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