Installation: Difference between revisions

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This article has information 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).

This article has information that should ease the installation of XDS and related programs like ([[XDS-viewer]], [[xdsstat]], [[XDSGUI|xdsgui]]). Generally, it is easiest if binaries (or links to binaries) 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). But it is mostly possible to install without administrative privileges - the exception is XDSGUI on Linux which may require installation of certain libraries by the administrator.

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# ln -sf XDS-INTEL64_Linux_x86_64/* .

</pre>

In case the above website is unavailable, there is a [https://{{SERVERNAME}}/pub/xds backup site].

If you don't have root rights, replace /usr/local/bin by $HOME/bin in the first line above, and make sure that $HOME/bin is in your $PATH (google "linux set path" or similar).

If you want to process data from the [[Eiger]] detector: see below for plugins that allow XDS to read the .h5 files. Similarly for gzip-ed CBF files as mostly collected at EMBL Hamburg.

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As root, the script copies the programs into /usr/local/bin/linux_bin, and links them to /usr/local/bin. As a normal user, they are downloaded to $HOME/bin/linux_bin, and linked to your $HOME/bin. In the latter case, make sure that $HOME/bin is in your $PATH.

Although CCP4 is not required by XDS, XSCALE or XDSGUI, some of the programs (namely XDSSTAT, and MTZ file creation in XDSCONV) need its tools (F2MTZ, ...) or libraries, or run its programs (POINTLESS and COOT can be run from XDSGUI). Therefore, CCP4 should be installed.

=== tools and helper programs for [[generate_XDS.INP]] and [[XDSGUI]], and libraries ===

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* 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 (by root), you can check the xdsgui binary with

ldd `which xdsgui` | grep found

and that should show you the libraries it didn't find. Your friendly system administrator knows the specific commands to install those libraries.

and that should show you the libraries it '''didn't''' find. Your friendly system administrator knows the specific commands to install those libraries.

N.B. this may list libpng15.so for the latest XDSGUI (compiled May 2023), but you can ignore that!

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sudo apt-file update

Versions of XDSGUI compiled before 2021: Ubuntu 20.04: If the Qt5 libraries are missing, use <code>sudo apt install libqt5gui5 libqt5printsupport5 libqt5opengl5</code>. On CentOS7, this would be <code>yum -y install qt5-qtbase-gui qt5-qtbase</code> .

On Ubuntu, XDSGUI may require <code>sudo apt install libxcb-xinerama0</code>

On Ubuntu, ~~latest~~ XDSGUI may require <code>sudo apt install libxcb-xinerama0</code>

<code>xxdiff</code> is likely available for your distribution - google for it, or try e.g.

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on RHEL6/CentOS6/SL6 systems, or

apt install xxdiff

on Ubuntu. If Ubuntu ~~20.04~~ doesn't find it, use the latest from http://archive.ubuntu.com/ubuntu/pool/universe/x/xxdiff/

on Ubuntu. If Ubuntu 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.

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[[generate_XDS.INP]] requires the [https://developer.apple.com/download/more/ Xcode command line tools] to be installed (free of charge): open a Terminal window, and enter <code>sudo xcode-select --install</code> (the download has a size of about 750MB; the downloader is much too pessimistic about the time it takes).

Although CCP4 is not required by XDS, XSCALE or XDSGUI, some of the programs (namely XDSSTAT, and MTZ file creation in XDSCONV) ~~require~~ its tools (F2MTZ, ...) or libraries, or run its programs (POINTLESS, COOT can be run from XDSGUI). Therefore, CCP4 should be installed. Open a Terminal and check the existence of the file .zprofile , and its content:<pre>

Although CCP4 is not required by XDS, XSCALE or XDSGUI, some of the programs (namely XDSSTAT, and MTZ file creation in XDSCONV) need its tools (F2MTZ, ...) or libraries, or run its programs (POINTLESS, COOT can be run from XDSGUI). Therefore, CCP4 should be installed. Open a Terminal and check the existence of the file .zprofile , and its content:<pre>

