Tip Generic snapshot autoPROC release date 20240123

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 Mac running OS X version 10.9 "Mavericks" but should work equally on later OS X versions (see wikipedia OS X page).

  • Please first check that the machine on which you are running the installation is running a supported OS X release by following Apple Support Finding your OS X version and build information

Note GPhL software will only run on Macs running OS X 10.9 onwards. Versions prior to 10.9 are NOT supported.

  • 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 20240123.

  • Installation is done from a user account software with administration privileges, 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. Mac OS X packages

  • Some of the infrastructure that will be required to provide some of the optional dependencies of autoPROC, are not installed by default.

  • Xcode will be required. If not already installed on your machine, Xcode is available through the "App Store".

    • Once installed, open Xcode and from the main Xcode tab in the finder bar, then select preferences. When the preferences window opens, select the Downloads tab and then select and install "command line options", or if you are running OS X 10.9 "Mavericks", type "xcode-select --install" from a terminal window.

    • From a terminal window execute the command:

sudo xcodebuild -license

  • X11 is also no longer supplied with OS X and needs to be installed.

    • Download the current X11 dmg file from https://www.xquartz.org/, double click on it to open and then follow the instructions to install.

  • Finally, we recommend that you ensure that the OS is up to date by applying OS-recommended updates (particular security patches).

3. Imagemagick

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

  • If you have either the MacPorts or fink package managers installed, then Imagemagick can be installed as follows:

If using MacPorts

sudo port install imagemagick

If using Fink

fink install imagemagick

4. CCP4 (and Coot)

Tip Skip this section if you already have a working CCP4 8.0 (and Coot) installation.

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

Note These instructions assume installation of CCP4 version 8.0.

  • On your Mac navigate to https://www.ccp4.ac.uk and then select Download.

    • Make sure you are looking at the Mac OS X pane.

    • Download the Package Manager by clicking on the orange Download Now! button.

    • This will download a file called macosx-x86_64_ccp4-8.0-setup.dmg to your Downloads folder

    • Navigate to the Downloads folder and double click on macosx-x86_64_ccp4-8.0-setup.dmg to open it.

    • This will open a large Setup icon, double click on the icon.

    • You may be asked "Are you sure you want to open it?" Click Open

    • You will now be asked Setup wants to make changes. Type your password to allow this.

Tip The CCP4 installation user must have administration privileges

  • 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.

    • The CCP4 suite (including Coot) will be installed in folder /Applications (no user choice!).

    • Make sure that the folder you give for Choose temporary for download: is writable.

  • 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.

    • Test that the coot executable has been installed correctly by running it and verifying that the GUI works:

coot

  • Optionally test that the ARP/wARP system has been installed correctly by running:

$warpbin/check_programs.sh $warpbin/auto_tracing.sh $warpbin
### You are running ARP/wARP 8.0 patch 1 ###

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.
Note
We 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.

5. 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):

If on Intel-based platform then

mkdir ~/xds; cd ~/xds
curl -O https://xds.mr.mpg.de/XDS-OSX_64.tar.gz
tar xzf XDS-OSX_64.tar.gz
curl -O https://xds.mr.mpg.de/XDS_html_doc.tar.gz
tar xf XDS_html_doc.tar.gz
rm *.tar.gz

If on Apple-M1 (ARM) platform then

mkdir ~/xds; cd ~/xds
curl -O https://xds.mr.mpg.de/XDS-Apple_M1.tar.gz
tar xzf XDS-Apple_M1.tar.gz
curl -O https://xds.mr.mpg.de/XDS_html_doc.tar.gz
tar xf XDS_html_doc.tar.gz
rm *.tar.gz

6. 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/

7. 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_20240123 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:
. /Applications/ccp4-8.0/bin/ccp4.setup-sh
# Add XDS to the user’s path:
export PATH="$PATH":~software/xds/XDS-OSX_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 /Applications/ccp4-8.0/bin/ccp4.setup-csh
# Add XDS to the user’s path:
set path=($path ~software/xds/XDS-OSX_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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