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→other programs: XDS-Viewer, XDSSTAT, XDSCC12, XDSGUI, XSCALE_ISOCLUSTER: ubuntu 20.04 xxdiff
(→other programs: XDS-Viewer, XDSSTAT, XDSCC12, XDSGUI, XSCALE_ISOCLUSTER: ubuntu 20.04 xxdiff) |
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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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ln -sf XDS-INTEL64_Linux_x86_64/* . | ln -sf XDS-INTEL64_Linux_x86_64/* . | ||
</pre> | </pre> | ||
In case the [ftp://ftp.mpimf-heidelberg.mpg.de/pub/kabsch above site] is unavailable, there is a [https://strucbio.biologie.uni-konstanz.de/pub/xds backup site]. | |||
=== other programs: [[XDS-Viewer]], [[XDSSTAT]], [[XDSCC12]], [[XDSGUI]], [[XSCALE_ISOCLUSTER]] === | === other programs: [[XDS-Viewer]], [[XDSSTAT]], [[XDSCC12]], [[XDSGUI]], [[XSCALE_ISOCLUSTER]] === | ||
... can be downloaded from | ... can be downloaded from https://{{SERVERNAME}}/pub/linux_bin/ . A simple way to obtain them is to create an empty folder, "cd" to that folder and then (as root) | ||
wget | wget https://{{SERVERNAME}}/pub/linux_bin/get_folder.sh | ||
chmod +x get_folder.sh | chmod +x get_folder.sh | ||
./get_folder.sh | ./get_folder.sh | ||
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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 | ||
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. <code>xds-viewer</code> needs libpng12.so.0 which can be installed with <code>yum install libpng12</code>. | ||
Ubuntu | |||
Ubuntu 18.04: if libQtOpenGL.so.4 is missing, use <code>sudo apt install libqt4-opengl</code>, and if libpng12.so is missing (xds-viewer needs it), install it from [https://packages.ubuntu.com/xenial/amd64/libpng12-0/download] . | |||
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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on RHEL6/CentOS6/SL6 systems, or | on RHEL6/CentOS6/SL6 systems, or | ||
apt-get install xxdiff | apt-get install xxdiff | ||
on Ubuntu. | on Ubuntu. If Ubuntu 20.04 doesn't find it, use the latest from http://archive.ubuntu.com/ubuntu/pool/universe/x/xxdiff/ | ||
An <code>xxdiff</code> binary that runs on CentOS7 (RHEL7, SL7) is provided by the <code>get_folder.sh</code> script. | An <code>xxdiff</code> binary that runs on CentOS7 (RHEL7, SL7) is provided by the <code>get_folder.sh</code> script. | ||
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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/* . | ||
Starting with macOS Catalina, you also need | |||
xattr -dr XDS-OSX_64/* | |||
if you get a security error popup (google "xattr com.apple.quarantine catalina"). | |||
=== other programs: [[XDS-Viewer]], [[XDSSTAT]], [[XDSCC12]], [[XDSGUI]], [[XSCALE_ISOCLUSTER]] === | === other programs: [[XDS-Viewer]], [[XDSSTAT]], [[XDSCC12]], [[XDSGUI]], [[XSCALE_ISOCLUSTER]] === | ||
... can be downloaded from | ... can be downloaded from https://{{SERVERNAME}}/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, | ||
curl -O -R | # 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 https://{{SERVERNAME}}/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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== Windows == | == Windows == | ||
The programs of the [[XDS]] package as well as [[XDSGUI]], [[XDSSTAT]], [[XDSCC12]] and so on may be run on 64bit Windows 10 within the [ | The programs of the [[XDS]] package as well as [[XDSGUI]], [[XDSSTAT]], [[XDSCC12]] and so on may be run on 64bit Windows 10 within the [https://docs.microsoft.com/windows/wsl/install-win10 Linux Subsystem for Windows] (WSL). This (easily!) installs a Ubuntu environment, which supports the apt package manager, so in principle any software available for Ubuntu may be installed (or other distros, see [https://blogs.msdn.microsoft.com/commandline/2017/05/11/new-distros-coming-to-bashwsl-via-windows-store/]). | ||
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 | before running the program. Running XDSGUI under WSL's Ubuntu may require installation of a few packages with e.g. | ||
sudo apt-get install libgomp1 libqtgui4 | sudo apt-get install libgomp1 libqtgui4 | ||
and [[generate_XDS.INP]] requires a number of packages (some of which are only for specific detectors!); I'd start with | (see [[XDSGUI#Libraries_and_software_that_the_program_depends_on|XDSGUI]] and above). | ||
[[generate_XDS.INP]] requires a number of packages (some of which are only for specific detectors!); I'd start with | |||
sudo apt-get install coreutils binutils gawk sed bc grep | sudo apt-get install coreutils binutils gawk sed bc grep | ||
and if required, also install python and hdf5-tools. | and if required, also install python and hdf5-tools. | ||
XDSSTAT and the conversion to MTZ files by XDSCONV require a CCP4 installation accessible by WSL. In principle, CCP4 may be installed within WSL (have not tested this), or on the Windows host. | XDSSTAT and the conversion to MTZ files by XDSCONV require a CCP4 installation accessible by WSL. In principle, CCP4 may be installed within WSL (have not tested this), or on the Windows host. | ||
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(Screenshot provided by Gustavo Lima) | (Screenshot provided by Gustavo Lima) | ||
A detailed [https://strucbio.biologie.uni-konstanz.de/pub/xds%20%20prog%20installation%20in%20WSL%20(Lata%20Panicker).pdf writeup for Ubuntu 20.04 LTS] was provided by Dr Lata Panicker, SO(G), BARC, India. | |||
== See also == | == See also == | ||
[[Cluster Installation]] | [[Cluster Installation]] | ||