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¶
pbindex
is provided by the pbbam package.
A simple way to install pbbam is with conda
.
Have a look at Setting up Bioconda, and follow the instructions in there
if you want to choose the conda route. Once those steps are followed,
and the resulting conda
environment is active, install pbbam
:
$ conda install pbbam
Upon success, you will be able to pass the path to the pbindex
executable to sm-analysis if needed (see below how).
Warning
Notice that, contrary to the suggestion given in PacBio & Bioconda,
the explicit selection of the bioconda
channel by means of the -c
option of conda install
(e.g., conda install -c bioconda ...
)
triggers a dependency error. DO NOT USE the -c bioconda
option,
just run conda install ...
instead, as explained in the main text.
Note
An alternative way to install pbindex
is through SMRT-link software server tool.
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 pbbam
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