Difference between revisions of "Installation"

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(other programs: XDS-Viewer, XDSSTAT, XDSCC12, XDSGUI, XSCALE_ISOCLUSTER)
(Windows)
 
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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].
 
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]]  ===
+
=== other programs: [[XDS-Viewer]], [[XDSSTAT]], [[XDSCC12]], [[XDSGUI]], [[XSCALE_ISOCLUSTER]], [[spot2pdb]], [[generate_XDS.INP]]  ===
... 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)
+
... 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
 
  wget https://{{SERVERNAME}}/pub/linux_bin/get_folder.sh
 
  wget https://{{SERVERNAME}}/pub/linux_bin/get_folder.sh
 
  chmod +x get_folder.sh
 
  chmod +x get_folder.sh
 
  ./get_folder.sh
 
  ./get_folder.sh
You may repeat this, as root, every now and then, to update the programs.
+
You may repeat this every now and then to update the programs.
  
==== infrastructure: tools and helper programs for [[generate_XDS.INP]] and [[XDSGUI]], and libraries ====
+
As root, the script copies the programs into /usr/local/bin/linux_bin, and links them to /usr/local/bin. As a normal user, they are downloaded to $HOME/bin/linux_bin, and linked to your $HOME/bin. In the latter case, make sure that $HOME/bin is in your $PATH.
 +
 
 +
Qt4 versions of xdsgui and xds-viewer are available as xdsgui.qt4 and xds-viewer.qt4, for old Linux distributions.
 +
 
 +
=== 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]]
 
* 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.  
 
* 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.  
  
 
Since XDSGUI depends on graphics packages that may need to be installed, you can check the xdsgui binary with
 
Since XDSGUI depends on graphics packages that may need to be installed, you can check the xdsgui binary with
  ldd `which xdsgui`
+
  ldd `which xdsgui` | grep found
and that should show you the libraries it found, and more importantly, those that it didn't find. Your friendly system administrator will then work out the specific commands to install those libraries; on RedHat-type distributions that would typically be e.g. <code>yum provides libXfixes.so.3</code> the output of which will tell you that this is in the libXfixes RPM.  
+
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.  
 +
 
 +
If in the case of Ubuntu you don't know the name of the package that provides a certain library, the
 +
  sudo apt-file search <name-of-library>
 +
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 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
+
Ubuntu 20.04: if libQtOpenGL.so.4 is missing (for the Qt4 binary of [[XDSGUI]]), use
 
  sudo add-apt-repository -y ppa:rock-core/qt4
 
  sudo add-apt-repository -y ppa:rock-core/qt4
 
  sudo apt update
 
  sudo apt update
 
  sudo apt install libqt4-opengl
 
  sudo apt install libqt4-opengl
 
Of course, this still requires installation of <code>xxdiff</code> (or alternative).
 
  
 
<code>xxdiff</code> is likely available for your distribution - google for it, or try e.g.
 
<code>xxdiff</code> is likely available for your distribution - google for it, or try e.g.
 
  yum -y install xxdiff
 
  yum -y install xxdiff
 
on RHEL6/CentOS6/SL6 systems, or
 
on RHEL6/CentOS6/SL6 systems, or
  apt-get install xxdiff
+
  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/
 
on Ubuntu. If Ubuntu 20.04 doesn't find it, use the latest from http://archive.ubuntu.com/ubuntu/pool/universe/x/xxdiff/
  
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== Mac OSX ==
 
== Mac OSX ==
  
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.
+
Attention: [[generate_XDS.INP]] requires the [https://developer.apple.com/download/more/ Xcode command line tools] to be installed (free of charge): open a Terminal window, and enter <code>sudo xcode-select --install</code>. You may 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>)
+
Become familiar with the concept and ways to run commands as "root" - google "mac osx become root". All the installation 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 for installation, 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
 
So, prepare the following steps by opening the Terminal window, and then
Line 72: Line 84:
 
if you get a security error popup (google "xattr com.apple.quarantine catalina").
 
if you get a security error popup (google "xattr com.apple.quarantine catalina").
  
