Dear ChimeraX team, Is there any way to install ChimeraX >= 1.8 on Linux without admin rights, like a generic Linux version that I can unpack at an arbitrary location? Our system is running Ubuntu 22.04 more specifically. Thank you! -- Ricardo Diogo Righetto
Hello，everyone. Who can give me the mac version of chimerax installation package? Now the chimera website is down. ---- 回复的原邮件 ---- | 发件人 | Ricardo Righetto via ChimeraX-users<chimerax-users@cgl.ucsf.edu> | | 日期 | 2024年06月17日 19:40 | | 收件人 | ChimeraX Users Help<chimerax-users@cgl.ucsf.edu> | | 抄送至 | | | 主题 | [chimerax-users] Installing ChimeraX on Linux without sudo | Dear ChimeraX team, Is there any way to install ChimeraX >= 1.8 on Linux without admin rights, like a generic Linux version that I can unpack at an arbitrary location? Our system is running Ubuntu 22.04 more specifically. Thank you! -- Ricardo Diogo Righetto
If the flatpak command is installed, you can install the flatpak version as a regular user. An administrator would need to install the flatpak command (sudo apt install flatpak), but after that you can update your version of ChimeraX any time. See https://www.cgl.ucsf.edu/chimerax/flatpak.html for details. Starting with 1.8, the flatpak version of ChimeraX is the generic Linux version. It is also possible to download the Ubuntu 22.04 deb package and extract the files using the dpkg-deb command. Move the usr/lib/ucsf-chimerax directory wherever you want, and make a symbolic link to the bin/ChimeraX program that you would use to run ChimeraX from the command line (do not add the ChimeraX bin directory to your path). Unfortunately, you still need sudo to install of the dependencies needed to run ChimeraX (which the dpkg-deb command can tell you). So it is simpler to have an administrator install ChimeraX (using sudo). If singularity/apptainer is installed your on your system, then it is also possible to build a container with ChimeraX and all of the dependencies in it. And run ChimeraX via that container. You need to get the right graphics driver in the container, so the container would be specific to your setup. An administrator would be needed to install the apptainer command if it isn't already installed. So sudo apt install is best, flatpak is a good second choice, and apptainer is a possible third choice. HTH, Greg On 6/17/2024 4:40 AM, Ricardo Righetto via ChimeraX-users wrote:
Dear ChimeraX team,
Is there any way to install ChimeraX >= 1.8 on Linux without admin rights, like a generic Linux version that I can unpack at an arbitrary location? Our system is running Ubuntu 22.04 more specifically.
Thank you!
-- Ricardo Diogo Righetto
_______________________________________________ ChimeraX-users mailing list --chimerax-users@cgl.ucsf.edu To unsubscribe send an email tochimerax-users-leave@cgl.ucsf.edu Archives:https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Hi Greg, thanks for the suggestions! We don't have flatpak available but I will ask our sysadmins to install it for the future. Before seeing your message, I ended up installing it like this: dpkg -x ucsf-chimerax_1.8ubuntu22.04_amd64.deb chimerax-1.8 (which is probably equivalent to using dpkg-deb) I then added the following environment variables: export PATH=chimerax-1.8/lib/ucsf-chimerax/bin:$PATH export LD_LIBRARY_PATH=chimerax-1.8/lib/ucsf-chimerax/lib:$LD_LIBRARY_PATH export LD_LIBRARY_PATH=chimerax-1.8/lib/ucsf-chimerax/lib64:$LD_LIBRARY_PATH I probably got lucky with the dependencies because everything worked smoothly. Perhaps some documentation on this method could be added to the website? Thank you! -- Ricardo Diogo Righetto Em qui., 20 de jun. de 2024 às 10:58, Greg Couch <gregc@cgl.ucsf.edu> escreveu:
If the flatpak command is installed, you can install the flatpak version as a regular user. An administrator would need to install the flatpak command (sudo apt install flatpak), but after that you can update your version of ChimeraX any time. See https://www.cgl.ucsf.edu/chimerax/flatpak.html for details. Starting with 1.8, the flatpak version of ChimeraX is the generic Linux version.
It is also possible to download the Ubuntu 22.04 deb package and extract the files using the dpkg-deb command. Move the usr/lib/ucsf-chimerax directory wherever you want, and make a symbolic link to the bin/ChimeraX program that you would use to run ChimeraX from the command line (do not add the ChimeraX bin directory to your path). Unfortunately, you still need sudo to install of the dependencies needed to run ChimeraX (which the dpkg-deb command can tell you). So it is simpler to have an administrator install ChimeraX (using sudo).
If singularity/apptainer is installed your on your system, then it is also possible to build a container with ChimeraX and all of the dependencies in it. And run ChimeraX via that container. You need to get the right graphics driver in the container, so the container would be specific to your setup. An administrator would be needed to install the apptainer command if it isn't already installed.
So sudo apt install is best, flatpak is a good second choice, and apptainer is a possible third choice.
HTH,
Greg On 6/17/2024 4:40 AM, Ricardo Righetto via ChimeraX-users wrote:
Dear ChimeraX team,
Is there any way to install ChimeraX >= 1.8 on Linux without admin rights, like a generic Linux version that I can unpack at an arbitrary location? Our system is running Ubuntu 22.04 more specifically.
