Blasr¶
The sm-analysis
program delegates the alignment of the input BAM
file to blasr
, which must be accessible at runtime. The blasr
program will be called on demand: if an aligned file is found,
the alignment process will be skipped for that file.
By default, blasr
is searched for in the PATH
. If it is
not found in the PATH
, you will receive a common runtime
error message:
[CRITICAL] [Errno 2] No such file or directory: 'blasr'
and the program will terminate.
In that case, the instructions in the following sections can help you.
Installing Blasr¶
Probably the easiest way to install blasr
is described in
PacBio & Bioconda. The instructions are in summary:
Install
conda
(see installing conda),Setup the
channels
(as described in bioconda channels), andInstall
blasr
:conda install -c bioconda blasr
Upon success, you will be able to pass the path to the blasr
executable to sm-analysis
if needed (see below for details).
Using blasr 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 blasr
by using a command
line option (-b/--blasr-path
) as follows:
sm-analysis --blasr-path /home/david/miniconda3/bin/blasr