Installation: Difference between revisions

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This article has some little script snippets that should ease the installation of XDS and related programs ([[XDS-viewer]], [[xdsstat]], [[XDSGUI|xdsgui]]). It is assumed that binaries (or links to binaries) should go to /usr/local/bin .
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).




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


To get the [[XDS]] package if you are an academic user,
=== [[XDS]] package ===
If you are an academic user, as root
<pre>
<pre>
  cd /usr/local/bin
  cd /usr/local/bin
Line 11: Line 12:
  ln -sf XDS-INTEL64_Linux_x86_64/* .
  ln -sf XDS-INTEL64_Linux_x86_64/* .
</pre>
</pre>
To get the script [[generate_XDS.INP]] from its XDSwiki article,
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].
<pre>
 
cd /usr/local/bin
=== other programs: [[XDS-Viewer]], [[XDSSTAT]], [[XDSCC12]], [[XDSGUI]], [[XSCALE_ISOCLUSTER]]  ===
wget http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/generate_XDS.INP -O - | \
... 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)
  sed -e s/\&nbsp\;/\ /g -e s/\&gt\;/\>/g -e s/\&lt\;/\</g -e s/amp\;//g -e s/\&quot\;/\"/g -e s/\&\#\1\6\0\;/\ /g | \
wget https://{{SERVERNAME}}/pub/linux_bin/get_folder.sh
  sed '/# end of generate_XDS.INP/,$d' | awk '/^#/,/rm -f tmp1 tmp2/' > generate_XDS.INP
  chmod +x get_folder.sh
  chmod +x generate_XDS.INP
./get_folder.sh
</pre>
 
Please note that to get the <code>strings</code> command, which is used by [[generate_XDS.INP]], on some Linux distributions (e.g. FC23) you need to install the <code>binutils</code> RPM package.
Please note that to get the <code>strings</code> command, which is used by [[generate_XDS.INP]], on some Linux distributions (e.g. FC23) you need to install the <code>binutils</code> RPM package.
To get [[XDS-Viewer]],
<pre>
cd /usr/local/bin
wget ftp://turn5.biologie.uni-konstanz.de/pub/xds-viewer-0.6.64bit -O xds-viewer
chmod a+x xds-viewer 
ln -sf xds-viewer xdsviewer
</pre>
To get [[XDSSTAT]],
<pre>
cd /usr/local/bin
wget ftp://turn5.biologie.uni-konstanz.de/pub/xdsstat-linux64.bz2 -O xdsstat.bz2
bunzip2 -f xdsstat.bz2
chmod a+x xdsstat
</pre>
To get [[XDSCC12]],
<pre>
cd /usr/local/bin
wget ftp://turn5.biologie.uni-konstanz.de/pub/xdscc12.rhel6.64 -O xdscc12
chmod a+x xdscc12
</pre>
To get [[XDSGUI]],
<pre>
cd /usr/local/bin
wget ftp://turn5.biologie.uni-konstanz.de/pub/xdsgui.rhel6.64 -O xdsgui
chmod a+x xdsgui
</pre>


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`
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 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. <code>xds-viewer</code> needs libpng12.so.0 which can be installed with <code>yum install libpng12</code>.
Ubuntu 14 users: please read http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/XDSGUI#Installation if you have a problem with missing libmng2.
 
Ubuntu 18.04: if libQtOpenGL.so.4 is missing, use <code>sudo apt install libqt4-opengl</code>, and if libpng12.so is missing (xds-viewer needs it), install it from [https://packages.ubuntu.com/xenial/amd64/libpng12-0/download] .
 
Of course, this still requires installation of <code>xxdiff</code> (or alternative), and for .h5 data: HDF5 package, and <code>H5ToXds</code> and/or [https://www.dectris.com/company/news/newsroom/news-details/process-eiger-data-with-xds-fast Neggia] library.


It is useful to install xxdiff or one of its alternatives (see below). The package 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
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on Ubuntu.
on Ubuntu.


On Centos7 (RHEL7, SL7) I went to http://rpmfind.net/linux/rpm2html/search.php?query=xxdiff and found that the Fedora 20 RPM can be installed using
An <code>xxdiff</code> binary that runs on CentOS7 (RHEL7, SL7) is provided by the <code>get_folder.sh</code> script.
yum install ftp://rpmfind.net/linux/fedora/linux/releases/20/Everything/x86_64/os/Packages/x/xxdiff-3.2-20.fc20.x86_64.rpm
Perhaps xxdiff will be available on EPEL some day - maybe it is available on RPMforge; I didn't check.


Alternatively, tkdiff may be installed, or other graphical comparison programs, like meld or kdiff3. vimdiff is also nice, and probably already installed.
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 [[Eiger|explained]], and <code>h5dump</code> should be installed by e.g. <code>yum -y install hdf5</code>.
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>.


