Installation: Difference between revisions
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'''To install [[XDSGUI]]''', please download from ftp://turn5.biologie.uni-konstanz.de/pub/xdsgui.dmg, install into $HOME/Applications and then | '''To install [[XDSGUI]]''', please download from ftp://turn5.biologie.uni-konstanz.de/pub/xdsgui.dmg, install into $HOME/Applications and then | ||
ln -s $HOME/Applications/xdsgui.app/Contents/MacOS/xdsgui $HOME/bin/xdsgui | 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/ - if you do not have administrator privileges, install it in $HOME/Applications and create a symlink to $HOME/bin in the same way as for XDS-Viewer and XDSGUI (see above). | |||
=== system-wide installation (requires root permission) === | === system-wide installation (requires root permission) === | ||
Revision as of 02:40, 23 June 2014
This article has some little script snippets that should ease the installation of XDS and related programs (XDS-viewer, xdsstat, xdsgui). It is assumed that binaries (or links to binaries) should go to /usr/local/bin .
Linux 64 bit
Log in as root, and then:
cd /usr/local/bin wget http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/generate_XDS.INP -O - | \ sed -e s/\ \;/\ /g -e s/\>\;/\>/g -e s/\<\;/\</g -e s/amp\;//g -e s/\"\;/\"/g -e s/\&\#\1\6\0\;/\ /g | \ sed '/# end of generate_XDS.INP/,$d' | awk '/^#/,/rm -f tmp1 tmp2/' > generate_XDS.INP chmod +x generate_XDS.INP
To get XDS,
cd /usr/local/bin wget ftp://ftp.mpimf-heidelberg.mpg.de/pub/kabsch/XDS-INTEL64_Linux_x86_64.tar.gz | tar xvf - ln -sf XDS-INTEL64_Linux_x86_64/* .
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, and then:
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,
wget ftp://ftp.mpimf-heidelberg.mpg.de/pub/kabsch/XDS-IA32_Linux_x86.tar.gz | tar xvf - ln -sf XDS-IA32_Linux_x86/* .
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)
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' >> .bashrc
- 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 , install into your $HOME/Applications, and then
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, install into $HOME/Applications and then
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/ - if you do not have administrator privileges, install it in $HOME/Applications and create a symlink to $HOME/bin in the same way as for XDS-Viewer and XDSGUI (see above).
system-wide installation (requires root permission)
sudo su
(enter your root password)
To get generate_XDS.INP:
cd /usr/local/bin curl -L -o - http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/generate_XDS.INP | \ sed -e s/\ \;/\ /g -e s/\>\;/\>/g -e s/\<\;/\</g -e s/amp\;//g -e s/\"\;/\"/g -e s/\&\#\1\6\0\;/\ /g | \ sed '/# end of generate_XDS.INP/,$d' | awk '/^#/,/rm -f tmp1 tmp2/' > generate_XDS.INP chmod +x generate_XDS.INP
To get XDS, for latest OS X (Mavericks):
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/* .
and for older OS X:
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; 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,
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 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.