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→XDS package: add z to Mac "tar xzvf " options since this seems to be req'd on old Macs
(→XDS package: add z to Mac "tar xzvf " options since this seems to be req'd on old Macs) |
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== 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 === | === [[XDS]] package === | ||
If you are an academic user, | 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 OSX == | ||
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echo you may have to "sudo su" first, to obtain administrator permissions! | 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 | sudo su | ||
which asks for the password and gives you administrator permissions. Then, | 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 | In order to enable [[Eiger]] data processing, the <code>get_folder.sh</code> script | ||
# copies Dectris' Neggia library into /usr/local/lib64 | # 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 [[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/ | Lastly, it is useful (for e.g. XDSGUI) to install <code>xxdiff</code> from http://furius.ca/downloads/xxdiff/releases/macosx/ | ||
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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 | ||