Installation

In the Sali Lab

If you are working in the Sali lab, you don’t need to build and install CryptoSite - it is already set up for you as a module. Just run module load cryptosite to load it.

Dependencies

All dependencies listed below are expected to be found in standard system paths. This may require setting PYTHONPATH, PATH and/or LD_LIBRARY_PATH environment variables. Note that Linux is the only platform for which all these dependencies are available, and so is the only platform on which CryptoSite currently functions.

  • Python 3.6 or later.

  • MODELLER plus the SOAP-Protein library. The soap_protein_od.hdf5 file needs to be placed into MODELLER’s modlib directory.

  • MUSCLE.

  • DSSP. It is expected that the mkdssp binary is in the PATH.

  • fpocket (version 2).

  • PatchDock.

  • IMP.

  • NCBI BLAST+ plus a local copy of the UniProt database for it to search against. To make this local database, gunzip the uniprot_trembl.fasta.gz and uniprot_sprot.fasta.gz files available from the UniProt website and combine them into a single uniprot text file. This then needs to be formatted for BLAST using the formatdb or makeblastdb tools in the BLAST software library.

  • USEARCH version 8.1 or later.

  • Biopython.

  • NumPy and SciPy.

  • scikit-learn. CryptoSite has been tested with versions 0.12, 0.14.1, 0.21.3, and 1.0.2 of scikit-learn. We can’t guarantee correct SVM results with other versions; at a minimum you should ensure that test/test_predict.py runs successfully.

  • AllosMod is needed to run part of the protocol.

  • nose is also needed to run the test suite (recommended but not essential).

In the Sali lab, running module load modeller muscle dssp fpocket patch_dock imp blast+ usearch will get all of these dependencies.

Building

Use make to build the library. Use make test to test the library, and make install to install it. In most cases you will need to tell make where to install (if running on a Linux cluster, CryptoSite will need to be installed on a network-accessible filesystem) and where your local copy of UniProt is, with something like make PREFIX=/shared/cryptosite UNIPROT=/database/uniprot install. See Makefile.include for all make variables that can be configured.