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→XDS package for Macs with Apple M processors: add cd /usr/local/bin
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== macOS == | == macOS == | ||
=== [[XDS]] package === | Become familiar with the concept and ways to run commands as "root" (administrator) - google "mac osx become root". Installation tasks that are run in a Terminal window require root privileges if the programs and their links are written to /usr/local/bin. | ||
Therefore, if /usr/local/bin does not yet exist, prepare the following steps by opening the Terminal window, and then | |||
sudo mkdir /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. Also, this requires modification of the $PATH, by a one-time | |||
mkdir $HOME/bin | |||
echo 'export PATH=$PATH:$HOME/bin' >> ~/.profile | |||
echo 'export PATH=$PATH:$HOME/bin' >> ~/.zprofile</code> | |||
=== [[XDS]] package for Intel Macs === | |||
If you are an academic user, | If you are an academic user, | ||
# obtain root privileges (it will ask for your password): | |||
sudo su | |||
cd /usr/local/bin | cd /usr/local/bin | ||
curl -L -o - https://xds.mr.mpg.de/XDS-OSX_64.tar.gz | tar xzvf - | curl -L -o - https://xds.mr.mpg.de/XDS-OSX_64.tar.gz | tar xzvf - | ||
ln -sf XDS-OSX_64/* . | ln -sf XDS-OSX_64/* . | ||
# release root permissions: | |||
exit | |||
(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 | Starting with macOS Catalina, you may also need | ||
xattr -dr XDS-OSX_64/* | sudo xattr -dr XDS-OSX_64/* | ||
if you get a security error popup (google "xattr com.apple.quarantine catalina"). | if you get a security error popup (google "xattr com.apple.quarantine catalina"). | ||
Then make sure that the binaries are in the search path for executables, as explained in https://xds.mr.mpg.de/html_doc/downloading.html . | Then make sure that the binaries are in the search path for executables, as also explained in https://xds.mr.mpg.de/html_doc/downloading.html . | ||
If you want to process .h5 files written by Eiger detectors on a Mac with Intel CPU, use the [https://{{SERVERNAME}}/pub/mac_bin/durin-plugin.so Durin plugin for Intel Mac processors] (source code [https://github.com/DiamondLightSource/durin available]) or the [https://{{SERVERNAME}}/pub/mac_bin/dectris-neggia.so Dectris-Neggia plugin for Intel Mac 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. | If you want to process .h5 files written by Eiger detectors on a Mac with Intel CPU, use the [https://{{SERVERNAME}}/pub/mac_bin/durin-plugin.so Durin plugin for Intel Mac processors] (source code [https://github.com/DiamondLightSource/durin available]) or the [https://{{SERVERNAME}}/pub/mac_bin/dectris-neggia.so Dectris-Neggia plugin for Intel Mac 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. | ||
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See [[Installation#other_programs:_XDS-viewer,_XDSSTAT,_XDSCC12,_XDSGUI,_XSCALE_ISOCLUSTER,_generate_XDS.INP|below]] for installation of these .so files. | See [[Installation#other_programs:_XDS-viewer,_XDSSTAT,_XDSCC12,_XDSGUI,_XSCALE_ISOCLUSTER,_generate_XDS.INP|below]] for installation of these .so files. | ||
==== | ==== XDS package for Macs with Apple M processors ==== | ||
The Intel Mac XDS programs also work on the Apple Silicon machines, but the libraries for e.g. reading data from Eiger detectors don't, and the native binaries are faster. | |||
Thus, change the above <code>curl</code> and <code>ln</code> commands to | |||
# become root (it will ask for your password): | |||
sudo su | |||
cd /usr/local/bin | |||
curl -L -o - https://xds.mr.mpg.de/XDS-Apple_M1.tar.gz | tar xzvf - | curl -L -o - https://xds.mr.mpg.de/XDS-Apple_M1.tar.gz | tar xzvf - | ||
ln -sf XDS-Apple_M1/* . | ln -sf XDS-Apple_M1/* . | ||
# release root permissions: | |||
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. | 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. | ||
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Only Terminal windows that are opened afterwards will have access to the CCP4 programs! | 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]] === | === other programs: [[XDS-viewer]], [[XDSSTAT]], [[XDSCC12]], [[XDSGUI]], [[XSCALE_ISOCLUSTER]], [[generate_XDS.INP]] === | ||
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chmod +x get_folder.sh | chmod +x get_folder.sh | ||
./get_folder.sh | ./get_folder.sh | ||
Release root privileges: | |||
exit | |||
If you want to update the programs some time later, just run these commands again. | If you want to update the programs some time later, just run these commands again. | ||