=== current versions of Konstanz programs outside the official XDS distribution ===
== Mac OSX ==
... can be downloaded from ftp://turn5.biologie.uni-konstanz.de/pub/linux_bin/ . A simple way is
wget -r ftp://turn5.biologie.uni-konstanz.de/pub/linux_bin/
chmod a+x turn5.biologie.uni-konstanz.de/pub/linux_bin/*
# next, move the binaries to the destination on your machine
Of course, this still requires installation of xxdiff (or alternative), and for .h5 data: HDF5 package, and H5ToXds and/or Neggia library.


== Mac (Intel) ==
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 [https://developer.apple.com/xcode/ Xcode] to be installed. '''Xcode''' is not installed by default, but can be downloaded free of charge from the Mac App Store: after installing Xcode, open '''Preferences''', select the '''Downloads''' tab, and click the '''Install''' next to '''Command Line Tools'''. Or: open a Terminal window and type <code>xcode-select --install</code>. This will bring up a prompt to install the necessary command line tools.
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>)


You also have to explicitly agree to the License terms when running a Command Line Tool for the first time.
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


I'm not sure if Xcode can be installed without administrator privileges; you may also wish to look at http://guide.macports.org/#installing.xcode .
=== [[XDS]] package ===
If you are an academic user,


=== personal installation (experimental writeup) ===
  echo you may have to "sudo su" first, to obtain administrator permissions!
 
  cd /usr/local/bin
'''Preparation''':
  curl -L -o - ftp://ftp.mpimf-heidelberg.mpg.de/pub/kabsch/XDS-OSX_64.tar.gz | tar xzvf -
* make sure your $PATH includes your $HOME/bin - the programs will be put into that directory. To achieve this, open a Terminal window, and then
<pre>
cd $HOME
  echo 'export PATH=$PATH:$HOME/bin' >> ~/.profile
</pre>
(I'm not sure if it should be .profile or .bashrc; I have seen it work with .profile but not with .bashrc on a Leopard system)
* create the $HOME/bin and $HOME/Applications directories. Still in the Terminal window, type
<pre>
mkdir $HOME/bin
mkdir $HOME/Applications
</pre>
'''To install [[generate_XDS.INP]]''':
<pre>
  cd $HOME/bin
curl -L -o - http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/generate_XDS.INP | \
  sed -e s/\&nbsp\;/\ /g -e s/\&gt\;/\>/g -e s/\&lt\;/\</g -e s/amp\;//g -e s/\&quot\;/\"/g -e s/\&\#\1\6\0\;/\ /g | \
  sed '/# end of generate_XDS.INP/,$d' | awk '/^#/,/rm -f tmp1 tmp2/' > generate_XDS.INP
chmod +x generate_XDS.INP
</pre>
'''To install [[XDS]]''':
<pre>
cd $HOME/bin
  curl -L -o - ftp://ftp.mpimf-heidelberg.mpg.de/pub/kabsch/XDS-OSX_64.tar.gz | tar xvf -
  ln -sf XDS-OSX_64/* .
  ln -sf XDS-OSX_64/* .
</pre>
'''To install [[XDS-Viewer]]''', click https://sourceforge.net/project/platformdownload.php?group_id=239755 , open up the downloaded XDS-Viewer.app by clicking, and then (once you see it in the Finder), go to the Terminal and
cp -pr /Volumes/XDS-Viewer/XDS-Viewer.app/ $HOME/Applications
ln -s $HOME/Applications/XDS-Viewer.app/Contents/MacOS/xds-viewer-bin $HOME/bin/xds-viewer
'''To install [[XDSSTAT]]''',
<pre>
cd $HOME/bin
curl -L -o xdsstat.bz2 ftp://turn5.biologie.uni-konstanz.de/pub/xdsstat-i386-mac.bz2
bunzip2 -f xdsstat.bz2
chmod a+x xdsstat
</pre>
'''To install [[XDSCC12]]''',
<pre>
cd $HOME/bin
curl -L -o xdscc12 ftp://turn5.biologie.uni-konstanz.de/pub/xdscc12-mac
chmod a+x xdscc12
</pre>
'''To install [[XDSGUI]]''', please download from ftp://turn5.biologie.uni-konstanz.de/pub/xdsgui.dmg, open up the downloaded xdsgui.app by clicking, and then (once you see it in the Finder), go to the Terminal and
cp -pr /Volumes/xdsgui/xdsgui.app/ $HOME/Applications
ln -s $HOME/Applications/xdsgui.app/Contents/MacOS/xdsgui $HOME/bin/xdsgui
Please also check [[XDSGUI#Installation]].
It is useful to install xxdiff from http://furius.ca/downloads/xxdiff/releases/macosx/xxdiff-4.0b1.osx.dmg (or newer). After downloading, open up the downloaded xxdiff.app by clicking, and then (once you see it in the Finder), go to the Terminal and
cp -pr /Volumes/xxdiff/xxdiff.app/ $HOME/Applications
ln -s $HOME/Applications/xxdiff.app/Contents/MacOS/xxdiff $HOME/bin/xxdiff
(the names of the files may not be entirely correct in these two lines)
=== system-wide installation (requires root permission) ===
To get [[generate_XDS.INP]]:
<pre>
cd /usr/local/bin
sudo sh -c 'curl -L -o - http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/generate_XDS.INP | \
  sed -e s/\&nbsp\;/\ /g -e s/\&gt\;/\>/g -e s/\&lt\;/\</g -e s/amp\;//g -e s/\&quot\;/\"/g -e s/\&\#\1\6\0\;/\ /g | \
  sed '/# end of generate_XDS.INP/,$d' | awk '/^#/,/rm -f tmp1 tmp2/' > generate_XDS.INP'
sudo chmod +x generate_XDS.INP
</pre>
To get [[XDS]]:
<pre>
cd /usr/local/bin
sudo sh -c 'curl -L -o - ftp://ftp.mpimf-heidelberg.mpg.de/pub/kabsch/XDS-OSX_64.tar.gz | tar xvf -'
sudo ln -sf XDS-OSX_64/* .
</pre>
To get [[XDS-Viewer]], click https://sourceforge.net/project/platformdownload.php?group_id=239755 , install in the usual graphical way to your /Applications and then
sudo ln -s /Applications/XDS-Viewer.app/Contents/MacOS/xds-viewer-bin /usr/local/bin/xds-viewer
To get [[XDSSTAT]],
<pre>
cd /usr/local/bin
sudo curl -L -o xdsstat.bz2 ftp://turn5.biologie.uni-konstanz.de/pub/xdsstat-i386-mac.bz2
sudo bunzip2 -f xdsstat.bz2
sudo chmod a+x xdsstat
</pre>


