-
diff --git a/scripts/determine_snakemake_env_options.sh b/scripts/determine_snakemake_env_options.sh
deleted file mode 100644
index 7980a6a..0000000
--- a/scripts/determine_snakemake_env_options.sh
+++ /dev/null
@@ -1,17 +0,0 @@
-#!/usr/bin/env bash
-
-# Determine which environment management options to use.
-env_options=""
-
-if test "$(command -v conda)"; then
-  env_options="--use-conda"
-
-elif test "$(command -v module)"; then
-  #env_options="--use-envmodules"
-  env_options=""
-
-else
-  env_options="--use-conda --use-singularity"
-
-fi
-
diff --git a/scripts/determine_snakemake_profile.sh b/scripts/determine_snakemake_profile.sh
deleted file mode 100644
index a14947e..0000000
--- a/scripts/determine_snakemake_profile.sh
+++ /dev/null
@@ -1,24 +0,0 @@
-#!/usr/bin/env bash
-
-# Determine what string to use to define Snakemake profile in current
-# environment.
-
-snakemake_profile=""
-
-if test "$(command -v sbatch)"; then
-    echo SLURM job scheduler detected.
-    snakemake_profile="slurm_amoebae"
-
-elif qstat -help; then
-    printf "(SUN/Univa) Grid Engine job scheduler detected."
-    snakemake_profile="sge_amoebae"
-
-elif pbs-config --version; then
-    printf "PBS-TORQUE job scheduler detected."
-    snakemake_profile="pbs-torque_amoebae"
-
-else
-    echo Unable to detect a job scheduler.
-    #exit 1
-
-fi
diff --git a/scripts/dry_run.sh b/scripts/dry_run.sh
deleted file mode 100644
index 9fc0917..0000000
--- a/scripts/dry_run.sh
+++ /dev/null
@@ -1,29 +0,0 @@
-#!/usr/bin/env bash
-
-# Determine what Snakemake profile to use.
-source scripts/determine_snakemake_profile.sh
-
-# Determine whether to use the --profile option at all.
-profile_option="--profile"
-if [ "$snakemake_profile" == "" ]; then
-  profile_option="--cores 1"
-fi
-
-# Determine which environment management options to use.
-source scripts/determine_snakemake_env_options.sh
-
-# Activate python virtual environment.
-source scripts/workflow_python_env_definition.sh
-
-# Run snakemake command.
-echo "Python version:" && \
-python3 --version && \
-echo "Snakemake version:" && \
-snakemake --version && \
-snakemake -n  --snakefile workflow/Snakefile && \
-snakemake plot_workflow -j 100 $env_options $profile_option $snakemake_profile \
---snakefile workflow/Snakefile --verbose
-
-# Deactivate python virtual environment.
-source scripts/deactivate_python_env.sh
-
diff --git a/scripts/install.sh b/scripts/install.sh
deleted file mode 100644
index a63b136..0000000
--- a/scripts/install.sh
+++ /dev/null
@@ -1,179 +0,0 @@
-#!/usr/bin/env bash
-
-# Script for setting up amoebae_example_workflow.
-
-# Start timing this script.
-SECONDS=0
-
-# Set to exit immediately if any commands return an error.
-set -e
-
-# Detect job scheduler.
-source scripts/determine_snakemake_profile.sh
-
-# Determine whether packages can be loaded using the 'module' command.
-if test "$(command -v module)"; then
-    # Use the 'module' command to load Python module.
-
-    # Load appropriate version of Python.
-    module load python/3.7
-
-else
-    # Print the version.
-    echo ""
-    echo Using this version of Python3:
-    python3 --version
-
-fi
-
-# Check that Python can be used.
-if test "$(command -v python3)"; then
-    echo ""
-else
-    echo Unable to access Python3.
-    exit 1
-fi
-
-# Define path to python environment directory.
-PYENVDIR=~/env_amoebae_workflow_setup_py
-
-# Set up a python environment with cookiecutter.
