Using external software with Doppio

How Doppio finds programs

Doppio (via the underlying CCP-EM Pipeliner) is designed to work with a wide range of external software programs. It finds them by searching for the program executables in the directories listed in the PATH environment variable. Full details of how to configure the CCP-EM Pipeliner are explained here, but in brief, to add a new piece of software you should do one of the following things:

  • Add the directory containing the program executables (typically called bin/) to your PATH, for example in a bash terminal you can run

    export PATH="/path/to/new/program/bin:$PATH"

    or put that line in your .bashrc file so it is run automatically when you start a new shell.

  • Add the directory containing the program executables to the "additional_program_paths" list in the CCP-EM Pipeliner settings file.

Then start Doppio and it should find the new software.

Note

Doppio does not check the versions of external programs that it finds. If your jobs fail, try updating to a newer version of the software. The job info in Doppio should usually specify what version is required. We will add automatic version checking in future.

Supported software

The following programs are supported in Doppio. They can be installed separately, or for convenience, a number of them can be installed at once using the scripts in the package-ccpem2 repository. An upcoming version of Doppio will add a tool to allow additional packages to be installed interactively from within the Doppio interface.

RELION

Required for many Doppio jobs, which all generally include “RELION” in the name or description.

We recommend using the latest stable version of RELION 5.0.

Installation: https://relion.readthedocs.io/en/release-5.0/Installation.html

Doppio will also work with RELION 4.0. This can be installed on its own, or the copy included in the CCP-EM v1 20221108 package can be used (see below).

ModelAngelo

Required for the ModelAngelo job.

Installation: Doppio can use the copy of ModelAngelo installed along with RELION 5 (see above) or you can install it separately: https://github.com/3dem/model-angelo

CCP4 v9.0

Provides programs used by the following jobs:

  • AceDRG

  • Atomic Model Validation

  • checkMySequence

  • DoubleHelix

  • em_placement

  • emplace_local

  • findMySequence

  • ModelCraft

  • Molprobity

  • Molrep

  • Privateer

  • Process predicted model

  • Refmac Servalcat

  • Servalcat difference map

  • Servalcat Trim

  • Slice

Note that the programs used by some of these jobs can also be installed on their own, for example by using the package-ccpem2 script.

Also note that some of these jobs require the very latest version of CCP4 (9.0.005, for the jobs in Doppio 1.2.0). You can update an existing installation by running ccp4um.

Download from https://www.ccp4.ac.uk/download

Installation: https://www.ccp4.ac.uk/download/installation.html

Known issues: https://www.ccp4.ac.uk/download/doc/known_issues_linux.html

CCP-EM v1, build 20221108

Required for the following jobs:

  • Confidence Map calculation

  • CryoEF particle orientation analysis

  • Flex-EM

  • LAFTER

  • ProShade

Download the last CCP-EM v1 nightly build for your OS from https://www.ccpem.ac.uk/download.php

Installation
tar -xzf ccpem-20221108-linux-x86_64.tar.gz (or ...-mac-x86_64.tar.gz on Mac) to unpack
cd ccpem-20221108
./install_ccpem.sh
source setup_ccpem.sh (or setup_ccpem.csh for csh)

Known issues https://www.ccpem.ac.uk/user_help/known_issues.php

Other software

The following programs are also supported. Links and more documentation will be added soon:

  • Cinderella

  • crYOLO

  • CryoDRGN

  • CTFFIND4

  • EMDA2

  • EMDB Validation Analysis

  • Icebreaker

  • LocScale

  • MotionCor2

  • Parakeet

  • REPIC

  • ResMap

  • RIBFIND2.0

  • TEMPy2.0

  • TEMPy-REFF