kineticsTools

The sm-analysis program delegates the identification of methylations to the ipdSummary program provided by the kineticsTools package.

By default, ipdSummary is searched for in the PATH. If it is not found in the PATH, you will receive the usual runtime error message:

[CRITICAL] [Errno 2] No such file or directory: 'ipdSummary'

and the program will terminate.

In that case, the instructions in the following sections can help you.

Installing kineticsTools

The kineticsTools package is written in Python. Unfortunately, at the time of this writing, there is no version of it in PyPI.

Therefore to use ipdSummary, we need to install kineticsTools and its dependencies from their GitHub repositories. This can be as follows. First activate the virtual environment where you have installed (or will install) PacBio Data Processing. Let us assume that PacBio Data Processing was installed inside a virtual environment located in:

/home/dave/.venvs/pdp

then, the activation must be done as usual with:

source /home/dave/.venvs/pdp/bin/activate

and now install the required packages with:

pip install git+https://github.com/PacificBiosciences/pbcore.git
pip install git+https://github.com/PacificBiosciences/pbcommand.git
pip install git+https://github.com/PacificBiosciences/kineticsTools.git

After this you will be able to use the ipdSummary executable to from sm-analysis automatically. If kineticsTools was installed in a different virtual environment, have a look at the following section.

Note

If, for some reason, the above mentioned repositories are not accesible, the installation can be carried out with the following lines that use alternative repositories:

pip install git+https://github.com/palao/pbcore.git
pip install git+https://github.com/palao/pbcommand.git
pip install git+https://github.com/palao/kineticsTools.git

Using ipdSummary installed in another virtual environment

Let us assume that PacBio Data Processing was installed inside a virtual environment located in:

/home/dave/.venvs/pdp

but kineticsTools was installed in:

/home/dave/.venvs/another

then, after activating the PacBio Data Processing’s virtual environment:

source /home/dave/.venvs/pdp/bin/activate

you can tell sm-analysis about ipdSummary by using a command line option (-i/--ipdsummary-path) as follows:

sm-analysis --ipdsummary-path /home/dave/.venvs/another/bin/ipdSummary