Installation: Difference between revisions

This article has some little script snippets that should ease the installation of XDS and related programs like ([[XDS-viewer]], [[xdsstat]], [[XDSGUI|xdsgui]]). It is assumed that binaries (or links to binaries) should go to /usr/local/bin . This means that you should do this as the administrator (root), or have sudo rights (Mac, and some Linux distros).

'''Log in as root''' - we need write permission for /usr/local/bin .

=== [[XDS]] package ===

If you are an academic user, as root

In case the [ftp://ftp.mpimf-heidelberg.mpg.de/pub/kabsch above site] is unavailable, there is a [https://strucbio.biologie.uni-konstanz.de/pub/xds backup site].

 

=== other programs: [[XDS-Viewer]], [[XDSSTAT]], [[XDSCC12]], [[XDSGUI]], [[XSCALE_ISOCLUSTER]]  ===

... can be downloaded from https://{{SERVERNAME}}/pub/linux_bin/ . A simple way to obtain them is to create an empty folder, "cd" to that folder and then (as root)

wget https://{{SERVERNAME}}/pub/linux_bin/get_folder.sh

  chmod +x get_folder.sh

./get_folder.sh

You may repeat this, as root, every now and then, to update the programs.

=== tools and helper programs for [[generate_XDS.INP]] and [[XDSGUI]], and libraries ===

* check and installation of Unix tools for [[generate_XDS.INP]] is shown at [[Generate_XDS.INP#Dependencies]]

* helper programs for [[XDSGUI]] are listed and discussed at [[XDSGUI#Dependencies]]. Nota bene: XDSGUI needs [[generate_XDS.INP]] unless you already have a working XDS.INP.  

  ldd `which xdsgui` | grep found

and that should show you the libraries it it didn't find. Your friendly system administrator will then work out the specific commands to install those libraries.

For RedHat-type distributions, that would typically be e.g.  

  yum provides libXfixes.so.3

the output of which will tell you that this is in the libXfixes RPM.  

command should find it for you (where <code><name-of-library></code> could e.g. be <code>libGLU.so.1</code>). This needs a one-time installation by

  sudo apt install apt-file

  sudo apt-file update

Ubuntu 18.04: if libQtOpenGL.so.4 is missing, use <code>sudo apt install libqt4-opengl</code>.

Ubuntu 20.04: if libQtOpenGL.so.4 is missing, use

But it would be better to use the [https://strucbio.biologie.uni-konstanz.de/pub/linux_bin/xdsgui_qt5 Qt5 binary of XDSGUI].

An <code>xxdiff</code> binary that runs on CentOS7 (RHEL7, SL7) is provided by the <code>get_folder.sh</code> script.

Alternatively, tkdiff may be installed, or other graphical comparison programs, like meld or kdiff3. vimdiff is also nice, and probably already installed.

For [[Eiger]] data processing, <code>H5ToXDS</code> should be installed as [[Eiger|explained]], and <code>h5dump</code> should be installed by e.g. <code>yum -y install hdf5</code>. Furthermore, you want the [https://www.dectris.com/company/news/newsroom/news-details/process-eiger-data-with-xds-fast Neggia] library or the [https://github.com/DiamondLightSource/durin Durin plugin].

Attention: [[generate_XDS.INP]] requires the [https://developer.apple.com/download/more/ Xcode command line tools] to be installed (free of charge). In my experience, you have to explicitly agree to the License terms when running a Command Line Tool (e.g. <code>strings</code>) for the first time.

Become familiar with the concept and ways to run commands as "root" - google "mac osx become root". All the tasks that are run in a Terminal window require root privileges, since some of the programs and their links are written to /usr/local/bin. (As an alternative that does not require root, one may create a directory $HOME/bin and use that for the programs and links. That would also require modification of the $PATH, by a one-time <code>echo 'export PATH=$PATH:$HOME/bin' >> ~/.profile</code>)

  mkdir /usr/local/bin  # only if /usr/local/bin was not created before

=== [[XDS]] package ===

echo you may have to "sudo su" first, to obtain administrator permissions!

  curl -L -o - ftp://ftp.mpimf-heidelberg.mpg.de/pub/kabsch/XDS-OSX_64.tar.gz | tar xzvf -

  ln -sf XDS-OSX_64/* .

Starting with macOS Catalina, you also need

  xattr -dr XDS-OSX_64/*

if you get a security error popup (google "xattr com.apple.quarantine catalina").

=== other programs: [[XDS-Viewer]], [[XDSSTAT]], [[XDSCC12]], [[XDSGUI]], [[XSCALE_ISOCLUSTER]]  ===

... can be downloaded from https://{{SERVERNAME}}/pub/mac_bin/ . A simple way to obtain them is is to open a Terminal, and type:

  sudo su

mkdir -p /usr/local/bin/mac_bin

cd /usr/local/bin/mac_bin

  ./get_folder.sh

If you want to update the programs some time later, just run these commands again.

In order to enable [[Eiger]] data processing, the <code>get_folder.sh</code> script

# copies [https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8/hdf5-1.8.7/bin/mac-intel-x86_64/utilities/h5dump version 1.8.7] of <code>h5dump</code> into /usr/local/bin

Lastly, it is useful (for e.g. XDSGUI) to install <code>xxdiff</code> from http://furius.ca/downloads/xxdiff/releases/macosx/

The programs of the [[XDS]] package as well as [[XDSGUI]], [[XDSSTAT]], [[XDSCC12]] and so on may be run on 64bit Windows 10 within the [https://docs.microsoft.com/windows/wsl/install-win10 Linux Subsystem for Windows] (WSL). This (easily!) installs a Ubuntu environment, which supports the apt package manager, so in principle any software available for Ubuntu may be installed (or other distros, see [https://blogs.msdn.microsoft.com/commandline/2017/05/11/new-distros-coming-to-bashwsl-via-windows-store/]).

Graphical Linux programs require installation of a X server like [https://sourceforge.net/projects/xming/files/latest/download Xming] or [https://sourceforge.net/projects/vcxsrv VcXsvr] on the Windows host. There are helpful writeups (e.g. [http://wsl-guide.org/en/latest/]). To use the X server, one has to say in the shell window

before running the program. Running XDSGUI under WSL's Ubuntu may require installation of a few packages with e.g.

(see [[XDSGUI#Libraries_and_software_that_the_program_depends_on|XDSGUI]] and above).

 

[[generate_XDS.INP]] requires a number of packages (some of which are only for specific detectors!); I'd start with

XDSSTAT and the conversion to MTZ files by XDSCONV require a CCP4 installation accessible by WSL. In principle, CCP4 may be installed within WSL (have not tested this), or on the Windows host.

[[File:Xds_win.PNG|1000px]]