To get [[XDSCC12]],
Starting with macOS Catalina, you also need
<pre>
  xattr -dr XDS-OSX_64/*
cd /usr/local/bin
if you get a security error popup (google "xattr com.apple.quarantine catalina").
  sudo curl -L -o xdscc12 ftp://turn5.biologie.uni-konstanz.de/pub/xdscc12-mac
sudo chmod a+x xdscc12
</pre>


To get [[XDSGUI]], please download from ftp://turn5.biologie.uni-konstanz.de/pub/xdsgui.dmg and then
=== other programs: [[XDS-Viewer]], [[XDSSTAT]], [[XDSCC12]], [[XDSGUI]], [[XSCALE_ISOCLUSTER]]  ===
  sudo ln -s /Applications/xdsgui.app/Contents/MacOS/xdsgui /usr/local/bin/xdsgui
... 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
Please also check [[XDSGUI#Installation]].
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://{{SERVERNAME}}/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.


It is useful to install xxdiff from http://furius.ca/downloads/xxdiff/releases/macosx/
In order to enable [[Eiger]] data processing, the <code>get_folder.sh</code> script
# copies Dectris' Neggia library into /usr/local/lib64
# 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


For [[Eiger]] data processing, [[Eiger#General_aspects|eiger2cbf-osx]] should be sym-linked into a directory in your $PATH, but under the name H5ToXds, and <code>h5dump</code> should be installed from a .dmg file.
Lastly, it is useful (for e.g. XDSGUI) to install <code>xxdiff</code> from http://furius.ca/downloads/xxdiff/releases/macosx/


=== Troubleshooting ===
=== Troubleshooting ===
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== 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 [http://www.pcworld.com/article/3050473/windows/heres-how-windows-10s-ubuntu-based-bash-shell-will-actually-work.html Linux Subsystem for Windows] (WSL). This (easily!) installs a Ubuntu 14.04.5 LTS environment, which supports the apt package manager, so in principle any software available for Ubuntu may be installed.
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/]).
[https://blogs.msdn.microsoft.com/commandline/2017/04/11/windows-10-creators-update-whats-new-in-bashwsl-windows-console/ Windows 10 Creators Update] (CU) allows to install (or update to) Ubuntu 16.04 (or other distros, see [https://blogs.msdn.microsoft.com/commandline/2017/05/11/new-distros-coming-to-bashwsl-via-windows-store/]), and fixes many bugs.


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://asria.pl/configure-graphic-and-sound-for-wsl-creators-update-for-ubuntu-16-04],[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] 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
  export DISPLAY=:0
  export DISPLAY=:0
before running the program. Running XDSGUI under WSL's Ubuntu 14.04 requires installation of a few packages with
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
  sudo apt-get install libgomp1 libqtgui4
and [[generate_XDS.INP]] requires a number of packages (some of which are only for specific detectors!); I'd start with
(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
  sudo apt-get install coreutils binutils gawk sed bc grep  
  sudo apt-get install coreutils binutils gawk sed bc grep  
and if required, also install python and hdf5-tools.
and if required, also install python and hdf5-tools.
The CU fixes many aspects of the interoperability between Windows and Linux, so is recommended. Without it, only single-processor xds runs smoothly, whereas the parallel xds_par stops with an error message.


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.
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.
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(Screenshot provided by Gustavo Lima)
(Screenshot provided by Gustavo Lima)
A detailed [https://strucbio.biologie.uni-konstanz.de/pub/xds%20%20prog%20installation%20in%20WSL%20(Lata%20Panicker).pdf writeup for Ubuntu 20.04 LTS] was provided by Dr Lata Panicker, SO(G), BARC, India.


== See also ==
== See also ==


[[Cluster Installation]]
[[Cluster Installation]]
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