-if [ ! -d "$PYENVDIR" ]; then
-  #virtualenv --no-download $PYENVDIR 
-  python3 -m venv $PYENVDIR 
-  source $PYENVDIR/bin/activate
-  pip install --upgrade pip
-  pip install cookiecutter
-  pip install -U pytest
-else
-  source $PYENVDIR/bin/activate
-fi
-
-
-if [ "$(uname)" == "Darwin" ]; then
-    printf "\nDetected MacOS."
-    # Do something under Mac OS X platform
-    echo "No further setup required."
-
-elif [ "$(expr substr $(uname -s) 1 5)" == "Linux" ]; then
-    printf "\nDetected Linux.\n\n"
-    # Do something under GNU/Linux platform
- 
-    # Determine what job scheduler is in use, and set up the appropriate
-    # SnakeMake profile.
-    if [ "$snakemake_profile" == "slurm_amoebae" ]; then
-        printf "\nSetting up config files for running SnakeMake with the SLURM job scheduler.\n\n"
-        # Install configuration files for running on a SLURM cluster
-        # (https://github.com/Snakemake-Profiles/slurm).
-
-        # Removing existing directory, if present.
-        if [ -d ~/.config/snakemake/slurm_amoebae ]; then
-            rm -rf ~/.config/snakemake/slurm_amoebae 
-        fi 
-
-        mkdir -p ~/.config/snakemake
-        cd ~/.config/snakemake
-        cookiecutter https://github.com/Snakemake-Profiles/slurm.git \
-            profile_name="slurm_amoebae" \
-            cluster_config="cluster_config.yaml"
-        cd -
-        # Now you can run snakemake as: snakemake --profile slurm_amoebae ...
-
-        # Copy amoebae_cluster_config.yaml example file from resources directory to
-        # profile files.
-        cp resources/example_slurm_cluster_config.yaml \
-        ~/.config/snakemake/slurm_amoebae/cluster_config.yaml
-
-        ## Update value of the cluster_config variable in the submission
-        ## python file with the name of the cluster_config.yaml file.
-        #sed -i 's/CLUSTER_CONFIG = \"\"/CLUSTER_CONFIG = \"cluster_config.yaml\"/g' \
-        #    ~/.config/snakemake/slurm_amoebae/slurm-submit.py 
-
-        # Copy over slurm-jobscript.sh file in the profile directory (this
-        # replaces the default script with a script that loads modules and
-        # activates a python virtual environment for every job).
-        cp resources/example_slurm-jobscript.sh \
-        ~/.config/snakemake/slurm_amoebae/slurm-jobscript.sh
-
-    elif [ "$snakemake_profile" == "sge_amoebae" ]; then
-        printf "\nSetting up config files for running SnakeMake with the (SUN/Univa) Grid Engine job scheduler.\n\n"
-
-        # Install configuration files for running on a cluster with the Grid
-        # Engine scheduler.
-
-        # Removing existing directory, if present.
-        if [ -d ~/.config/snakemake/sge_amoebae ]; then
-            rm -rf ~/.config/snakemake/sge_amoebae 
-        fi 
-
-        mkdir -p ~/.config/snakemake
-        cd ~/.config/snakemake
-        # Make profile directory using cookiecutter to install from GitHub.
-        cookiecutter https://github.com/Snakemake-Profiles/sge.git \
-            profile_name="sge_amoebae"
-        # Make Python scripts in profile executable.
-        chmod a+x ~/.config/snakemake/sge_amoebae/*.py
-        # Change back to previous directory.
-        cd -
-        # Now you can run snakemake as: snakemake --profile sge_amoebae ...
-
-
-    elif [ "$snakemake_profile" == "pbs-torque" ]; then
-        # Install configuration files for running on a cluster with the
-        # PBS-TORQUE scheduler.
-
-        printf "\nSetting up config files for running SnakeMake with the
-        PBS-TORQUE job scheduler.\n\n"
-
-        # Removing existing directory, if present.
