Installing mspypeline

An installation of python is required to use this package. Python can be installed as part of the Anaconda distribution, which is recommended, or via python (python 3.7). Then mspypeline needs to be installed using a terminal (e.g. the terminal provided by anaconda - anaconda prompt).

Anaconda installation (recommended)

When installing mspypeline via Anaconda, one can choose two possible options to do so.

1. Either a new virtual conda environment is created and mspypeline is installed therein. This can be achieved e.g. by running the following code in a terminal:

# create new environment called mspypeline and install mspypeline package
# + all required packages
conda create --name mspypeline python=3.7 mspypeline -c conda-forge -c siheming

# activate the newly created environment
conda activate mspypeline

# in the activated environment the python package mspypeline can be called, the GUI
# can be started or the package can be imported

With a new virtual environment in which python 3.7, mspypeline and all other required packages are installed, it is necessary to activate this environment before an analysis from the terminal in order to use mspypeline. Once the installation is performed and the environment is activated an analysis can be started following the next steps.

2. Otherwise, mspypeline can be installed into the base conda environment. This can be achieved e.g. by running the following code in a terminal:

conda install -c conda-forge -c siheming mspypeline

With this base installation of mspypeline and all required packages it is possible to immediately start an analysis following the next steps.

pip(PyPI) installation

The mspypeline python package can optionally also be installed from PyPI and one can choose two possible installation options.

1. Either a new virtual python environment is created and mspypeline is installed therein. Since the python version cannot be changed by pip make sure that the correct python version ist installed. This can be achieved e.g. by running the following code in a terminal (might differ based on your OS system):

# create new environment called mspypeline
python3 -m venv mypypeline

# activate the newly created environment
source activate mspypeline

# install the mspypeline package + all required package within the environment
pip install mspypeline

With a new virtual environment in which python, mspypeline and all other required packages are installed, it is necessary to activate this environment before an analysis from the terminal in order to use mspypeline. Once the installation is performed and the environment is activated an analysis can be started following the next steps.

2. Otherwise, mspypeline can be installed into the base environment. This can be achieved e.g. by running the following code in a terminal:

pip install mspypeline

With this base installation of mspypeline and all required packages it is possible to immediately start an analysis following the next steps.

Obtaining Sources

Get the source code by cloning the github project:

git clone https://github.com/siheming/mspypeline.git

Download Sources from PyPI.

Download Sources from conda.

Python support

Currently supported python versions are 3.7 and 3.8.

Dependencies

• numpy >= 1.17.4

• pandas >= 1.0.0

• scipy >= 1.3.1

• matplotlib >= 3.1.1

• scikit-learn >= 0.22.1

• tzlocal >= 2.0.0

• ruamel_yaml >= 0.15.46

• matplotlib-venn >= 0.11.5

• adjusttext >= 0.7.3.1

• plotly >= 4.6.0

Optional Dependencies for R packages

some plots might require additional R packages to be installed. Because of that additional dependencies are required for those plots.

• rpy2 >= 3.4.5