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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 . |
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| 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,
| | |
| <pre>
| | === other programs: [[XDS-Viewer]], [[XDSSTAT]], [[XDSCC12]], [[XDSGUI]], [[XSCALE_ISOCLUSTER]] === |
| cd /usr/local/bin | | ... can be downloaded from ftp://turn5.biologie.uni-konstanz.de/pub/linux_bin/ . A simple way to obtain them is |
| wget http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/generate_XDS.INP -O - | \
| | wget ftp://turn5.biologie.uni-konstanz.de/pub/linux_bin/get_folder.sh |
| sed -e s/\ \;/\ /g -e s/\>\;/\>/g -e s/\<\;/\</g -e s/amp\;//g -e s/\"\;/\"/g -e s/\&\#\1\6\0\;/\ /g | \
| | chmod +x get_folder.sh |
| sed '/# end of generate_XDS.INP/,$d' | awk '/^#/,/rm -f tmp1 tmp2/' > generate_XDS.INP
| | ./get_folder.sh |
| chmod +x generate_XDS.INP | | |
| </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. |
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| To get [[XDS-Viewer]],
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| <pre>
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| cd /usr/local/bin
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| wget ftp://turn5.biologie.uni-konstanz.de/pub/xds-viewer-0.6.64bit -O xds-viewer
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| chmod a+x xds-viewer
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| ln -sf xds-viewer xdsviewer
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| </pre>
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| To get [[XDSSTAT]],
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| <pre>
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| cd /usr/local/bin
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| wget ftp://turn5.biologie.uni-konstanz.de/pub/xdsstat-linux64.bz2 -O xdsstat.bz2
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| bunzip2 -f xdsstat.bz2
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| chmod a+x xdsstat
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| </pre>
| |
| To get [[XDSCC12]],
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| <pre>
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| cd /usr/local/bin
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| wget ftp://turn5.biologie.uni-konstanz.de/pub/xdscc12.rhel6.64 -O xdscc12
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| chmod a+x xdscc12
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| </pre>
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| To get [[XDSGUI]],
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| <pre>
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| cd /usr/local/bin
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| wget ftp://turn5.biologie.uni-konstanz.de/pub/xdsgui.rhel6.64 -O xdsgui
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| chmod a+x xdsgui
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| </pre>
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| 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 |
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| 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 14 users: please read http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/XDSGUI#Installation if you have a problem with missing libmng2. |
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| 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.
| | 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. |
| | |
| | <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. |
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| 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
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| Perhaps xxdiff will be available on EPEL some day - maybe it is available on RPMforge; I didn't check.
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| 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. |
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| 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>. |
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| === current versions of programs outside the official XDS distribution ===
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| ... can be downloaded from ftp://turn5.biologie.uni-konstanz.de/pub/linux_bin/ . A simple way is
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| wget -r ftp://turn5.biologie.uni-konstanz.de/pub/linux_bin/
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| chmod a+x turn5.biologie.uni-konstanz.de/pub/linux_bin/*
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| # next, move the binaries to the destination on your machine
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| Of course, this still requires installation of xxdiff (or alternative), and for .h5 data: HDF5 package, and H5ToXds and/or Neggia library.
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| == Mac (Intel) == | | == Mac (Intel) == |
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| Attention: [[generate_XDS.INP]] requires the [https://developer.apple.com/download/more/ Xcode command line tools] to be installed (free of charge). | | 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. |
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| You also have to explicitly agree to the License terms when running a Command Line Tool (e.g. <code>strings</code>) for the first time.
