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

... 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

=== 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.

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

 

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

 

sudo add-apt-repository -y ppa:rock-core/qt4

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

  apt install xxdiff

on Ubuntu. If Ubuntu 20.04 doesn't find it, use the latest from http://archive.ubuntu.com/ubuntu/pool/universe/x/xxdiff/

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].

== Mac OSX ==

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>)

So, prepare the following steps by opening the Terminal window, and then

  sudo su                    # this will make you root, and ask for your password

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

If you are an academic user,

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

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

  # any folder would do; here we use /usr/local/bin/mac_bin

  curl -O -R https://{{SERVERNAME}}/pub/mac_bin/get_folder.sh

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

# copies [[Eiger#General_aspects|eiger2cbf-osx]] into /usr/local/bin, but under the name <code>H5ToXds</code>

# 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