Installation: Difference between revisions

Installation (view source)

Revision as of 11:14, 27 July 2021

1,123 bytes added , 27 July 2021

m

→‎other programs: XDS-viewer, XDSSTAT, XDSCC12, XDSGUI, XSCALE_ISOCLUSTER, generate_XDS.INP

Kay

Bureaucrats

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 === other programs: [[XDS-Viewer]], [[XDSSTAT]], [[XDSCC12]], [[XDSGUI]], [[XSCALE_ISOCLUSTER]], [[spot2pdb]], [[generate_XDS.INP]]  ===
 ... 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
-  wget https://{{SERVERNAME}}/pub/linux_bin/get_folder.sh
+  wget -N https://{{SERVERNAME}}/pub/linux_bin/get_folder.sh
   chmod +x get_folder.sh
   ./get_folder.sh
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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.
-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> (Ubuntu: <code>apt install hdf5-tools</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].
+For [[Eiger]] data processing, a h5dump binary (version 1.10 req'd for HDF5 data from DLS) and <code>H5ToXDS</code> is installed by the <code>get_folder.sh</code> script into /usr/local/bin. If the script is not used, <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> (Ubuntu: <code>apt install hdf5-tools</code>) - but make sure that h5dump is version 1.10 or higher when processing HDF5 data from DLS.
+Furthermore, you want the [https://www.dectris.com/company/news/newsroom/news-details/process-eiger-data-with-xds-fast Neggia] library (does not work for HDF5 data from DLS) or the [https://github.com/DiamondLightSource/durin Durin plugin]. These may be installed through the <code>get_folder.sh</code> script, in <code>/usr/local/lib64</code>.
 == Mac OSX ==
-Attention: [[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>. You may 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): open a Terminal window, and enter <code>sudo xcode-select --install</code> (for Big Sur, the download has a size of about half a GB; the downloader is much too pessimistic about the time it takes).
+Although CCP4 is not required by XDS itself, some of the programs (XDSSTAT, and MTZ file creation in XDSCONV) use CCP4 tools or libraries. 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
+kay@Kays-MacBook-Air-2018 ~ % cat .zprofile
+source /Users/kay/.profile
+# Added by CCP4 package manager:
+. '/Applications/ccp4-7.1/bin/ccp4.setup-sh'
+</pre>If the file does not exist, create it with the contents indicated above; you have to adapt it to your user name and the CCP4 version.
 Become familiar with the concept and ways to run commands as "root" - google "mac osx become root". All the installation 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 for installation, 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>)
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 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 and DLS's Durin library into <code>/usr/local/lib64</code>
-# copies [[Eiger#General_aspects|eiger2cbf-osx]] into /usr/local/bin, but under the name <code>H5ToXds</code> ([https://www.globalphasing.com GlobalPhasing's] hdf2mini-cbf would be preferable but needs [https://www.globalphasing.com/autoproc/ autoPROC] license)
+# copies [https://www.globalphasing.com GlobalPhasing's] <code>hdf2mini-cbf</code> into <code>/usr/local/bin</code>, but under the name <code>H5ToXds</code> (consider getting a [https://www.globalphasing.com/autoproc/ autoPROC] license!)
-# 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 (a 1.10 version is required for Eiger data from DLS)
+# copies <code>h5dump</code> [https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.12/hdf5-1.12.1/bin/unix/hdf5-1.12.1-Std-macos11_64-clang.tar.gz] into <code>/usr/local/bin</code>
 A [https://{{SERVERNAME}}/pub/mac_bin/XDS-Viewer-macOS10.13.dmg 10.13] Qt5 version of XDS-viewer (compiled by T. Hauß) works on macOS Catalina, and is installed by <code>get_folder.sh</code>. Older Macs need [https://{{SERVERNAME}}/pub/mac_bin/XDS-Viewer-0.6 this version]; newer macOS should install [https://{{SERVERNAME}}/pub/mac_bin/XDS-Viewer-macOS10.15.dmg 10.15]. For XDSGUI, the [https://{{SERVERNAME}}/pub/mac_bin/xdsgui_qt4.dmg Qt4 version] is still the default, but a [https://{{SERVERNAME}}/pub/mac_bin/xdsgui_qt5.dmg Qt5 version] is available.
-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/ . I had to go to System Preferences > Security & Privacy > Privacy and add <code>xxdiff</code> to the programs with full disk access.
 === Troubleshooting ===
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 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] or [https://mobaxterm.mobatek.net/ Mobaxterm] on the Windows host. There are helpful writeups (e.g. [https://wiki.ubuntu.com/WSL#Running_Graphical_Applications] and [http://wsl-guide.org/en/latest/]). VcXsrc seems to have a problem with coot for some people (see [https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=COOT;6ef4a967.2011 WSL2 installation] and responses). To use the X server with WSL, one has to say in the shell window
   export DISPLAY=:0
-before running the program. Running XDSGUI under WSL's Ubuntu may require installation of a few packages with e.g.
+before running the program. Running [[XDSGUI]] under WSL's Ubuntu 20.04 may require installation of a few packages with e.g.
-  sudo apt-get install libgomp1 libqtgui4
+  sudo apt-get install libgomp1 libqtgui4 binutils
-(see [[XDSGUI#Libraries_and_software_that_the_program_depends_on|XDSGUI]] and above).
+(see [[XDSGUI#Libraries_and_software_that_the_program_depends_on|XDSGUI]] and above). If required, also install python and hdf5-tools.
-[[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
-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.
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   sudo chown MYWSLNAME /opt/xtal
-A few libraries are needed before CCP4 installation (tcsh is needed by CCP4, the others are mostly graphics libraries):
+A few libraries are needed before CCP4 installation (tcsh is needed by CCP4; most of the others are graphics libraries; binutils provides <code>strings</code>):
-  sudo apt install tcsh libqt5opengl5 libqt5printsupport5 libqt5gui5 libxcb-render0 libxcb-shm0 libglu1-mesa libgomp1
+  sudo apt install tcsh libqt5opengl5 libqt5printsupport5 libqt5gui5 libxcb-render0 libxcb-shm0 libglu1-mesa libgomp1 binutils
-When installing CCP4, let it "modify the environment" for you. If you forgot this, insert a line into your ~/.bashrc :
+When installing CCP4, let it "modify command line environment" for you (on one of the very first screens of the installation GUI). If you forgot this, insert a line into your ~/.bashrc :
   source /opt/xtal/ccp4-7.1/bin/ccp4.setup-sh
 afterwards (this is not WSL specific, but is just Linux). I created a file in the Windows filesystem (replace MYUSERNAME with your Windows user name):