Installation: Difference between revisions
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Perhaps xxdiff will be available on EPEL some day - maybe it is available on RPMforge; I didn't check. | 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 | Alternatively, tkdiff may be installed, or other graphical comparison programs, like meld or kdiff3. | ||
== Linux 32 bit == | == Linux 32 bit == | ||
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on Ubuntu. | on Ubuntu. | ||
Alternatively, tkdiff may be used. | Alternatively, tkdiff may be used, or kdiff3, or meld. | ||
== Mac (Intel) == | == Mac (Intel) == | ||
Revision as of 12:34, 16 September 2015
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 64 bit
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
To get XDS-Viewer,
cd /usr/local/bin wget ftp://turn5.biologie.uni-konstanz.de/pub/xds-viewer-0.6 -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 XDSGUI,
cd /usr/local/bin wget ftp://turn5.biologie.uni-konstanz.de/pub/xdsgui.rhel6.64 -O xdsgui chmod a+x xdsgui
If this binary does not work for you: there is also a statically linked binary called xdsgui.rhel5.64 , at the FTP site. 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 . 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.
Linux 32 bit
Log in as root - we need write permission for /usr/local/bin .
To get the XDS package,
wget -O - ftp://ftp.mpimf-heidelberg.mpg.de/pub/kabsch/XDS-IA32_Linux_x86.tar.gz | tar xzvf - ln -sf XDS-IA32_Linux_x86/* .
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
To get XDS-Viewer,
wget ftp://turn5.biologie.uni-konstanz.de/pub/xds-viewer-0.6 -O xds-viewer ln -sf xds-viewer xdsviewer
To get XDSSTAT,
wget ftp://turn5.biologie.uni-konstanz.de/pub/xdsstat-linux32.bz2 -O xdsstat.bz2 bunzip2 -f xdsstat.bz2 chmod a+x xdsstat
To get XDSGUI,
cd /usr/local/bin wget ftp://turn5.biologie.uni-konstanz.de/pub/xdsgui.rhel6.32 -O xdsgui chmod a+x xdsgui
If this binary does not work for you: there is also a statically linked binary called xdsgui.rhel5.32 . 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 . The package is likely available for your distribution - google for it, or try e.g.
yum -y install xxdiff
on RedHat systems, or
apt-get install xxdiff
on Ubuntu.
Alternatively, tkdiff may be used, or kdiff3, or meld.
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”. 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 $HOME echo 'export PATH=$HOME:$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, for latest OS X (Mavericks):
cd $HOME/bin curl -L -o - ftp://ftp.mpimf-heidelberg.mpg.de/pub/kabsch/XDS-OSX10.9.1_Darwin13.0.0.tar.gz | tar xvf - ln -sf XDS-OSX10.9.1_Darwin13.0.0/* .
(for older OS X, like Leopoard, Snow Leopard, Lion, Mountain Lion, that would be
cd $HOME/bin curl -L -o - ftp://ftp.mpimf-heidelberg.mpg.de/pub/kabsch/XDS-OSX10.5.8_Darwin9.8.0.tar.gz | tar xvf - ln -sf XDS-OSX10.5.8_Darwin9.8.0/* .
There is also a 32bit tarfile at the same site, for OS X 10.4.11 - Tiger; the installation would be similar)
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 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 . 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, for latest OS X (Mavericks):
cd /usr/local/bin sudo sh -c 'curl -L -o - ftp://ftp.mpimf-heidelberg.mpg.de/pub/kabsch/XDS-OSX10.9.1_Darwin13.0.0.tar.gz | tar xvf -' sudo ln -sf XDS-OSX10.9.1_Darwin13.0.0/* .
and for older OS X:
cd /usr/local/bin sudo sh -c 'curl -L -o - ftp://ftp.mpimf-heidelberg.mpg.de/pub/kabsch/XDS-OSX10.5.8_Darwin9.8.0.tar.gz | tar xvf -' sudo ln -sf XDS-OSX10.5.8_Darwin9.8.0/* .
(There is also a 32bit tarfile at the same site, for OS X 10.4.11; the installation would be similar)
To get XDS-Viewer, click https://sourceforge.net/project/platformdownload.php?group_id=239755 , install in the usual way 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 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/
Windows
Sorry, neither XDS nor XDSGUI is currently available for Windows.