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:

  1. Install conda (see installing conda),

  2. Setup the channels (as described in bioconda channels), and

  3. Install 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