-        if [ -d ~/.config/snakemake/pbs-torque_amoebae ]; then
-            rm -rf ~/.config/snakemake/pbs-torque_amoebae
-        fi 
-
-        mkdir -p ~/.config/snakemake
-        cd ~/.config/snakemake
-        # Make profile directory using cookiecutter to install from GitHub.
-        cookiecutter https://github.com/Snakemake-Profiles/pbs-torque.git \
-            profile_name="pbs-torque_amoebae"
-        # Make Python scripts in profile executable.
-        chmod a+x ~/.config/snakemake/pbs-torque_amoebae/*.py
-        # Change back to previous directory.
-        cd -
-        # Now you can run snakemake as: snakemake --profile pbs-torque_amoebae ...
-
-    else
-        printf "\nUnable to automatically set up config files for submitting
-        jobs through the job scheduler on this system. You must do this
-        manually.\n\n"
-    fi
-
-
-elif [ "$(expr substr $(uname -s) 1 10)" == "MINGW32_NT" ]; then
-    printf "\nDetected Windows."
-    # Do something under 32 bits Windows NT platform
-    echo "This software has not been tested on Windows, as it has been designed to run on linux clusters."
-    exit 1
-
-elif [ "$(expr substr $(uname -s) 1 10)" == "MINGW64_NT" ]; then
-    printf "\nDetected Windows."
-    # Do something under 64 bits Windows NT platform
-    echo "This software has not been tested on Windows, as it has been designed to run on linux clusters."
-    exit 1
-fi
-
-
-
-#######################################################
-
-# Deactivate and remove Python environment.
-deactivate
-rm -rf $PYENVDIR
-
-
-#######################################################
-# Report how much time it took for this script to run.
-echo ""
-ELAPSED="Setting up this workflow took the following amount of time: $(($SECONDS / 3600))hrs $((($SECONDS / 60) % 60))min $(($SECONDS % 60))sec"
-echo $ELAPSED
-
-
diff --git a/scripts/quantify_test_coverage.py b/scripts/quantify_test_coverage.py
deleted file mode 100644
index 2c7202c..0000000
--- a/scripts/quantify_test_coverage.py
+++ /dev/null
@@ -1,42 +0,0 @@
-#!/usr/bin/env python3
-
-import glob
-import os
-import matplotlib.pyplot as plt; plt.rcdefaults()
-import numpy as np
-import matplotlib.pyplot as plt
-
-
-# Count how many function definitions there are.
-funct_def_count = 0
-for d in ['amoebaelib', 'misc_scripts']:
-    for f in glob.glob(os.path.join(d, '*.py')):
-        with open(f) as infh:
-            for i in infh:
-                if i.startswith("def "):
-                    #print(i.strip())
-                    funct_def_count += 1
-print("Total number of function definitions: " + str(funct_def_count))
-
-# Count how many functions have tests in files in the tests directory.
-tested_def_count = 0
-for d in ['tests']:
-    for f in glob.glob(os.path.join(d, '*.py')):
-        with open(f) as infh:
-            contents = infh.read()
-            split_on_defs = contents.split()
-            for i in infh:
-                if i.startswith("def "):
-                    #print(i.strip())
-                    funct_def_count += 1
-
-objects = ('Total Defs', 'Tested Defs')
-y_pos = np.arange(len(objects))
-performance = [funct_def_count, 0]
-
-plt.bar(y_pos, performance, align='center', alpha=0.5)
-plt.xticks(y_pos, objects)
-plt.ylabel('Def count')
-plt.title('Test coverage')
-
-plt.show()
diff --git a/scripts/run_data_setup.sh b/scripts/run_data_setup.sh
deleted file mode 100644
index 852fc7a..0000000
--- a/scripts/run_data_setup.sh
+++ /dev/null
@@ -1,22 +0,0 @@
-#!/usr/bin/env bash
-
-# Determine what Snakemake profile to use.
-source scripts/determine_snakemake_profile.sh
-
-# Determine whether to use the --profile option at all.
