Transcriptic Python Library
The Transcriptic Python Library (TxPy) provides a Python interface for managing Transcriptic organizations, projects, runs, datasets and more. One can either interface with our library through the bundled command line interface (CLI) or through a Jupyter notebook using a Python client.
We recommend using the Jupyter interface as it provides a nice rendering and presentation of the objects, as well as provide additional analysis and properties functions specific to the Transcriptic objects.
Transcriptic is the robotic cloud laboratory for the life sciences. https://www.transcriptic.com
TxPy is separated into three main components: 1) Core. The core modules
provide a barebones client for making calls to the Transcriptic webapp
to create and obtain data. This can be done via the
api object or
via the command-line using the CLI. 2) Jupyter. This module provides a
Jupyter-centric means for interacting with objects returned from the
Transcriptic webapp such as Run, Project and Dataset. 3) Analysis. This
module provides some basic analysis wrappers around datasets returned
from the webapp using standard Python scientific libraries.
For a barebones CLI install, you’ll do:
pip install transcriptic
We recommend installing the
jupyter module for Jupyter-centric
pip install transcriptic[jupyter]
Lastly, we recommend installing the
analysis module for a
pip install transcriptic[analysis]
Alternatively, if you’re interested in contributing or living at the edge:
git clone https://github.com/transcriptic/transcriptic.git cd transcriptic pip install .[jupyter,analysis]
to upgrade to the latest version using pip or check whether you’re already up to date:
pip install transcriptic --upgrade
Then, login to your Transcriptic account:
$ transcriptic login Email: email@example.com Password: Logged in as firstname.lastname@example.org (example-lab)
To enable auto-completion for the Transcriptic CLI, you’ll need to download an appropriate auto-complete file and add it your shell configuration.
Here’s an example script for installing it on a bash shell in your
export INSTALL_DIR=~/.config && mkdir -p $INSTALL_DIR curl -L https://raw.githubusercontent.com/strateos/transcriptic/master/autocomplete/bash.sh > $INSTALL_DIR/tx_complete.sh && chmod +x $INSTALL_DIR/tx_complete.sh echo ". $INSTALL_DIR/tx_complete.sh" >> ~/.bash_profile
- Ubuntu and Fedora note: Modify your
- Zsh note: Use
bash.sh. Modify your
- Fish note: Use
tx-complete.fish. Skip the last step.
See the Transcriptic Developer Documentation for detailed information about how to use this package, including learning about how to package protocols and build releases.
Note that direct analysis and submission of Autoprotocol is currently restricted. Please contact email@example.com if you would like to do so.
Read Contributing for more information on contributing to TxPy.