=== other programs: [[XDS-Viewer]], [[XDSSTAT]], [[XDSCC12]], [[XDSGUI]], [[XSCALE_ISOCLUSTER]]  ===
+
=== other programs: [[XDS-viewer]], [[XDSSTAT]], [[XDSCC12]], [[XDSGUI]], [[XSCALE_ISOCLUSTER]], [[generate_XDS.INP]]  ===
 
... can be downloaded from https://{{SERVERNAME}}/pub/mac_bin/ . A simple way to obtain them is is to open a Terminal, and type:
 
... 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
 
  sudo su
Line 89: Line 101:
 
# 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  
 
# 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/
+
A Qt5 version of XDS-viewer (provided by T. Hauß) is available for MacOS [https://{{SERVERNAME}}/pub/mac_bin/XDS-Viewer-macOS10.13.dmg 10.13], and for [https://{{SERVERNAME}}/pub/mac_bin/XDS-Viewer-macOS10.15.dmg 10.15] and newer. Users must decide which DMG they install. The Qt4 version is still the default.
 +
 
 +
Lastly, it is useful (for e.g. XDSGUI) to install <code>xxdiff</code> from http://furius.ca/downloads/xxdiff/releases/macosx/ .
  
 
=== Troubleshooting ===
 
=== Troubleshooting ===
Line 113: Line 127:
 
== Windows ==
 
== Windows ==
  
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/]).
+
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, or preferably WSL2). This (easily!) installs e.g. an 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
+
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] or [https://mobaxterm.mobatek.net/ Mobaxterm] on the Windows host. There are helpful writeups (e.g. [http://wsl-guide.org/en/latest/]). VcXsrc seems to have a problem with coot for some people (see [https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=COOT;6ef4a967.2011 WSL2 installation] and responses). To use the X server, one has to say in the shell window
 
  export DISPLAY=:0
 
  export DISPLAY=:0
 
before running the program. Running XDSGUI under WSL's Ubuntu may require installation of a few packages with e.g.
 
before running the program. Running XDSGUI under WSL's Ubuntu may require installation of a few packages with e.g.

Latest revision as of 08:50, 24 November 2020

This article has some little script snippets that should ease the installation of XDS and related programs like (XDS-viewer, xdsstat, 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).


Linux

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

XDS package

If you are an academic user, as root

 cd /usr/local/bin
 wget -O- ftp://ftp.mpimf-heidelberg.mpg.de/pub/kabsch/XDS-INTEL64_Linux_x86_64.tar.gz | tar xzvf -
 ln -sf XDS-INTEL64_Linux_x86_64/* .

In case the above site is unavailable, there is a backup site.

other programs: XDS-Viewer, XDSSTAT, XDSCC12, XDSGUI, XSCALE_ISOCLUSTER, spot2pdb, generate_XDS.INP

... can be downloaded from https://strucbio.biologie.uni-konstanz.de/pub/linux_bin/ . A simple way to obtain them is to create an empty folder, "cd" to that folder and then

wget https://strucbio.biologie.uni-konstanz.de/pub/linux_bin/get_folder.sh
chmod +x get_folder.sh
./get_folder.sh

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

As root, the script copies the programs into /usr/local/bin/linux_bin, and links them to /usr/local/bin. As a normal user, they are downloaded to $HOME/bin/linux_bin, and linked to your $HOME/bin. In the latter case, make sure that $HOME/bin is in your $PATH.

Qt4 versions of xdsgui and xds-viewer are available as xdsgui.qt4 and xds-viewer.qt4, for old Linux distributions.

tools and helper programs for generate_XDS.INP and XDSGUI, and libraries

Since XDSGUI depends on graphics packages that may need to be installed, you can check the xdsgui binary with

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.

If in the case of Ubuntu you don't know the name of the package that provides a certain library, the

 sudo apt-file search <name-of-library> 

command should find it for you (where <name-of-library> could e.g. be libGLU.so.1). 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 sudo apt install libqt4-opengl.

