Container for EncoMPASS development and maintenance

Development of the EncoMPASS database was carried out using multiple applications, whose dependencies are collected in a container in Singularity/Apptainer format.

This repository does not include the scientific software itself.

The file Ubuntu1804-EncoMPASS.def contains the definition file to build this container. There is also a link to a pre-built container image for the amd64 architecture.

To use the apps below, install them in a local folder writable by you and run the container while mounting that folder as /EncoMPASS (see the option --bind in the Singularity/Apptainer user guide).

Singularity documentation: https://sylabs.io/guides/latest/user-guide/ Apptainer documentation: https://apptainer.org/docs

List of applications supported by this container

Commands should be run inside the container, or passed as an argument to it (or to an explicit singularity exec command). Don't forget to escape the $ sign as \$ (shell variables are defined inside the container).

AnAnaS 1.1

Link: https://team.inria.fr/nano-d/software/ananas/
Pre-compiled static executable.
Test command line:

$ ananas $ENCOMPASS_DIR/1okc.pdb

CESymm 2.2.3 and QuatSymm 2.2.3

Link: https://github.com/rcsb/symmetry
Java packages, with shell script wrappers; original scripts modified to use 30G of max allocatable memory (backed up as run_*_small.sh).
Test command line:

$ runCESymm.sh -J $ENCOMPASS_DIR/1okc.pdb --stats

CESymm 2.1.0 and QuatSymm 2.1.0 are also available in the container.

DSSP 3.1.5 and HSSP 3.1.5

Link: https://github.com/cmbi/dssp https://github.com/cmbi/hssp
Dynamically linked executable, built in the container.
Test command line:

$ mkdssp -i $ENCOMPASS_DIR/1okc.pdb

Fr-TM-Align

Link: http://cssb.biology.gatech.edu/skolnick/files/FrTMalign/index.html
Static executable, built in the container.
Test command line:

$ frtmalign $ENCOMPASS_DIR/1okc.pdb <other_pdb>

MUSCLE 3.8.31

Link: https://www.drive5.com/muscle/downloads.htm
Pre-compiled static executable.
Test command line:

$ muscle3.8.31_i86linux64 -in <inputfile> -out <outputfile>

MUSCLE 5.1.0

Link: https://github.com/rcedgar/muscle/releases/download/5.1.0/muscle5.1.linux_intel64 Pre-compiled static executable. Test command line:

$ muscle5.1.linux_intel64 -align <inputfile> -output <outputfile>

PPM

Link: n/a
Static executable, built in the container.
Test command line:

$ immers < test.inp

Symd 1.3w and 1.61

Link: n/a
Pre-compiled static executables.
Test command line:

$ symd1.61-linux $ENCOMPASS_DIR/1okc.pdb