Detailed Installation Guide

Installation guide is divided in two phases: checking the prerequisites and main package installation.

mcpartools works under Linux operating system.

If you are familiar with python and pip tool, simply type following command to install the package:

$ pip install mcpartools

If your are a less advanced user, read the rest of the page.

Installation guide is divided in two phases: prerequisites (mainly Python installation) and main package installation.

There are two groups of users: administrators and regular ones. For regular users we assume that they can write files to their home directory, but not necessary elsewhere. We assume that administrators can log in as root user, execute commands via sudo or have some other way to create files system-wide.

We expect that mcpartools will mostly be used by regular users on computing clusters. This is the reason why installation instruction is lengthy and detailed, explaining how to deal with lack of administrator rights.

Prerequisites - python interpreter

First we need to check if Python interpreter is installed. Try if one of following commands (printing Python version) works:

$ python --version
$ python3 --version

At the time of writing Python language interpreter has two popular versions: 2.x (Python 2) and 3.x (Python 3) families. Command python invokes either Python 2 or 3, while python3 can invoke only Python 3.

mcpartools supports most of the modern Python versions, mainly: 2.7, 3.2, 3.4, 3.5 and 3.6. Check if your interpreter version is supported.

If none of python and python3 commands are present, then Python interpreter has to be installed.

We suggest to use the newest version available for your Linux distribution (from 3.x family).

User installation

In case Python is missing and you are regular user, the best would be contact somebody with administrator rights and ask to install Python interpreter in the system.

Installation of Python without administrator rights is however possible, but in case something goes wrong it will require expert knowledge.

As an user you will need to download Python interpreter source code (written in C language) and compile it. For that purpose you will need a C language compiler (i.e. gcc) and some other tools (i.e. make). These tools are usually installed by somebody with administrator rights. Python installer might not complain about missing SSL libraries (i.e. libssl-dev) and will compile successfully, but we recommend to install it (SSL libraries) before, to have easier installation of pip package manager in the next steps.

When installing as user we advice to unpack downloaded source code in $HOME/tmp directory and keep it there. It may be needed for upgrade or deinstallation purpose.

Let us install Python 2.7 into $HOME/usr/py27 directory. First let us create $HOME/tmp directory and step into it:

$ mkdir -p $HOME/tmp
$ cd $HOME/tmp

Now its time to download and unpack source code package. We show an example with 2.7.12 version, but newer one can be problably found on https://www.python.org/downloads/source/

$ wget https://www.python.org/ftp/python/2.7.12/Python-2.7.12.tgz
$ tar -zxf Python-2.7.12.tgz
$ cd Python-2.7.12

Finally let us start compilation process (it might take couple of minutes). This process might be interrupted by some error message. Do not hesitate to find a professional help to fix it:

$ ./configure --prefix=$HOME/usr/py27
$ make
$ make install

Python2.7 is now installed into $HOME/usr/py27 directory. In order to execute python interpreter, you need to provide full path to the executable file, i.e.:

$ $HOME/usr/py27/bin/python --version

In a similar way python3.x can be installed.

Administrator installation

The best way is to use your package manager.

  • apt-get install python3 (python 3) or apt-get install python (python 2) for Debian and Ubuntu
  • dnf install python3 (python 3) or dnf install python (python 2) for Fedora
  • yum install python3 (python 3) or yum install python (python 2) for CentOS and SLC

Single file distribution

mcpartools is shipped as a single file executable. It can be downloaded from https://github.com/DataMedSci/mcpartools/releases webpage using the web browser or via command line (here an example with 0.1.4 version is found, newer versions should also be available):

$ wget https://github.com/DataMedSci/mcpartools/releases/download/v0.1.4/generatemc.pyz -O generatemc

After downloading the file, make sure it has executable bits set:

$ chmod ugo+x generatemc

When new version if released, replace downloaded file with newer one.

As mcpartools doesn’t have any mechanism of automatic updates, we recommend to use installation using pip tool, described below. It makes easy upgrade and uninstallation procedure.

Prerequisites - pip tool

pip is a tool for installing and managing Python packages. It downloads the packages from central Internet repository and installs them in a similar way as apps are downloaded on your smartphone by Google Play or Apple Store.

Try the following commands (printing pip version):

$ pip --version
$ pip3 --version

In a similar way to python interpreter pip is a tool for Python 2 or 3, while pip3 works exclusively for Python 3. If none of these commands are present, then pip has to be installed.

User installation

Follow the instruction from here https://pip.pypa.io/en/stable/installing/, mainly - download installation script using your web browser, or by typing in the terminal:

$ wget https://bootstrap.pypa.io/get-pip.py

# openssl for python2

Now use your python interpreter to execute downloaded script. It will install pip in your home directory:

$ python get-pip.py --user

Try if pip command is available by typing:

$ $HOME/.local/bin/pip --version

If this method fails you can also try to use a ensurepip approach. It works with Python versions: 2.7 (starting from 2.7.9), 3.4 and newer. To install pip, simply type:

$ python -m ensurepip

Administrator installation

Follow the package installation for your system. On some systems instructions mentioned below have to be prefixed with sudo command.

  • apt-get install python3-pip (python 3) or apt-get install python-pip (python 2) for Debian and Ubuntu
  • dnf install python3-pip (python 3) or dnf install python-pip (python 2) for Fedora
  • yum install python3-pip (python 3) or yum install python-pip (python 2) for CentOS and SLC

pip package installation

Now it is time to install mcpartools package. It consists of executable file called generatemc and bunch of necessary code files.

User installation

User installation will put the mcpartools under hidden directory $HOME/.local.

To install the package, type in the terminal:

$ pip install mcpartools --user

If pip command is missing on your system, replace pip with pip3 in abovementioned instruction.

To upgrade the mcpartools to newer version, simply type:

$ pip install --upgrade mcpartools --user

To completely remove mcpartools from your system, use following command:

$ pip uninstall mcpartools

In most of modern systems all executables found in $HOME/.local/bin directory (generatemc executable will be saved there) can be called like normal Linux commands (i.e. ls, cd). It means that after installation you should be able to simply type in terminal: generatemc to use this package

$ generatemc --help

If this is not the case, please prefix the command with $HOME/.local/bin and call it in the following way:

$ $HOME/.local/bin/generatemc --help

Administrator installation

Administrator installation is very simple, but requires to save some files in system-wide directories (i.e. /usr). On some systems commands mentioned below have to be prefixed with sudo command:

$ pip install mcpartools

To upgrade the mcpartools to newer version, simply type:

$ pip install --upgrade mcpartools

To completely remove mcpartools from your system, use following command:

$ pip uninstall mcpartools

Now generatemc script should be installed for all users and can be invoked by typing:

$ generatemc --help