Ubuntu 20.04: if libQtOpenGL.so.4 is missing (for the Qt4 binary of XDSGUI), use

sudo add-apt-repository -y ppa:rock-core/qt4
sudo apt update
sudo apt install libqt4-opengl

xxdiff is likely available for your distribution - google for it, or try e.g.

yum -y install xxdiff

on RHEL6/CentOS6/SL6 systems, or

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/

An xxdiff binary that runs on CentOS7 (RHEL7, SL7) is provided by the get_folder.sh 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, H5ToXDS should be installed as explained, and h5dump should be installed by e.g. yum -y install hdf5. Furthermore, you want the Neggia library or the Durin plugin.

Mac OSX

Attention: generate_XDS.INP requires the Xcode command line tools to be installed (free of charge): open a Terminal window, and enter sudo xcode-select --install. You may have to explicitly agree to the License terms when running a Command Line Tool (e.g. strings) for the first time.

Become familiar with the concept and ways to run commands as "root" - google "mac osx become root". All the installation 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 for installation, one may create a directory $HOME/bin and use that for the programs and links. That would also require modification of the $PATH, by a one-time echo 'export PATH=$PATH:$HOME/bin' >> ~/.profile)

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

sudo su                    # this will make you root, and ask for your password
mkdir /usr/local/bin  # only if /usr/local/bin was not created before

XDS package

If you are an academic user,

echo you may have to "sudo su" first, to obtain administrator permissions!
cd /usr/local/bin
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, generate_XDS.INP

... can be downloaded from https://strucbio.biologie.uni-konstanz.de/pub/mac_bin/ . A simple way to obtain them is is to open a Terminal, and type:

sudo su

which asks for the password and gives you administrator permissions. Then,

# any folder would do; here we use /usr/local/bin/mac_bin
mkdir -p /usr/local/bin/mac_bin
cd /usr/local/bin/mac_bin
curl -O -R https://strucbio.biologie.uni-konstanz.de/pub/mac_bin/get_folder.sh
chmod +x get_folder.sh
./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 get_folder.sh script

  1. copies Dectris' Neggia library into /usr/local/lib64
  2. copies eiger2cbf-osx into /usr/local/bin, but under the name H5ToXds
  3. copies version 1.8.7 of h5dump into /usr/local/bin

A Qt5 version of XDS-viewer (provided by T. Hauß) is available for MacOS 10.13, and for 10.15 and newer. Users must decide which DMG they install. The Qt4 version is still the default.

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

Troubleshooting

If any of the commands

ls -l /usr/local/bin/generate_XDS.INP
ls -l /usr/local/bin/xdsgui
ls -l /usr/local/bin/xds-viewer
# in the same way, check the other programs that should be used

returns a message like file or directory not found then this means that you do not have the symlink. But even if these commands do not return errors, you should also check the targets of the symlink:

ls -l /Applications/xdsgui.app/Contents/MacOS/xdsgui
ls -l /Applications/XDS-Viewer.app/Contents/MacOS/xds-viewer-bin 

Again, these commands should not return an error message. If they do, the programs are not installed in the location where the symlink points to. You'll have to either install the programs properly (in /Applications) or make the symlink point to the correct location.

A quick way is also

which generate_XDS.INP xdsgui xds xds-viewer xdsstat xdscc12

and this should return a line for each of the programs asked for.

Windows

The programs of the XDS package as well as XDSGUI, XDSSTAT, XDSCC12 and so on may be run on 64bit Windows 10 within the Linux Subsystem for Windows (WSL, or preferably WSL2). This (easily!) installs e.g. an Ubuntu environment, which supports the apt package manager, so in principle any software available for Ubuntu may be installed (or other distros, see [1]).

Graphical Linux programs require installation of a X server like Xming or VcXsvr or Mobaxterm on the Windows host. There are helpful writeups (e.g. [2]). VcXsrc seems to have a problem with coot for some people (see WSL2 installation and responses). To use the X server, one has to say in the shell window

export DISPLAY=:0

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

sudo apt-get install libgomp1 libqtgui4

(see XDSGUI and above).

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

sudo apt-get install coreutils binutils gawk sed bc grep 

and if required, also install python and hdf5-tools.

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.

Xds win.PNG

(Screenshot provided by Gustavo Lima)

A detailed writeup for Ubuntu 20.04 LTS was provided by Dr Lata Panicker, SO(G), BARC, India.

See also

Cluster Installation