Installation: Difference between revisions

<pre>

  cd /usr/local/bin

</pre>

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.

=== 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

  chmod +x get_folder.sh

  ./get_folder.sh

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.

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

* 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.  

  ldd `which xdsgui` | grep found

For RedHat-type distributions, that would typically be e.g.  

   sudo apt-file update

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

on RHEL6/CentOS6/SL6 systems, or

  apt install xxdiff

An <code>xxdiff</code> binary that runs on CentOS7 (RHEL7, SL7) is provided by the <code>get_folder.sh</code> script.

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. Also, this requires modification of the $PATH, by a one-time  

  mkdir $HOME/bin

=== [[XDS]] package for Intel Macs ===

  # obtain root privileges (it will ask for your password):

  sudo su

  cd /usr/local/bin

  curl -L -o - https://xds.mr.mpg.de/XDS-OSX_64.tar.gz | tar xzvf -

(If you don't have root privileges and run in $HOME/bin, only the curl and ln commands have to be run)

Starting with macOS Catalina, you may also need

if you get a security error popup (google "xattr com.apple.quarantine catalina").

  # become root (it will ask for your password):

  sudo su

  exit

If you want to process .h5 files written by Eiger detectors, use the [https://{{SERVERNAME}}/pub/mac_bin/durin-plugin-Apple-arm64.so Durin plugin for Apple ARM64 processors] (source code [https://github.com/DiamondLightSource/durin available]) or the [https://{{SERVERNAME}}/pub/mac_bin/dectris-neggia-Apple-arm64.so Dectris-Neggia plugin for Apple ARM64 processors] (source code [https://github.com/dectris/neggia available]). The latter may be faster, but does not work on data collected at Diamond Light Source. The former should in principle work for all HDF5 data.   

See [[Installation#other_programs:_XDS-viewer,_XDSSTAT,_XDSCC12,_XDSGUI,_XSCALE_ISOCLUSTER,_generate_XDS.INP|below]] for installation of these .so files.

[[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).

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

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

source $HOME/.profile

# Added by CCP4 package manager:

</pre>If the file does not exist, create it - the easiest way is:

<pre>

# or

# depending on which CCP4 version you have installed

</pre>The <code>get_folder.sh</code> script (below) checks the CCP4 setup, and creates the necessary files if needed.

Only Terminal windows that are opened afterwards will have access to the CCP4 programs!

=== other programs: [[XDS-viewer]], [[XDSSTAT]], [[XDSCC12]], [[XDSGUI]], [[XSCALE_ISOCLUSTER]], [[generate_XDS.INP]]  ===

... 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

  # any folder would do; here we use /usr/local/bin/mac_bin

  mkdir -p /usr/local/bin/mac_bin

  chmod +x get_folder.sh

  ./get_folder.sh

  exit

If you want to update the programs some time later, just run these commands again.

# 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 <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>

For XDSGUI, you have a choice between the version for Intel Macs and that for Silicon Macs. Both do work on Silicon Macs, except for the plugin libraries - for these, the correct version (ending with -Apple-arm64.so) must be used together with xdsgui_mac_silicon.  

=== Troubleshooting ===

== Windows ==

A lot of technical detail is at [https://docs.microsoft.com/en-us/windows/wsl/compare-versions] .

=== WSL2 ===

If you want to install CCP4 as a regular user, you need (as this is Linux! And replace MYWSLNAME with your WSL user name):

  sudo apt install tcsh libqt5opengl5 libqt5printsupport5 libqt5gui5 libxcb-render0 libxcb-shm0 libglu1-mesa libgomp1 binutils

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 :

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):

  cd /mnt/c/Users/MYUSERNAME/

to make the shelx* programs work (see https://github.com/microsoft/WSL/issues/4694 ), and to make "vsyscall=emulate" appear in /proc/cmdline. After creating the file, WSL2 must be restarted with "wsl.exe --shutdown" (or the machine booted).

== See also ==

[[Cluster Installation]]