diff --git a/README.md b/README.md
index 4b2be88..523e5fd 100755
--- a/README.md
+++ b/README.md
@@ -23,14 +23,16 @@ Iszatt J.(2023).Phanatic(v2.2.0)[Source code].Github:https://github.com/JoshuaIs
 ```
 
 ## Installation
+To run this pipeline you first need a working docker installation. 
+
 Install using pip
 ```sh
-
+pip install Phanatic==2.2.0
 ```
 
 Run the help command to see options 
 ```sh
-
+phanatic.py -h
 ```
 
 ## Output
diff --git a/pip/LICENSE.md b/pip/LICENSE.md
new file mode 100755
index 0000000..0ad25db
--- /dev/null
+++ b/pip/LICENSE.md
@@ -0,0 +1,661 @@
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+OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
+THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+PURPOSE.  THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
+IS WITH YOU.  SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
+ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+  16. Limitation of Liability.
+
+  IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
+THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
+USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
+DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
+PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
+EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
+SUCH DAMAGES.
+
+  17. Interpretation of Sections 15 and 16.
+
+  If the disclaimer of warranty and limitation of liability provided
+above cannot be given local legal effect according to their terms,
+reviewing courts shall apply local law that most closely approximates
+an absolute waiver of all civil liability in connection with the
+Program, unless a warranty or assumption of liability accompanies a
+copy of the Program in return for a fee.
+
+                     END OF TERMS AND CONDITIONS
+
+            How to Apply These Terms to Your New Programs
+
+  If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+  To do so, attach the following notices to the program.  It is safest
+to attach them to the start of each source file to most effectively
+state the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+    <one line to give the program's name and a brief idea of what it does.>
+    Copyright (C) <year>  <name of author>
+
+    This program is free software: you can redistribute it and/or modify
+    it under the terms of the GNU Affero General Public License as published
+    by the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU Affero General Public License for more details.
+
+    You should have received a copy of the GNU Affero General Public License
+    along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
+Also add information on how to contact you by electronic and paper mail.
+
+  If your software can interact with users remotely through a computer
+network, you should also make sure that it provides a way for users to
+get its source.  For example, if your program is a web application, its
+interface could display a "Source" link that leads users to an archive
+of the code.  There are many ways you could offer source, and different
+solutions will be better for different programs; see section 13 for the
+specific requirements.
+
+  You should also get your employer (if you work as a programmer) or school,
+if any, to sign a "copyright disclaimer" for the program, if necessary.
+For more information on this, and how to apply and follow the GNU AGPL, see
+<https://www.gnu.org/licenses/>.
diff --git a/pip/Phanatic.egg-info/PKG-INFO b/pip/Phanatic.egg-info/PKG-INFO
new file mode 100644
index 0000000..e07c521
--- /dev/null
+++ b/pip/Phanatic.egg-info/PKG-INFO
@@ -0,0 +1,18 @@
+Metadata-Version: 2.1
+Name: Phanatic
+Version: 2.2.0
+Summary: Python package to run de novo bacteriophage assembly container.
+Home-page: https://github.com/JoshuaIszatt/Phanatic
+Author: Joshua Iszatt
+Author-email: joshiszatt@gmail.com
+License: AGPL-3.0
+Classifier: Development Status :: 2 - Pre-Alpha
+Classifier: License :: OSI Approved :: GNU Affero General Public License v3
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.6
+Classifier: Programming Language :: Python :: 3.7
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Requires-Python: >=3.6
+License-File: LICENSE.md
diff --git a/pip/Phanatic.egg-info/SOURCES.txt b/pip/Phanatic.egg-info/SOURCES.txt
new file mode 100644
index 0000000..f170603
--- /dev/null
+++ b/pip/Phanatic.egg-info/SOURCES.txt
@@ -0,0 +1,9 @@
+LICENSE.md
+setup.py
+Phanatic/__init__.py
+Phanatic/main.py
+Phanatic.egg-info/PKG-INFO
+Phanatic.egg-info/SOURCES.txt
+Phanatic.egg-info/dependency_links.txt
+Phanatic.egg-info/entry_points.txt
+Phanatic.egg-info/top_level.txt
\ No newline at end of file
diff --git a/pip/Phanatic.egg-info/dependency_links.txt b/pip/Phanatic.egg-info/dependency_links.txt
new file mode 100644
index 0000000..8b13789
--- /dev/null
+++ b/pip/Phanatic.egg-info/dependency_links.txt
@@ -0,0 +1 @@
+
diff --git a/pip/Phanatic.egg-info/entry_points.txt b/pip/Phanatic.egg-info/entry_points.txt
new file mode 100644
index 0000000..95c29b7
--- /dev/null
+++ b/pip/Phanatic.egg-info/entry_points.txt
@@ -0,0 +1,2 @@
+[console_scripts]
+phanatic.py = Phanatic.main:main
diff --git a/pip/Phanatic.egg-info/top_level.txt b/pip/Phanatic.egg-info/top_level.txt
new file mode 100644
index 0000000..a2fb3e6
--- /dev/null
+++ b/pip/Phanatic.egg-info/top_level.txt
@@ -0,0 +1 @@
+Phanatic
diff --git a/pip/Phanatic/__init__.py b/pip/Phanatic/__init__.py
new file mode 100755
index 0000000..e69de29
diff --git a/pip/Phanatic/main.py b/pip/Phanatic/main.py
new file mode 100755
index 0000000..1c58800
--- /dev/null
+++ b/pip/Phanatic/main.py
