System requirements

Currently only UNIX-based systems supported. Should work both on Linux and OS X.

We recommend using a computer cluster but Assembline can be also run on a standalone workstation.

Warning

Some scripts might not work on OS X. All tests were performed with bash (i.e. not tested in other shells).

Installation with Anaconda

Installation should take less than 1 hour.

Install dependencies

UCSF Chimera 1.14 (https://www.cgl.ucsf.edu/chimera/download.html)

chimera command must be available in your command line.
Xlink Analyzer plugin to Chimera, version 1.1 and higher (https://www.embl-hamburg.de/XlinkAnalyzer/XlinkAnalyzer.html)

It is only needed on your local workstation for input preparation and analysis.

Install Anaconda

Anaconda is a free and open-source distribution of the Python and R programming languages for scientific computing, which aims to simplify package management and deployment.

We will use Anaconda to create a “virtual environment” in which Assembline will be installed.

Download and install version for Python 3 from https://www.anaconda.com/distribution/

Create virtual Anaconda environment

conda create --name Assembline python=3.8

Install Python dependencies

Activate (“enter”) the environment:
source activate Assembline
or depending on your computer setup:
conda activate Assembline

Install Integrative Modeling Platform (IMP) version at least 2.14:

conda config --add channels conda-forge
conda install -y imp=2.16.0

Install other dependencies:

conda install -y scipy numpy scikit-learn matplotlib pandas
conda install -y -c salilab pyrmsd
conda install -y -c conda-forge hdbscan

[optional] Install Modeller. Only needed for building full atom representation of loops modelled as flexible beads
conda install -y -c salilab modeller
Follow the displayed instruction to edit lib/modeller-9.25/modlib/modeller/config.py inserting your Modeller license key

Install Gnuplot

[optional] Install Gnuplot. Only needed for analysis steps.
conda install -y -c conda-forge gnuplot

Install R

The easiest is to install R in your Anaconda environment:

conda install -y r-base r-fdrtool r-psych r-ggplot2 r-tidyr r-data.table

If for any reason you want to install R separately, install R from https://www.r-project.org/ and make sure:

Rscript is available in your command line.

The following R packages are installed:

fdrtool

psych

ggplot2

tidyr

data.table

Install Assembline

conda install -y -c kosinskilab assembline

For your information - this will also install some external dependencies:

PDBX https://github.com/soedinglab/pdbx
PDB_TOOLS https://github.com/haddocking/pdb-tools

Warning

Always activate the environment before using the software by:

source activate Assembline

or depending on your computer setup:

conda activate Assembline

For developers

Create the environment and install all dependencies, but do not install Assembline from Anaconda.

Instead:

Clone our repositories:

In your software_dir:

git clone git@git.embl.de:kosinski/efitter.git
git clone git@git.embl.de:kosinski/pyxlinks.git
git clone git@git.embl.de:kosinski/pdb_utils.git
mkdir Assembline
cd Assembline
git clone git@git.embl.de:kosinski/imp_utils1.git
git clone git@git.embl.de:kosinski/SuperConfig.git

Clone PDBX and PDB-TOOLS

In your software_dir:

git clone https://github.com/soedinglab/pdbx.git
git clone https://github.com/haddocking/pdb-tools.git

Setup before running

After installation run sth like the below every time before using the pipeline:

module load Anaconda3
source activate Assembline
export PYTHONPATH=<your path>Assembline/SuperConfig:$PYTHONPATH
export PYTHONPATH=<your path>Assembline/imp_utils1:$PYTHONPATH
export PYTHONPATH=<your path>pyxlinks:$PYTHONPATH
export PYTHONPATH=<your path>situs_utils:$PYTHONPATH
export PYTHONPATH=<your path>pdb_utils:$PYTHONPATH
export PYTHONPATH=<your path>/pdb-tools/:$PYTHONPATH
export PYTHONPATH=<your path>/pdbx:$PYTHONPATH

of course replacing the path with your path.

And, use the full paths to the scripts:

Assembline scripts are located in Assembline/imp_utils1/scripts

Efitter scripts (those used for generating and analyzing fit libraries) are in efitter/scripts

Explanations:

git clone - creates local copies of software in so-called “git repositories” e.g. at git.embl.de