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 sm-analysis program itself will terminate.

In that case, the instructions in the following sections can help you.

Installing Blasr

Probably the easiest way to install blasr is with conda. Have a look at Setting up Bioconda. Once those steps are followed, and the resulting conda environment is active, install blasr:

$ conda install blasr

Upon success, you will be able to pass the path to the blasr executable to sm-analysis if needed (see below for details).

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

At the time of this writing, SMRT-link software server tool does not contain the blasr executable.

Using blasr 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 pbbioconda 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 blasr by using a command line option (sm-analysis -b) as follows:

$ sm-analysis --blasr-path /home/dave/miniconda3/bin/blasr