-profile_option="--profile"
-if [ "$snakemake_profile" == "" ]; then
-  profile_option="--cores 1"
-fi
-
-# Determine which environment management options to use.
-source scripts/determine_snakemake_env_options.sh
-
-# Activate python virtual environment.
-source scripts/workflow_python_env_definition.sh
-
-# Run snakemake command.
-snakemake get_ref_seqs -j 100 $env_options $profile_option $snakemake_profile --verbose
-
-# Deactivate python virtual environment.
-source scripts/deactivate_python_env.sh
diff --git a/scripts/run_fwd_only.sh b/scripts/run_fwd_only.sh
deleted file mode 100644
index b37d5f8..0000000
--- a/scripts/run_fwd_only.sh
+++ /dev/null
@@ -1,22 +0,0 @@
-#!/usr/bin/env bash
-
-# Determine what Snakemake profile to use.
-source scripts/determine_snakemake_profile.sh
-
-# Determine whether to use the --profile option at all.
-profile_option="--profile"
-if [ "$snakemake_profile" == "" ]; then
-  profile_option="--cores 1"
-fi
-
-# Determine which environment management options to use.
-source scripts/determine_snakemake_env_options.sh
-
-# Activate python virtual environment.
-source scripts/workflow_python_env_definition.sh
-
-# Run snakemake command.
-snakemake get_fwd_hit_seqs -j 100 $env_options $profile_option $snakemake_profile --verbose
-
-# Deactivate python virtual environment.
-source scripts/deactivate_python_env.sh
diff --git a/scripts/run_workflow.sh b/scripts/run_workflow.sh
deleted file mode 100644
index 03bf9a1..0000000
--- a/scripts/run_workflow.sh
+++ /dev/null
@@ -1,23 +0,0 @@
-#!/usr/bin/env bash
-
-# Determine what Snakemake profile to use.
-source scripts/determine_snakemake_profile.sh
-
-# Determine whether to use the --profile option at all.
-profile_option="--profile"
-if [ "$snakemake_profile" == "" ]; then
-  profile_option="--cores 1"
-fi
-
-# Determine which environment management options to use.
-source scripts/determine_snakemake_env_options.sh
-
-# Activate python virtual environment.
-source scripts/workflow_python_env_definition.sh
-
-# Run snakemake command.
-snakemake -j 100 $env_options $profile_option $snakemake_profile --verbose
-
-# Deactivate python virtual environment.
-source scripts/deactivate_python_env.sh
-
diff --git a/scripts/uninstall.sh b/scripts/uninstall.sh
deleted file mode 100644
index 4e0bc19..0000000
--- a/scripts/uninstall.sh
+++ /dev/null
@@ -1,19 +0,0 @@
-#!/usr/bin/env bash
-# Script for removing all files associated with amoebae.
-
-# Define a function to confirm with the user before deleting files.
-confirm() {
-    echo -n "Do you want to run $*? [N/y] "
-    read -N 1 REPLY
-    echo
-    if test "$REPLY" = "y" -o "$REPLY" = "Y"; then
-        "$@"
-    else
-        echo "Cancelled by user"
-    fi
-}
-
-# Remove files.
-
-confirm rm -rf ../amoebae
-
diff --git a/scripts/unlock_workflow.sh b/scripts/unlock_workflow.sh
deleted file mode 100644
index e63f7e9..0000000
--- a/scripts/unlock_workflow.sh
+++ /dev/null
@@ -1,10 +0,0 @@
-#!/usr/bin/env bash
-
-# Activate python virtual environment.
-source scripts/workflow_python_env_definition.sh
-
-# Run snakemake in python virtual environment.
-snakemake --unlock --cores 1
-
-# Deactivate python virtual environment.
-source scripts/deactivate_python_env.sh
diff --git a/scripts/workflow_python_env_definition.sh b/scripts/workflow_python_env_definition.sh
deleted file mode 100644
index 241678c..0000000
--- a/scripts/workflow_python_env_definition.sh
+++ /dev/null
@@ -1,131 +0,0 @@
-#!/usr/bin/env bash
-
-# Script for building and accessing virtual environments for running snakemake.
