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 sm-analysis program itself will stop.
In that case, the instructions in the following sections can help you.
Installing Pbindex¶
Probably the easiest way to install pbindex
is with conda
.
Have a look at Setting up Bioconda. Once those steps are followed,
and the resulting conda
environment is active, install 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 how).
Using Pbindex from sm-analysis¶
Let us assume that PacBio Data Processing was installed inside a virtual environment located in:
/home/dave/.venvs/pdp
and let us assume that pbbioconda
was installed in:
/home/dave/miniconda3
then, after activating the PacBio Data Processing’s virtual environment:
source /home/dave/.venvs/pdp/bin/activate
you can tell sm-analysis
about pbindex
by using a command
line option (sm-analysis -p
) as follows:
sm-analysis --pbindex-path /home/dave/miniconda3/bin/pbindex