Installation

The latest stable version of Digger may be downloaded from PyPI. Digger requires Python 3.9 or above.

Development versions are available from GitHub.

Digger requires BLAST to be installed. If you use conda/anaconda on Linux or Mac we recommend installing BLAST with conda:

> conda install bioconda::blast

Alternatively, please follow the link for installation instructions and see the note below. No BLAST databases are needed: just the executable.

The installation instructions at NCBI ask you to browse to the link https://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/. Browsers are ceasing support for FTP, and you may find that your browser won’t open the page. The easiest approach in this case is to use curl to download the file. curl is included in all Windows 10 and 11 installations.

will list the latest versions available for download. For Windows, for example, you will see a filename similar to ncbi-blast-2.12.0+-win64.exe.

will download the file to your current directory. You will need to modify the filename to reflect the listed version.

Once BLAST has been installed, following NCBI’s instructions, please verify by typing blastn -help at the command line: if everything is ok, it should provide usage instructions. On Windows you will need to open a new command window to run the command.

If you encounter the error Cannot allocate memory, this is coming from BLAST makeblastdb. Please set the environment variable BLASTDB_LMDB_MAP_SIZE=100000000.

If you encounter the error Error while loading shared libraries: libnsl.so.1, the shared library libnsl.so.1 needs to be installed. The precise instructions to do so are platform specific, but you should be able to obtain guidance through a Google search.

The easiest way to install Digger itself is with pip:

> pip install receptor-digger --user

Digger requires the Python packages receptor-utils and biopython. These should be installed automatically by pip.