Tip These instructions are for Ubuntu 16.04 64bit,
Generic snapshot autoPROC release date 20240710

Please note this version of autoPROC is for academic users and its download, installation and use is conditional on acceptance of the licence conditions. Please carefully review these licence conditions before download, installation or use.

1. Introduction

  • These instructions have been prepared on an updated Ubuntu 16.04 LTS x86_64 kernel version.

  • Please first check that the machine where you are doing the installation is actually running under a 64 bit Ubuntu OS. To do this run the commands:

lsb_release -a; uname -m
No LSB modules are available.
Distributor ID: Ubuntu
Description: Ubuntu 16.04.X LTS
Release: 16.04
Codename: xenial
x86_64

Tip This page uses green bold text for the commands you type, blue italic text for the output produced and red italics for comments. The command prompt is omitted to make copy/paste easier. Some long lines may be wrapped in your display but if you use copy and paste the commands should work fine.

  • If the commands do not result in reports of Ubuntu and a version 16.04 and x86_64 then you are looking at the wrong page! Please go back and select your OS.

  • This page will show the complete process of how to install and test Global Phasing’s automated data processing suite, autoPROC, specifically the Generic snapshot autoPROC version release date 20240710.

  • Apart from step 2, installation is done from a user account software (without root privilege), using the bash shell and assuming that the browser downloads to the ~/Downloads directory.

  • You will probably have to adapt the procedure in places as you are likely to be installing in a different location and possibly with a different shell. You may also have already installed other software such as CCP4 and XDS. If so then you should use your existing installations.

2. Ubuntu packages

Note
Ubuntu package installation must be done as root.

  • Although not absolutely required by autoPROC, ImageMagick is highly recommended in order to make use of the full functionality of autoPROC.

  • If not already installed, this may be installed as follows (see also official Ubuntu documentation about sudo):

sudo apt-get install imagemagick

Note
The rest of these instructions should be performed as an unprivileged user: NOT 'root'.

  • We will use the user account called software.

3. CCP4

Tip Skip this section if you already have a working CCP4 8.0 installation.

  • A functional installation of the CCP4 suite is an absolute requirement for autoPROC.

Note These instructions assume installation of CCP4 version 8.0.

  • CCP4 should be installed in a non-root account (here software).

  • Follow the link to https://www.ccp4.ac.uk and then select Download from the "SOFTWARE" pull-down.

    • The page starts Here you can download the latest version of the CCP4 Software Suite, version 8.0, code name Addingham.

    • Make sure you are looking at the GNU/Linux pane.

    • Then download the Package Manager (64 bit) using the orange Download Now! button.

    • Download the ccp4sm.tar.gz file and unpack it in a directory ~/ccp4. These are my commands to do this:

mkdir ~/ccp4; cd ~/ccp4
tar xvf ~/Downloads/ccp4sm.tar.gz

  • Then launch the CCP4 package manager GUI:

./ccp4sm

  • You should see the CCP4 Software Suite Setup: follow the instructions.

    • Select CCP4 Program Suite v8.0.

    • If you are a publically funded academic institution or you have a valid commercial SHELX licence: select SHELX.

    • If you are a publically funded academic institution or you have a valid commercial ARP/wARP licence: select ARP/wARP v8.0.

    • Agree to CCP4 terms and conditions (if not done before).

    • Confirm the ARP/wARP licence (if appropriate) and agree to its terms and conditions.

    • Set the location for the installation to ~/ccp4.

  • CCP4 package should be downloaded and installed: have a cup of coffee!

    • The installation process will automatically install all CCP4 updates available at the time of installation. Post-installation, we would strongly recommend that you keep your CCP4 installation updated by applying new updates as they are released by CCP4 (either through running ccp4i2, ccp4i or ccp4um).

  • If you want to test the installation see quick test of the CCP4 installation.

4. XDS

Tip XDS is an absolute requirement for autoPROC

  • Please see https://xds.mr.mpg.de/ for a full description of XDS, in particular note that "For industrial usage of XDS a license is required"

  • Download XDS binaries from https://xds.mr.mpg.de/html_doc/downloading.html (for academic users) or through the appropriate channels for commercial users. Then unpack them in ~/xds. The following commands achieve this (for academic users):

mkdir ~/xds; cd ~/xds
wget https://xds.mr.mpg.de/XDS-INTEL64_Linux_x86_64.tar.gz
tar xzf XDS-INTEL64_Linux_x86_64.tar.gz
wget https://xds.mr.mpg.de/XDS_html_doc.tar.gz
tar xf XDS_html_doc.tar.gz
rm *.tar.gz

5. autoPROC software installation

  • This section is omitted from the "Generic" pages included as files in the distribution because to see this page the install must have already been done.

  • For details please consult the specific page available at your download page, see https://www.globalphasing.com/

6. GPhL Software user access

  • For users to access autoPROC they need to invoke the autoPROC setup script (as well as having set up the CCP4 suite and having XDS available on their PATH).

  • A good way to do this is to create a soft link called autoPROC_latest to the directory for the installation we have just made:
    [genericdirnot]

cd ~/GPhL
rm -f autoPROC_latest
ln -s autoPROC_snapshot_20240710 autoPROC_latest

  • The soft link is useful because it means that when in the future you install a new version of the software, the soft link can be updated so that users automatically use the latest version of the software (but the previous version will still be available if wanted).

  • Once you have created the soft link, bash users can enable access to the software by adding the following lines to their ~/.bashrc file:

# Provide access to autoPROC:
. ~software/GPhL/autoPROC_latest/setup.sh
# Set up CCP4:
. ~software/ccp4/ccp4-8.0/bin/ccp4.setup-sh
# Add XDS to the user’s path:
export PATH="$PATH":~software/xds/XDS-INTEL64_Linux_x86_64

  • csh or tcsh users can enable access to the software by adding the following lines to their ~/.cshrc file:

# Provide access to autoPROC:
source ~software/GPhL/autoPROC_latest/setup.csh
# Set up CCP4:
source ~software/ccp4/ccp4-8.0/bin/ccp4.setup-csh
# Add XDS to the user’s path:
set path=($path ~software/xds/XDS-INTEL64_Linux_x86_64)

Note

  • If you have a site-specific special mechanism to provide access to software then this should be used instead!

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