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