-# If you are running this on a cluster that uses the Conda package manager,
-# make sure that you have activated a Conda environment using an appropriate
-# version of Python.
-
-# Determine snakemake profile name.
-source scripts/determine_snakemake_profile.sh
-
-# Determine whether packages can be loaded using the 'module' command.
-if test "$(command -v module)"; then
-    # Use the 'module' command to load Python and Singularity modules.
-
-    # Load appropriate version of Python.
-    # (tested using 3.7.4).
-    module load python/3.7
-
-    # Load an appropriate version of Singularity.
-    module load singularity/3.6
-
-else
-    # Print the versions.
-    echo ""
-    echo Using this version of Python:
-    python3 --version
-    echo ""
-    echo Using this version of Singularity:
-    singularity --version
-
-fi
-
-# Check that Python can be used.
-if test "$(command -v python3)"; then
-    echo ""
-else
-    echo Unable to access Python3.
-    exit 1
-fi
-
-# Check that Singularity can be used.
-if test "$(command -v singularity)"; then
-    echo ""
-else
-    echo Unable to access Singularity.
-    #exit 1
-fi
-
-# Define path to directory to contain python virtual environment files
-# (installation of dependencies)
-DIR=~/env_amoebae_snakemake_workflow
-
-# Build the virtual environment, if necessary.
-
-if test "$(command -v conda)"; then
-  echo Conda is available.
-
-  # Install dependencies in virtual environment using conda.
-  if ! test "$(conda info --envs | grep "conda_env_amoebae_snakemake_workflow")"; then
-    #conda create --name conda_env_amoebae_snakemake_workflow python=3.7.4
-    #source activate conda_env_amoebae_snakemake_workflow
-
-    # Check that mamba is installed.
-    if ! test "$(command -v mamba)"; then
-        echo Installing mamba.
-        # Install Mamba for making snakemake install easier.
-        conda install -c conda-forge mamba
-    fi
-
-    echo ""
-    echo Setting up environment for snakemake with mamba.
-    echo ""
-
-
-    # Create conda environment for snakemake with mamba.
-    mamba create -c conda-forge -c bioconda \
-        -n conda_env_amoebae_snakemake_workflow \
-            snakemake \
-            matplotlib \
-            numpy \
-            graphviz \
-            requests \
-            pulp \
-
-    echo Environment set up. Re-run to activate.
-    exit 1
-
-  else
-    # Otherwise, just activate the environment.
-    echo Attempting to activate conda environment from script.
-
-    # Get the path to the conda base environment.
-    conda_base_env=$(conda info | grep -i 'base environment' | tr -s ' ' | cut -d' ' -f5)
-    # Source conda from the base environment so that it can be used in a
-    # subshell.
-    source $conda_base_env/etc/profile.d/conda.sh
-    # Activate the conda environment.
-    conda activate conda_env_amoebae_snakemake_workflow
-
-    # Add profile path to $PATH.
-    export PATH=$PATH:~/.config/snakemake/$snakemake_profile
-
-  fi
-
-else
-  # Install dependencies in virtual environment using pip.
-  if [ ! -d "$DIR" ]; then
-    python3 -m venv $DIR 
-    source $DIR/bin/activate
-    pip install --upgrade pip
-    pip install setuptools wheel
-    pip install requests
-    pip install \
-    numpy \
-    biopython==1.77 \
-    gffutils==0.10.1 \
-    pypdf2==1.26.0 \
-    reportlab==3.5.51 \
-    pandoc==2.0a4 \
-    pandas==1.1.3 \
-    matplotlib==3.3.2 \
-    graphviz==0.14.2 \
-    snakemake==5.26.1
-
-  else
-    # Otherwise, just activate the environment.
-    source $DIR/bin/activate
-  fi
-fi
-
-