Transcriptic Python Library

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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

Setup

Organization

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.

Installation

For a barebones CLI install, you’ll do:

.. code-block:: bash

pip install transcriptic

We recommend installing the jupyter module for Jupyter-centric navigation:

.. code-block:: bash

pip install transcriptic[jupyter]

Lastly, we recommend installing the analysis module for a full-fledged experience:

.. code-block:: bash

pip install transcriptic[analysis]

Alternatively, if you’re interested in contributing or living at the edge:

.. code-block:: bash

git clone https://github.com/strateos/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:

.. code-block:: bash

pip install transcriptic --upgrade

Then, login to your Transcriptic account:

.. code-block:: bash

$ transcriptic login Email: [email protected] Password: Logged in as [email protected] (example-lab)

Tab Completion

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
``~/.config`` directory.

.. code-block:: bash

   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 ``~/.bashrc`` instead of
   ``~/.bash_profile``
-  Zsh note: Use ``autocomplete/zsh.sh`` instead of ``bash.sh``. Modify
   your ``~/.zshrc`` instead of ``~/.bash_profile``
-  Fish note: Use ``autocomplete/fish.sh`` instead of ``bash.sh``.
   Change ``$INSTALL_DIR`` to ``~/.config/fish/completions`` and rename
   ``tx-complete.sh`` to ``tx-complete.fish``. Skip the last step.

Documentation
-------------

CLI
~~~

See the `Transcriptic Developer
Documentation <https://developers.strateos.com/docs/getting-started-with-the-cli>`__
for detailed information about how to use this package, including
learning about how to package protocols and build releases.

Jupyter
~~~~~~~

Click on the |Binder| icon to open an interactive notebook environment
for using the library.

Developer
~~~~~~~~~

View `Developer Specific
Documentation <http://transcriptic.readthedocs.io/en/latest/>`__

Permissions
-----------

Note that direct analysis and submission of Autoprotocol is currently
restricted. Please contact [email protected] if you would like to do
so.

Contributing
------------

Read `Contributing <http://transcriptic.readthedocs.io/en/latest/contributing.html>`__ for more information on contributing to TxPy.

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