kay@Kays-MacBook-Air-2018 ~ % ls -l .zprofile

-rw-r--r-- 1 kay staff 107 7 Mär 09:41 .zprofile

@@ Line 1: / Line 1: @@
-This article has information 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).
+This article has information that should ease the installation of XDS and related programs like ([[XDS-viewer]], [[xdsstat]], [[XDSGUI|xdsgui]]). Generally, it is easiest if binaries (or links to binaries) 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). But it is mostly possible to install without administrative privileges - the exception is XDSGUI on Linux which may require installation of certain libraries by the administrator.
@@ Line 15: / Line 15: @@
 # ln -sf XDS-INTEL64_Linux_x86_64/* .
 </pre>
 In case the above website is unavailable, there is a [https://{{SERVERNAME}}/pub/xds backup site].
+If you don't have root rights, replace /usr/local/bin by $HOME/bin in the first line above, and make sure that $HOME/bin is in your $PATH (google "linux set path" or similar).
 If you want to process data from the [[Eiger]] detector: see below for plugins that allow XDS to read the .h5 files. Similarly for gzip-ed CBF files as mostly collected at EMBL Hamburg.
@@ Line 27: / Line 29: @@
 As root, the script copies the programs into /usr/local/bin/linux_bin, and links them to /usr/local/bin. As a normal user, they are downloaded to $HOME/bin/linux_bin, and linked to your $HOME/bin. In the latter case, make sure that $HOME/bin is in your $PATH.
+Although CCP4 is not required by XDS, XSCALE or XDSGUI, some of the programs (namely XDSSTAT, and MTZ file creation in XDSCONV) need its tools (F2MTZ, ...) or libraries, or run its programs (POINTLESS and COOT can be run from XDSGUI). Therefore, CCP4 should be installed.
 === tools and helper programs for [[generate_XDS.INP]] and [[XDSGUI]], and libraries ===
@@ Line 32: / Line 36: @@
 * 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 (by root), you can check the xdsgui binary with
   ldd `which xdsgui` | grep found
-and that should show you the libraries it didn't find. Your friendly system administrator knows the specific commands to install those libraries.
+and that should show you the libraries it '''didn't''' find. Your friendly system administrator knows the specific commands to install those libraries.
 N.B. this may list libpng15.so for the latest XDSGUI (compiled May 2023), but you can ignore that!
@@ Line 48: / Line 52: @@
    sudo apt-file update
-Versions of XDSGUI compiled before 2021: Ubuntu 20.04: If the Qt5 libraries are missing, use <code>sudo apt install libqt5gui5 libqt5printsupport5 libqt5opengl5</code>. On CentOS7, this would be <code>yum -y install qt5-qtbase-gui qt5-qtbase</code> .
+On Ubuntu, XDSGUI may require <code>sudo apt install libxcb-xinerama0</code>
-On Ubuntu, latest XDSGUI may require <code>sudo apt install libxcb-xinerama0</code>
 <code>xxdiff</code> is likely available for your distribution - google for it, or try e.g.
@@ Line 56: / Line 58: @@
 on RHEL6/CentOS6/SL6 systems, or
   apt install xxdiff
-on Ubuntu. If Ubuntu 20.04 doesn't find it, use the latest from http://archive.ubuntu.com/ubuntu/pool/universe/x/xxdiff/
+on Ubuntu. If Ubuntu 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.
@@ Line 128: / Line 130: @@
 [[generate_XDS.INP]] requires the [https://developer.apple.com/download/more/ Xcode command line tools] to be installed (free of charge): open a Terminal window, and enter <code>sudo xcode-select --install</code> (the download has a size of about 750MB; the downloader is much too pessimistic about the time it takes).
-Although CCP4 is not required by XDS, XSCALE or XDSGUI, some of the programs (namely XDSSTAT, and MTZ file creation in XDSCONV) require its tools (F2MTZ, ...) or libraries, or run its programs (POINTLESS, COOT can be run from XDSGUI). Therefore, CCP4 should be installed. Open a Terminal and check the existence of the file .zprofile , and its content:<pre>
+Although CCP4 is not required by XDS, XSCALE or XDSGUI, some of the programs (namely XDSSTAT, and MTZ file creation in XDSCONV) need its tools (F2MTZ, ...) or libraries, or run its programs (POINTLESS, COOT can be run from XDSGUI). Therefore, CCP4 should be installed. Open a Terminal and check the existence of the file .zprofile , and its content:<pre>
 kay@Kays-MacBook-Air-2018 ~ % ls -l .zprofile
 -rw-r--r--  1 kay   staff  107  7 Mär 09:41 .zprofile