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.
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 2.7 or later (Python 3 should also be OK).
- MODELLER plus the
SOAP-Protein library.
The
soap_protein_od.hdf5
file needs to be placed into MODELLER'smodlib
directory. - MUSCLE.
- DSSP. It is expected that the
:command:`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
theuniprot_trembl.fasta.gz
anduniprot_sprot.fasta.gz
files available from the UniProt website and combine them into a singleuniprot
text file. This then needs to be formatted for BLAST using theformatdb
ormakeblastdb
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.
Use make PYTHON=python3
or make PYTHON=python2
to build the library
(depending on which version of Python you want to use).
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.