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→XDS package: add z to Mac "tar xzvf " options since this seems to be req'd on old Macs
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(→XDS package: add z to Mac "tar xzvf " options since this seems to be req'd on old Macs) |
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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 . | 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 . This means that you should do this as the administrator (root), or have sudo rights (Mac, and some Linux distros). | ||
== Linux == | == Linux == | ||
Log in as root - we need write permission for /usr/local/bin . | '''Log in as root''' - we need write permission for /usr/local/bin . | ||
=== [[XDS]] package === | |||
If you are an academic user, as root | |||
<pre> | <pre> | ||
cd /usr/local/bin | cd /usr/local/bin | ||
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=== other programs: [[XDS-Viewer]], [[XDSSTAT]], [[XDSCC12]], [[XDSGUI]], [[XSCALE_ISOCLUSTER]] === | === other programs: [[XDS-Viewer]], [[XDSSTAT]], [[XDSCC12]], [[XDSGUI]], [[XSCALE_ISOCLUSTER]] === | ||
... can be downloaded from ftp://turn5.biologie.uni-konstanz.de/pub/linux_bin/ . A simple way to obtain them is | ... can be downloaded from ftp://turn5.biologie.uni-konstanz.de/pub/linux_bin/ . A simple way to obtain them is to create an empty folder, "cd" to that folder and then (as root) | ||
wget ftp://turn5.biologie.uni-konstanz.de/pub/linux_bin/get_folder.sh | wget ftp://turn5.biologie.uni-konstanz.de/pub/linux_bin/get_folder.sh | ||
chmod +x get_folder.sh | chmod +x get_folder.sh | ||
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ldd `which xdsgui` | 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. <code>yum provides libXfixes.so.3</code> the output of which will tell you that this is in the libXfixes RPM. | 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. <code>yum provides libXfixes.so.3</code> the output of which will tell you that this is in the libXfixes RPM. | ||
Ubuntu 14 users: please read | Ubuntu 14 users: please read [[XDSGUI#Installation|XDSGUI]] if you have a problem with missing libmng2. Ubuntu 16.04 and 18.04: if libQtOpenGL.so.4 is missing, use <code>sudo apt install libqt4-opengl</code>. | ||
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. | 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. | ||
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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>. | 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>. | ||
== Mac OSX == | |||
== Mac | |||
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. | 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. | ||
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. | 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. (As an alternative that does not require root, one may create a directory $HOME/bin and use that for the programs and links. That would also require modification of the $PATH, by a one-time <code>echo 'export PATH=$PATH:$HOME/bin' >> ~/.profile</code>) | ||
So, prepare the following steps by opening the Terminal window, and then | |||
su # this will ask for password | sudo su # this will make you root, and ask for your password | ||
mkdir /usr/local/bin # only if /usr/local/bin was not created before | mkdir /usr/local/bin # only if /usr/local/bin was not created before | ||
=== [[XDS]] package === | |||
If you are an academic user, | |||
echo you may have to "sudo su" first, to obtain administrator permissions! | |||
cd /usr/local/bin | cd /usr/local/bin | ||
curl -L -o - ftp://ftp.mpimf-heidelberg.mpg.de/pub/kabsch/XDS-OSX_64.tar.gz | tar | curl -L -o - ftp://ftp.mpimf-heidelberg.mpg.de/pub/kabsch/XDS-OSX_64.tar.gz | tar xzvf - | ||
ln -sf XDS-OSX_64/* . | ln -sf XDS-OSX_64/* . | ||
=== other programs: [[XDS-Viewer]], [[XDSSTAT]], [[XDSCC12]], [[XDSGUI]], [[XSCALE_ISOCLUSTER]] === | === other programs: [[XDS-Viewer]], [[XDSSTAT]], [[XDSCC12]], [[XDSGUI]], [[XSCALE_ISOCLUSTER]] === | ||
... can be downloaded from ftp://turn5.biologie.uni-konstanz.de/pub/mac_bin/ . A simple way to obtain them is | ... can be downloaded from ftp://turn5.biologie.uni-konstanz.de/pub/mac_bin/ . A simple way to obtain them is is to open a Terminal, and type: | ||
sudo su | |||
which asks for the password and gives you administrator permissions. Then, | |||
# any folder would do; here we use /usr/local/bin/mac_bin | |||
mkdir -p /usr/local/bin/mac_bin | |||
cd /usr/local/bin/mac_bin | |||
curl -O -R ftp://turn5.biologie.uni-konstanz.de/pub/mac_bin/get_folder.sh | curl -O -R ftp://turn5.biologie.uni-konstanz.de/pub/mac_bin/get_folder.sh | ||
chmod +x get_folder.sh | chmod +x get_folder.sh | ||
./get_folder.sh | ./get_folder.sh | ||
If you want to update the programs some time later, just run these commands again. | |||
In order to enable [[Eiger]] data processing, the <code>get_folder.sh</code> script | |||
# copies Dectris' Neggia library into /usr/local/lib64 | |||
# copies [[Eiger#General_aspects|eiger2cbf-osx]] into /usr/local/bin, but under the name <code>H5ToXds</code> | |||
# copies [https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8/hdf5-1.8.7/bin/mac-intel-x86_64/utilities/h5dump version 1.8.7] of <code>h5dump</code> into /usr/local/bin | |||
Lastly, it is useful (for e.g. XDSGUI) to install <code>xxdiff</code> from http://furius.ca/downloads/xxdiff/releases/macosx/ | |||
=== Troubleshooting === | === Troubleshooting === | ||
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[https://blogs.msdn.microsoft.com/commandline/2017/04/11/windows-10-creators-update-whats-new-in-bashwsl-windows-console/ Windows 10 Creators Update] (CU) allows to install (or update to) Ubuntu 16.04 (or other distros, see [https://blogs.msdn.microsoft.com/commandline/2017/05/11/new-distros-coming-to-bashwsl-via-windows-store/]), and fixes many bugs. | [https://blogs.msdn.microsoft.com/commandline/2017/04/11/windows-10-creators-update-whats-new-in-bashwsl-windows-console/ Windows 10 Creators Update] (CU) allows to install (or update to) Ubuntu 16.04 (or other distros, see [https://blogs.msdn.microsoft.com/commandline/2017/05/11/new-distros-coming-to-bashwsl-via-windows-store/]), and fixes many bugs. | ||
Graphical Linux programs require installation of a X server like [https://sourceforge.net/projects/xming/files/latest/download Xming] or [https://sourceforge.net/projects/vcxsrv VcXsvr] on the Windows host. There are helpful writeups (e.g. | Graphical Linux programs require installation of a X server like [https://sourceforge.net/projects/xming/files/latest/download Xming] or [https://sourceforge.net/projects/vcxsrv VcXsvr] on the Windows host. There are helpful writeups (e.g. [http://wsl-guide.org/en/latest/]). To use the X server, one has to say in the shell window | ||
export DISPLAY=:0 | export DISPLAY=:0 | ||
before running the program. Running XDSGUI under WSL's Ubuntu 14.04 requires installation of a few packages with | before running the program. Running XDSGUI under WSL's Ubuntu 14.04 requires installation of a few packages with | ||