Installation

Although installing lts_workflows_sm_scrnaseq itself should be easy enough, installing the workflow dependencies requires that you perform some manual steps. The number of steps depend on the installation route you take. For instance, the conda installation will install all python3 dependencies on the fly.

Hint

Whatever installation route you choose, it is recommended to create conda environments for python2 and python3 packages. The workflow will be executed from the python3 environment and by default is configured to load a python2 environment named py2.7. You can modify the python2 environment name in the configuration setting config[‘conda’][‘python2’].

Stable release from conda

Note

Make sure your channel order complies with the instructions provided by bioconda. In short, your ~/.condarc file should have the following channel configuration:

channels:
  - bioconda
  - conda-forge
  - defaults

The workflow depends on a couple of python2 packages that cannot be added as requirement to conda. Therefore, these packages must be installed manually.

$ conda create -n py2.7 python=2.7 rpkmforgenes=1.0.1 rseqc=2.6.4

To install lts_workflows_sm_scrnaseq, create a new environment, activate it and install the package:

$ conda create -n lts-workflows-sm-scrnaseq python=3.6
$ source activate lts-workflows-sm-scrnaseq
$ conda install -c scilifelab-lts lts-workflows-sm-scrnaseq

This is the preferred method to install lts_workflows_sm_scrnaseq, as it will always install the most recent stable release.

You can also create a new environment with lts_workflows_sm_scrnaseq as a dependency:

$ conda create -n lts-workflows-sm-scrnaseq -c scilifelab-lts lts-workflows-sm-scrnaseq python=3.6

From sources

The sources for lts_workflows_sm_scrnaseq can be downloaded from the Bitbucket repo.

$ git clone git@bitbucket.org:scilifelab-lts/lts-workflows-sm-scrnaseq.git

Once you have a copy of the source, you can install it with:

$ cd lts-workflows-sm-scrnaseq
$ python setup.py install

You can also install in development mode with:

$ python setup.py develop

See the section on Development for more information.

You can setup the python 2 packages as in the previous section, or by using the environment file lts_workflows_sm_scrnaseq/environment-27.yaml:

$ conda env create -n py2.7 -f lts_workflows_sm_scrnaseq/environment-27.yaml

Tests

If lts_workflows_sm_scrnaseq has been installed as a module, run

$ pytest -v -rs -s --pyargs lts_workflows_sm_scrnaseq

In order to load the pytest options provided by the module, the full path to the test suite needs to be given:

$ pytest -v -rs -s /path/to/lts_workflows_sm_scrnaseq/tests

See Test-based development for more information.