Installation

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Revision as of 12:07, 9 December 2014 by Kay (talk | contribs) (→‎Linux 32 bit: fix wget tar pipe)
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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). 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,

 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/\&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

To get XDS-Viewer,

 cd /usr/local/bin
 wget ftp://turn5.biologie.uni-konstanz.de/pub/xds-viewer-0.6 -O 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 RedHat systems, or

apt-get install xxdiff

on Ubuntu.

Alternatively, tkdiff may be used.

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/\&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

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.

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”.

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 $HOME/bin
 curl -L -o - http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/generate_XDS.INP | \
   sed -e s/\&nbsp\;/\ /g -e s/\&gt\;/\>/g -e s/\&lt\;/\</g -e s/amp\;//g -e s/\&quot\;/\"/g -e s/\&\#\1\6\0\;/\ /g | \
   sed '/# end of generate_XDS.INP/,$d' | awk '/^#/,/rm -f tmp1 tmp2/' > generate_XDS.INP
 chmod +x generate_XDS.INP
 

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/\&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
 

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.