@@ -0,0 +1,108 @@
+def main():
+
+    import os
+    import sys
+    import subprocess
+    import argparse
+    import random
+    import pandas as pd
+
+    # Did you know prompts
+    prompts = [
+        "Phanatic currently only supports short, paired end, illumina reads (default 'PE_illumina_150').",
+        "I (J. Iszatt) made Phanatic to assemble S. aureus phage genomes as part of my PhD project.",
+        "This is a short read assembler primarily designed for bacteriophage",
+        "My favourite bacteriophage is a Silviavirus named Koomba-kaat_1",
+        "You can use your own config file to customise the assembly and functions"
+    ]
+    random_prompt = random.choice(prompts)
+
+    # Creating function to check directory path
+    def valid_dir(dir_path):
+        if not os.path.isdir(dir_path):
+            raise argparse.ArgumentTypeError(
+                f"{dir_path} is not a valid directory path")
+        if not os.access(dir_path, os.R_OK):
+            raise argparse.ArgumentTypeError(
+                f"{dir_path} is not a readable directory")
+        return dir_path
+
+    def valid_file(file_path):
+        if not os.path.isfile(file_path):
+            raise argparse.ArgumentTypeError(
+                f"{file_path} is not a valid file path")
+        if not os.access(file_path, os.R_OK):
+            raise argparse.ArgumentTypeError(
+                f"{file_path} is not a readable file")
+        return file_path
+
+    # Parsing arguments
+    image = 'iszatt/phanatic:2.2.0'
+    parser = argparse.ArgumentParser(description=f"Easy short read assembly. Joshua J Iszatt: https://github.com/JoshuaIszatt")
+
+    # Input/output options
+    parser.add_argument('-i', '--input', type=valid_dir, help='Input reads files')
+    parser.add_argument('-o', '--output', type=valid_dir, help='Direct output to this location')
+    parser.add_argument('-r', '--reads', type=str, choices=['PE_illumina_150'], default='PE_illumina_150', help='Pipeline options')
+    parser.add_argument('-c', '--config', type=valid_file, help='Use config file to customise assembly')
+    parser.add_argument('-v', '--version', action="store_true", help='Print the docker image version')
+    parser.add_argument('--show_console', action="store_true", help='Include this flag to write output to console')
+    parser.add_argument('--manual', action="store_true", help='Enter container interactively')
+    args = parser.parse_args()
+
+    # Printing version
+    if args.version:
+        print(image)
+        sys.exit(0)
+
+    # Obtaining absolute paths if entered correctly
+    if args.input and args.output:
+        input_path = os.path.abspath(args.input)
+        output_path = os.path.abspath(args.output)
+    elif args.input and not args.output:
+        sys.exit("No output directory specified\nRun --help to see options")
+    elif args.output and not args.input:
+        sys.exit("No input directory specified\nRun --help to see options")
+    else:
+        sys.exit("No input or output directories specified\nRun --help to see options")
+        
+
+    # Printing command variables
+    print(
+        f"Program run: {image}",
+        f"Input path: {input_path}",
+        f"Output path: {output_path}",
+        f"Reads type: {args.reads}",
+        ">>>",
+        f"Did you know:",
+        f"{random_prompt}",
+        ">>>\n",
+        sep='\n'
+        )
+
+    # Copying config file to output dir
+    if args.config:
+        print(f"Using {args.config} file \n")
+        os.system(f"cp {args.config} {args.output}/config.ini")
+
+    if args.show_console:
+        docker = "docker run"
+    else:
+        docker = "docker run -d"
+
+    # Running docker
+    if args.manual: 
+        os.system(f"docker exec -it \
+            $(docker run -d \
+            -v {input_path}:/assemble/input \
+            -v {output_path}:/assemble/output \
+            {image} sleep 1d) bash")
+    else:
+        command = ["%s -v %s:/assemble/input -v %s:/assemble/output %s /assemble/bin/assemble.sh" %
+                (docker, input_path, output_path, image)]
+        result = subprocess.Popen(command, shell=True)
+        print(command)
+
+
+if __name__ == "__main__":
+    exit(main())
\ No newline at end of file
diff --git a/pip/dist/Phanatic-2.2.0.tar.gz b/pip/dist/Phanatic-2.2.0.tar.gz
new file mode 100644
index 0000000..d565f57
Binary files /dev/null and b/pip/dist/Phanatic-2.2.0.tar.gz differ
diff --git a/pip/setup.py b/pip/setup.py
new file mode 100755
index 0000000..0584e6b
--- /dev/null
+++ b/pip/setup.py
@@ -0,0 +1,30 @@
+from setuptools import find_packages, setup
+
+setup(
+    name="Phanatic",
+    version="2.2.0",
+    description="Python package to run de novo bacteriophage assembly container.",
+    url="https://github.com/JoshuaIszatt/Phanatic",
+    author="Joshua Iszatt",
+    author_email="joshiszatt@gmail.com",
+    license="AGPL-3.0",
+    classifiers=[
+        "Development Status :: 2 - Pre-Alpha",
+        "License :: OSI Approved :: GNU Affero General Public License v3",
+        "Programming Language :: Python :: 3",
+        "Programming Language :: Python :: 3.6",
+        "Programming Language :: Python :: 3.7",
+        "Programming Language :: Python :: 3.8",
+        "Programming Language :: Python :: 3.9",
+        "Programming Language :: Python :: 3.10",
+    ],
+    install_requires=[""],
+    python_requires=">=3.6",
+    packages=find_packages(),
+    data_files=[("", ["LICENSE.md"])],
+    entry_points={
+        'console_scripts': [
+            'phanatic.py = Phanatic.main:main',
+        ],
+    },
+)
\ No newline at end of file