Thank you!
-- Ricardo Diogo Righetto
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Dear all, For information/documentation: This is how I do it on CentOS9/RHEL9/AlmaLinux9 systems: rpm2cpio ucsf-chimerax-1.8-1.el9.x86_64.rpm | cpio -idmv (rpm2cpio is part of the rpm package) Here is an example environment using environment modules: module-whatis {UCSF ChimeraX} prepend-path PATH /gpfs/cssb/software/rhel9/x86_64/chimerax/1.8.0/usr/bin prepend-path MANPATH /gpfs/cssb/software/rhel9/x86_64/chimerax/1.8.0/usr/share/man prepend-path LD_LIBRARY_PATH /gpfs/cssb/software/rhel9/x86_64/chimerax/1.8.0/usr/libexec/UCSF-ChimeraX/lib Since ChimeraX 1.8 (and other recent Qt6 software) I needed the missing library xcb-util-cursor - missing libxcb-cursor.so.0 library error when starting ChimeraX. This is part of the distribution and you have to ask your IT to install it or do it by yourself and adapt the LD_LIBRARY_PATH. This is also maybe specific to graphical login nodes where we start ChimeraX like: set-alias chimerax {vglrun +xcb /gpfs/cssb/software/rhel9/x86_64/chimerax/1.8.0/usr/bin/chimerax} Cheers, Wolfgang From: "Ricardo Righetto via ChimeraX-users" <chimerax-users@cgl.ucsf.edu> To: "Greg Couch" <gregc@cgl.ucsf.edu> Cc: "ChimeraX Users Help" <chimerax-users@cgl.ucsf.edu> Sent: Friday, 21 June, 2024 17:18:48 Subject: [EXT] [chimerax-users] Re: Installing ChimeraX on Linux without sudo Hi Greg, thanks for the suggestions! We don't have flatpak available but I will ask our sysadmins to install it for the future. Before seeing your message, I ended up installing it like this: dpkg -x ucsf-chimerax_1.8ubuntu22.04_amd64.deb chimerax-1.8 (which is probably equivalent to using dpkg-deb) I then added the following environment variables: export PATH=chimerax-1.8/lib/ucsf-chimerax/bin:$PATH export LD_LIBRARY_PATH=chimerax-1.8/lib/ucsf-chimerax/lib:$LD_LIBRARY_PATH export LD_LIBRARY_PATH=chimerax-1.8/lib/ucsf-chimerax/lib64:$LD_LIBRARY_PATH I probably got lucky with the dependencies because everything worked smoothly. Perhaps some documentation on this method could be added to the website? Thank you! -- Ricardo Diogo Righetto Em qui., 20 de jun. de 2024 às 10:58, Greg Couch < [ mailto:gregc@cgl.ucsf.edu | gregc@cgl.ucsf.edu ] > escreveu: If the flatpak command is installed, you can install the flatpak version as a regular user. An administrator would need to install the flatpak command (sudo apt install flatpak), but after that you can update your version of ChimeraX any time. See [ https://www.cgl.ucsf.edu/chimerax/flatpak.html | https://www.cgl.ucsf.edu/chimerax/flatpak.html ] for details. Starting with 1.8, the flatpak version of ChimeraX is the generic Linux version. It is also possible to download the Ubuntu 22.04 deb package and extract the files using the dpkg-deb command. Move the usr/lib/ucsf-chimerax directory wherever you want, and make a symbolic link to the bin/ChimeraX program that you would use to run ChimeraX from the command line (do not add the ChimeraX bin directory to your path). Unfortunately, you still need sudo to install of the dependencies needed to run ChimeraX (which the dpkg-deb command can tell you). So it is simpler to have an administrator install ChimeraX (using sudo). If singularity/apptainer is installed your on your system, then it is also possible to build a container with ChimeraX and all of the dependencies in it. And run ChimeraX via that container. You need to get the right graphics driver in the container, so the container would be specific to your setup. An administrator would be needed to install the apptainer command if it isn't already installed. So sudo apt install is best, flatpak is a good second choice, and apptainer is a possible third choice. HTH, Greg On 6/17/2024 4:40 AM, Ricardo Righetto via ChimeraX-users wrote: BQ_BEGIN Dear ChimeraX team, Is there any way to install ChimeraX >= 1.8 on Linux without admin rights, like a generic Linux version that I can unpack at an arbitrary location? Our system is running Ubuntu 22.04 more specifically. Thank you! -- Ricardo Diogo Righetto _______________________________________________ ChimeraX-users mailing list -- [ mailto:chimerax-users@cgl.ucsf.edu | chimerax-users@cgl.ucsf.edu ] To unsubscribe send an email to [ mailto:chimerax-users-leave@cgl.ucsf.edu | chimerax-users-leave@cgl.ucsf.edu ] Archives: [ https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ | https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ ] BQ_END _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
participants (4)
-
Greg Couch -
Lugmayr, Wolfgang -
Ricardo Righetto -
胡小华