| | 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. |
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| === personal installation (experimental writeup) ===
| | Thus, prepare the steps by opening the Terminal window, and then |
| | su # this will ask for password |
| | mkdir /usr/local/bin # only if /usr/local/bin was not created before |
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| '''Preparation''':
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| * 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
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| <pre>
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| cd $HOME
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| echo 'export PATH=$PATH:$HOME/bin' >> ~/.profile
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| </pre> | | </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)
| | '''To install [[XDS]]''', |
| * create the $HOME/bin and $HOME/Applications directories. Still in the Terminal window, type
| |
| <pre> | | <pre> |
| mkdir $HOME/bin
| | cd /usr/local/bin |
| mkdir $HOME/Applications
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| </pre>
| |
| '''To install [[generate_XDS.INP]]''':
| |
| <pre>
| |
| cd $HOME/bin | |
| curl -L -o - http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/generate_XDS.INP | \
| |
| sed -e s/\ \;/\ /g -e s/\>\;/\>/g -e s/\<\;/\</g -e s/amp\;//g -e s/\"\;/\"/g -e s/\&\#\1\6\0\;/\ /g | \
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| sed '/# end of generate_XDS.INP/,$d' | awk '/^#/,/rm -f tmp1 tmp2/' > generate_XDS.INP
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| chmod +x generate_XDS.INP
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|
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| </pre>
| |
| '''To install [[XDS]]''':
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| <pre>
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| cd $HOME/bin
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| curl -L -o - ftp://ftp.mpimf-heidelberg.mpg.de/pub/kabsch/XDS-OSX_64.tar.gz | tar xvf - | | 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> | | </pre> |
|
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|
| '''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
| | === other programs: [[XDS-Viewer]], [[XDSSTAT]], [[XDSCC12]], [[XDSGUI]], [[XSCALE_ISOCLUSTER]] === |
| cp -pr /Volumes/XDS-Viewer/XDS-Viewer.app/ $HOME/Applications
| | ... can be downloaded from ftp://turn5.biologie.uni-konstanz.de/pub/mac_bin/ . A simple way to obtain them is |
| ln -s $HOME/Applications/XDS-Viewer.app/Contents/MacOS/xds-viewer-bin $HOME/bin/xds-viewer
| |
| | | |
| '''To install [[XDSSTAT]]''',
| | curl -O -R ftp://turn5.biologie.uni-konstanz.de/pub/mac_bin/get_folder.sh |
| <pre>
| | chmod +x get_folder.sh |
| cd $HOME/bin
| | ./get_folder.sh |
| curl -L -o xdsstat.bz2 ftp://turn5.biologie.uni-konstanz.de/pub/xdsstat-i386-mac.bz2 | |
| bunzip2 -f xdsstat.bz2
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| chmod a+x xdsstat
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| </pre>
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|
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| '''To install [[XDSCC12]]''',
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| <pre>
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| cd $HOME/bin
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| curl -L -o xdscc12 ftp://turn5.biologie.uni-konstanz.de/pub/xdscc12-mac
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| 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
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| cp -pr /Volumes/xdsgui/xdsgui.app/ $HOME/Applications
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| ln -s $HOME/Applications/xdsgui.app/Contents/MacOS/xdsgui $HOME/bin/xdsgui
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|
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| 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
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| cp -pr /Volumes/xxdiff/xxdiff.app/ $HOME/Applications | |
| ln -s $HOME/Applications/xxdiff.app/Contents/MacOS/xxdiff $HOME/bin/xxdiff
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| | |
| (the names of the files may not be entirely correct in these two lines)
| |
| | |
| === system-wide installation (requires root permission) ===
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|
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| To get [[generate_XDS.INP]]:
| | Using the Finder window which should have opened automagically, install XDSGUI and XDS-Viewer graphically, by pulling them into the Applications folder. |
| <pre>
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| cd /usr/local/bin
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| sudo sh -c 'curl -L -o - http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/generate_XDS.INP | \
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| sed -e s/\ \;/\ /g -e s/\>\;/\>/g -e s/\<\;/\</g -e s/amp\;//g -e s/\"\;/\"/g -e s/\&\#\1\6\0\;/\ /g | \
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| sed '/# end of generate_XDS.INP/,$d' | awk '/^#/,/rm -f tmp1 tmp2/' > generate_XDS.INP'
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| sudo chmod +x generate_XDS.INP
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| </pre>
| |
| | |
| To get [[XDS]]:
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| <pre>
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| cd /usr/local/bin
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| sudo sh -c 'curl -L -o - ftp://ftp.mpimf-heidelberg.mpg.de/pub/kabsch/XDS-OSX_64.tar.gz | tar xvf -'
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| sudo ln -sf XDS-OSX_64/* .
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| </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
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| sudo ln -s /Applications/XDS-Viewer.app/Contents/MacOS/xds-viewer-bin /usr/local/bin/xds-viewer
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|
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| To get [[XDSSTAT]],
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| <pre>
| |
| cd /usr/local/bin
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| sudo curl -L -o xdsstat.bz2 ftp://turn5.biologie.uni-konstanz.de/pub/xdsstat-i386-mac.bz2
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| sudo bunzip2 -f xdsstat.bz2
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| sudo chmod a+x xdsstat
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| </pre>
| |
| | |
| To get [[XDSCC12]],
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| <pre>
| |
| cd /usr/local/bin
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| sudo curl -L -o xdscc12 ftp://turn5.biologie.uni-konstanz.de/pub/xdscc12-mac
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| sudo chmod a+x xdscc12
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| </pre>
| |
| | |
| 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
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|
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| Please also check [[XDSGUI#Installation]].
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|
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|
| It is useful to install xxdiff from http://furius.ca/downloads/xxdiff/releases/macosx/ | | It is useful to install xxdiff from http://furius.ca/downloads/xxdiff/releases/macosx/ |