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→infrastructure: tools and helper programs for generate_XDS.INP and XDSGUI, and libraries
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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 | ||
You may repeat this, as root, every now and then, to update the programs. | |||
=== tools and helper programs for [[generate_XDS.INP]] and [[XDSGUI]], and libraries === | |||
* check and installation of Unix tools for [[generate_XDS.INP]] is shown at [[Generate_XDS.INP#Dependencies]] | |||
* helper programs for [[XDSGUI]] are listed and discussed at [[XDSGUI#Dependencies]]. Nota bene: XDSGUI needs [[generate_XDS.INP]] unless you already have a working XDS.INP. | |||
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` | grep found | ||
and that should show you the libraries it | and that should show you the libraries it it didn't find. Your friendly system administrator will then work out the specific commands to install those libraries. | ||
For RedHat-type distributions, that would typically be e.g. | |||
yum provides libXfixes.so.3 | |||
the output of which will tell you that this is in the libXfixes RPM. | |||
If in the case of Ubuntu you don't know the name of the package that provides a certain library, the | |||
sudo apt-file search <name-of-library> | |||
command should find it for you (where <code><name-of-library></code> could e.g. be <code>libGLU.so.1</code>). This needs a one-time installation by | |||
sudo apt install apt-file | |||
sudo apt-file update | |||
Ubuntu 18.04: if libQtOpenGL.so.4 is missing, use <code>sudo apt install libqt4-opengl</code>. | |||
Ubuntu 20.04: if libQtOpenGL.so.4 is missing, use | |||
sudo add-apt-repository -y ppa:rock-core/qt4 | |||
sudo apt update | |||
sudo apt install libqt4-opengl | |||
But it would be better to use the [https://strucbio.biologie.uni-konstanz.de/pub/linux_bin/xdsgui_qt5 Qt5 binary of XDSGUI]. | |||
<code>xxdiff</code> is likely available for your distribution - google for it, or try e.g. | <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 | ||
apt | apt 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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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. | ||
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>. Furthermore, you want the [https://www.dectris.com/company/news/newsroom/news-details/process-eiger-data-with-xds-fast Neggia] library or the [https://github.com/DiamondLightSource/durin Durin plugin]. | ||
== Mac OSX == | == Mac OSX == | ||
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curl -L -o - ftp://ftp.mpimf-heidelberg.mpg.de/pub/kabsch/XDS-OSX_64.tar.gz | tar xzvf - | 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, | ||
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mkdir -p /usr/local/bin/mac_bin | mkdir -p /usr/local/bin/mac_bin | ||
cd /usr/local/bin/mac_bin | cd /usr/local/bin/mac_bin | ||
curl -O -R | 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 | ||
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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]] | ||