F/LOSS part of the dependencies can be installed from standard Debian/Ubuntu repositories.
List of such dependencies is found at dependencies/Ubuntu-20.04/run.sh.
Some Python modules have to be installed from PyPI.
List of such dependencies is found at dependencies/PyPI/run.sh.
Jackal and Rosetta have to be installed with their executables accessible in $PATH.
Jackal does not seem to have version numbers, I have downloaded my copy on 2022-02-08.
Rosetta's version 2021.16.61629 has been used.
Some computations use temporary files and directories.
They are created using mktemp and later on removed.
Default place for mktemp to store these temporary files and directories is /tmp, but this could be overridden by setting TMPDIR environment variable.
To generate contacts map for PDB files of interest, the following steps have to be performed:
-
Extract contacts for each of the PDB files:
$ snakemake vorocontacts/<PDB_ID_1>.tab vorocontacts/<PDB_ID_2>.tab ...
Here <PDB_ID_1>, <PDB_ID_2>, ... correspond to 4-symbol PDB IDs (letters have to be in uppercase).
-
Generate the map for the processed PDB files:
$ bin/S1-contact-map --contacts-with alignments/pdb_seqres-PF07654.hmmsearch <PDB_ID_1> <PDB_ID_2> ... > map.tab
Copyright 2022 Andrius Merkys
Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.