Installation: Difference between revisions
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This will then use process-level parallelization instead of thread-level parallelization, and works rather well. | This will then use process-level parallelization instead of thread-level parallelization, and works rather well. | ||
XDSSTAT and the conversion to MTZ files by XDSCONV require a CCP4 installation. | |||
Revision as of 13:55, 12 December 2016
This article has some little script snippets that should ease the installation of XDS and related programs (XDS-viewer, xdsstat, xdsgui). It is assumed that binaries (or links to binaries) should go to /usr/local/bin .
Linux
Log in as root - we need write permission for /usr/local/bin .
To get the XDS package if you are an academic user,
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/* .
To get the script generate_XDS.INP from its XDSwiki article,
cd /usr/local/bin wget http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/generate_XDS.INP -O - | \ sed -e s/\ \;/\ /g -e s/\>\;/\>/g -e s/\<\;/\</g -e s/amp\;//g -e s/\"\;/\"/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
Please note that to get the strings command, which is used by generate_XDS.INP, on some Linux distributions (e.g. FC23) you need to install the binutils RPM package.
To get XDS-Viewer,
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
To get XDSSTAT,
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
To get XDSCC12,
cd /usr/local/bin wget ftp://turn5.biologie.uni-konstanz.de/pub/xdscc12.rhel6.64 -O xdscc12 chmod a+x xdscc12
To get XDSGUI,
cd /usr/local/bin wget ftp://turn5.biologie.uni-konstanz.de/pub/xdsgui.rhel6.64 -O xdsgui chmod a+x xdsgui
Since XDSGUI depends on graphics packages that may need to be installed, you can check the xdsgui binary with
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. yum provides libXfixes.so.3 the output of which will tell you that this is in the libXfixes RPM.
Ubuntu 14 users: please read http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/XDSGUI#Installation if you have a problem with missing libmng2.
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.
yum -y install xxdiff
on RHEL6/CentOS6/SL6 systems, or
apt-get install xxdiff
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
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.
For Eiger data processing, H5ToXDS should be installed as explained, and h5dump should be installed by e.g. yum -y install hdf5.
Mac (Intel)
Attention: generate_XDS.INP requires 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 xcode-select --install. This will bring up a prompt to install the necessary command line tools.
You also have to explicitly agree to the License terms when running a Command Line Tool for the first time.
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 .
personal installation (experimental writeup)
Preparation:
- 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
cd $HOME echo 'export PATH=$PATH:$HOME/bin' >> ~/.profile
(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
mkdir $HOME/bin mkdir $HOME/Applications
To install generate_XDS.INP:
cd $HOME/bin curl -L -o - http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/generate_XDS.INP | \ sed -e s/\ \;/\ /g -e s/\>\;/\>/g -e s/\<\;/\</g -e s/amp\;//g -e s/\"\;/\"/g -e s/\&\#\1\6\0\;/\ /g | \ sed '/# end of generate_XDS.INP/,$d' | awk '/^#/,/rm -f tmp1 tmp2/' > generate_XDS.INP chmod +x generate_XDS.INP
To install XDS:
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/* .
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,
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
To install XDSCC12,
cd $HOME/bin curl -L -o xdscc12 ftp://turn5.biologie.uni-konstanz.de/pub/xdscc12-mac chmod a+x xdscc12
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 $HOME/bin/xxdiff
(the names of the files may not be entirely correct in these two lines)
system-wide installation (requires root permission)
To get generate_XDS.INP:
cd /usr/local/bin sudo sh -c 'curl -L -o - http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/generate_XDS.INP | \ sed -e s/\ \;/\ /g -e s/\>\;/\>/g -e s/\<\;/\</g -e s/amp\;//g -e s/\"\;/\"/g -e s/\&\#\1\6\0\;/\ /g | \ sed '/# end of generate_XDS.INP/,$d' | awk '/^#/,/rm -f tmp1 tmp2/' > generate_XDS.INP' sudo chmod +x generate_XDS.INP
To get XDS:
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/* .
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,
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
To get XDSCC12,
cd /usr/local/bin sudo curl -L -o xdscc12 ftp://turn5.biologie.uni-konstanz.de/pub/xdscc12-mac sudo chmod a+x xdscc12
To get XDSGUI, please download from ftp://turn5.biologie.uni-konstanz.de/pub/xdsgui.dmg and then
sudo ln -s /Applications/xdsgui.app/Contents/MacOS/xdsgui /usr/local/bin/xdsgui
Please also check XDSGUI#Installation.
It is useful to install xxdiff from http://furius.ca/downloads/xxdiff/releases/macosx/
For Eiger data processing, eiger2cbf-osx should be sym-linked into a directory in your $PATH, but under the name H5ToXds, and h5dump should be installed from a .dmg file.
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
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.
Windows
The programs of the XDS package as well as XDSGUI, XDSSTAT and so on may be run on 64bit Windows10 within the Linux Subsystem for Windows. This installs a Ubuntu 14.04.5 LTS environment, which supports the apt package manager.
Graphical Linux programs require installation of a X server like Xming on the Windows host. To use it, one has to say in the shell window
export DISPLAY=:0
XDSGUI requires
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
sudo apt-get install coreutils binutils gawk sed bc grep
and if required, also install python and hdf5-tools.
Unfortunately, only single-processor xds runs smoothly, whereas the parallel xds_par stops with an error message. This is the workaround:
- since xds_par does not work anyway, just copy the xds binary over the xds_par binary so that it is available under both names
- in XDS.INP, specify MAXIMUM_NUMBER_OF_JOBS= <number of cores>
This will then use process-level parallelization instead of thread-level parallelization, and works rather well.
XDSSTAT and the conversion to MTZ files by XDSCONV require a CCP4 installation.