Installation

Table of Contents

• Install the h1s package
• Setup HaMStR-oneSeq
• Update HaMStR-oneSeq
• Uninstall HaMStR-oneSeq

HaMStR-oneSeq is distributed as a python package called h1s. It is compatible with Python ≥ v3.7.

Install the h1s package

You can install h1s using pip:

python3 -m pip install h1s

or, in case you do not have admin rights, and don't use package systems like Anaconda to manage environments you need to use the --user option:

python3 -m pip install --user h1s

and then add the following line to the end of your ~/.bashrc or ~/.bash_profile file, restart the current terminal to apply the change (or type source ~/.bashrc):

export PATH=$HOME/.local/bin:$PATH

Setup HaMStR-oneSeq

After installing h1s, you need to setup HaMStR-oneSeq to get its dependencies and pre-calculated data.

You can do it by just running this command

setup1s -o /output/path/for/oneSeq/data

or, in case you are using Anaconda

setup1s -o /output/path/for/oneSeq/data --conda

You should have the sudo password ready, otherwise some missing dependencies cannot be installed. See dependency list for more info. If you do not have root privileges, ask your admin to install those dependencies using setup1s --lib command.

Pre-calculated data set of HaMStR-oneSeq will be saved in /output/path/for/oneSeq/data. The path to this directory will be stored within installed hamstr1s package and is required for many hamstr1s functions.

After the setup run successfully, you can start using HaMStR-oneSeq.

For debugging the setup, please create a log file by running the setup as e.g. setup1s | tee log.txt for Linux/MacOS or setup1s --conda | tee log.txt for Anaconda and send us that log file, so that we can trouble shoot the issues. Most of the problems can be solved by just re-running the setup.

Update HaMStR-oneSeq

python3 -m pip install --upgrade h1s

Or

python3 -m pip install --user --upgrade h1s

if you have installed h1s with --user option.

In most of the cases, you don't need to run seupt1s again. Your old data will still be available.

Uninstall HaMStR-oneSeq

remove1s [--data]

This command will uninstall h1s and all the data or files saved within the installed hamstr1s directory (optional, only when --data option is used).

If you see this warning

WARNING: Skipping h1s as it is not installed.

probably you have multiple versions of Python running on your machine. In this case, you can manually uninstall h1s by using the command

pip uninstall h1s

and delete the installed folder h1s within your Python library directory.