Pbindex¶
The sm-analysis program delegates the indexing of one-molecule
BAM files to pbindex, which must be accessible at runtime.
By default, pbindex is searched for in the PATH. If it is
not found in the PATH, you will receive an informative runtime
error message:
[CRITICAL] [Errno 2] No such file or directory: 'pbindex'
and the program will stop.
In that case, the instructions in the following sections can help you.
Installing Pbindex¶
Probably the easiest way to install pbindex is described in
PacBio & Bioconda. The instructions are basically:
Install
conda(see installing conda),Setup the
channels(as described in bioconda channels), andInstall
pbbam:conda install -c bioconda pbbam
Upon success, you will be able to pass the path to the pbindex
executable to sm-analysis if needed (see below for details).
Using Pbindex from sm-analysis¶
Let us assume that PacBio Data Processing was installed inside a virtual environment located in:
/home/david/.venvs/pdp
and let us assume that pbbioconda was installed in:
/home/david/miniconda3
then, after activating the PacBio Data Processing’s virtual environment:
source /home/david/.venvs/pdp/bin/activate
you can tell sm-analysis about pbindex by using a command
line option (-p/--pbindex-path) as follows:
sm-analysis --pbindex-path /home/david/miniconda3/bin/pbindex