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