Installing the Spatial Transcriptomics pipeline

These are the general instructions for installing the st_pipeline from scratch on you compute environment. All the commands can be performed as a user with no elevated permissions.

Check that you have Anaconda installed, and that it is using python 2.7

python -c "import sys; print sys.version"

Example output:

2.7.12 |Anaconda custom (64-bit)| (default, Jul  2 2016, 17:42:40) [GCC 4.4.7 20120313 (Red Hat 4.4.7-1)]

Here one can see that the python version is 2.7.12, and that Anaconda is installed. This shows an example of output when Anaconda is not installed:

2.7.10 (default, Oct 23 2015, 19:19:21) [GCC 4.2.1 Compatible Apple LLVM 7.0.0 (clang-700.0.59.5)]

If Anaconda is not installed on your system, it can be downloaded from the following link: Important! Download the python 2.7 version

https://www.continuum.io/downloads#linux

Direct link for wget or curl (at the time of writing) https://repo.continuum.io/archive/Anaconda2-4.1.1-Linux-x86_64.sh

wget https://repo.continuum.io/archive/Anaconda2-4.1.1-Linux-x86_64.sh

To run the installer, type the following command (the numbers might change depending on the current version at the time of download):

bash Anaconda2-4.1.1-Linux-x86_64.sh

During the installation you will be asked if you want to pre-append the Anaconda path to your path. Choose yes. If you do not choose yes, run the following command:

echo export PATH="~/anaconda2/bin:$PATH" > ~/.bash_profile

OR

Edit your ~/.bash_profile directly by entering the following text using your favourite text editor:

export PATH="~/anaconda2/bin:$PATH"

To make sure that the changes have been regestired by the shell you can either:

Log out from the server and then log back in

OR

Type

source ~/.bash_profile

After doing this, we need to install a couple of packages using anaconda to use the pipeline. Type the following commands:

conda install nomkl

conda install pysam

We then create a virtual environment from which we will run the pipeline in. Type the following command:

conda create -n pipeline python=2.7 anaconda

The name for the virtual environment that we have just created is specified by the -n flag. Here is is called pipeline, but this can be anything that you want to name it. To run the pipeline, this virtual environment must be activated. To activate the virtual environment, enter the following command:

source activate pipeline

Where pipeline is the name of your virtual environment (here the virtual environment is called pipeline). To deactivate the virtual environment, type the following command:

source deactivate

You need to obtain the pipeline from github to use it. The following steps will tell you how to perform this.

Change to your home directory

cd

Clone the repository from github

git clone git://github.com/SpatialTranscriptomicsResearch/st_pipeline.git

Change into the st_pipeline directory

cd st_pipeline

Activate the virtual environment (if not already active)

source activate pipeline

Install the pipeline

python setup.py build

python setup.py install

Alternatively, you can simply install the pipeline using PyPy:

``pip install stpipeline`

Now the pipeline is installed and ready to be run.