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SCIPION

SCIPION uses software that needs Nvidia GPU acceleration. Appropriate hardware and driver are required.

Scipion plugins included in SBGrid (30+).

Note that this plugins are already linked to SBGrid available titles (capsules)*

  • aretomo
  • bsoft
  • chimerax
  • cistem
  • cryoassess
  • cryocare
  • cryodrgn
  • cryosparc (CryoSPARC installation not included in SBGrid, you need to link your own**)
  • deepfinder
  • dynamo
  • eman2
  • emantomo
  • emfacilities
  • emready
  • fidder
  • gapstop
  • gautomatch
  • gctf
  • imod
  • membrain
  • motioncorr
  • novactf
  • pwem
  • pyworkflowtests
  • relion
  • reliontomo
  • repic
  • tardis
  • sphire
  • tomo
  • tomosegmemtv
  • warp
  • topaz
  • xmipptomo (no longer supported by Scipion devs)
  • xmipp3

IMPORTANT NOTE: if you miss any plugin or a newer version, you can always request SBGrid team to install/update it, but DO NOT try to do it on your own, as it might not work as expected (most of plugin installs need a fine-tunning to work properly with SBGrid installed software).

*Note that if you are a commercial user, some of the titles linked to Scipion plugin may not be available for you (Sphire/CryOLO, Chimerax, etc), in that case, you will see the plugin in Scipion but you will not be able to run the protocols as the underneath title unfortunatly is not available for you on SBGrid.

**The scipion-em-cryoSPARC2 plugin is provided in Scipion, but CryoSPARC is not available in SBGrid, so you can not use CryoSPARC directly. However, if you want to use CryoSPARC in Scipion, link a CryoSPARC installation outside of SBGrid to the scipion-em-cryoSPARC2 plugin following the instructions on its GitHub repository (skip step 1): https://github.com/scipion-em/scipion-em-cryosparc2?tab=readme-ov-file#installing-the-plugin.

For more info on available, installed and version of the plugins, check the complete list of Scipion plugins: scipion installp --help

Running tutorials without write privileges

Scipion tutorials (https://scipion-em.github.io/docs/docs/user/user-documentation.html#tutorials) are launched by typing, for example scipion tutorial intro into the terminal. However, these tutorials will try and download the tutorial data into the $SCIPION_HOME/data/tests directory. Many SBGrid 'site' installations will have the /programs directory set as 'read and execute' only, with no write permissions in the /programs tree.

To be able to run Scipion tutorials without write privileges in the /programs tree, Scipion needs to have its configuration file modified to save tests in a directory with write privileges.

The configuration file is located at ~/.config/scipion/scipion.conf and should look similar to this: 

[DIRS_LOCAL]
SCIPION_USER_DATA = ~/ScipionUserData
SCIPION_LOGS = %(SCIPION_USER_DATA)s/logs
SCIPION_TMP = %(SCIPION_USER_DATA)s/tmp

[PACKAGES]
EM_ROOT = software/em
XMIPP_HOME = %(EM_ROOT)s/xmipp
CHIMERA_HOME = %(EM_ROOT)s/chimera-1.13.1
CHIMERA_HEADLESS_HOME = %(EM_ROOT)s/chimera_headless
VMD_HOME = %(EM_ROOT)s/vmd

[VARIABLES]
SCIPION_NOTES_PROGRAM =
SCIPION_NOTES_ARGS =
SCIPION_NOTES_FILE = notes.txt
SCIPION_NOTIFY = False
VIEWERS = {"Volume":["pyworkflow.em.viewers.viewers_data.DataViewer"]}

Open the file in your favourite editor, and add a line

SCIPION_TESTS = ~/scipion/tests

in the "DIRS_LOCAL" section. You can specify any directory you want the tutorials to be saved, provided you have write privileges in the directory.

Your modified ~/.config/scipion/scipion.conf file should now look similar to this: 

[DIRS_LOCAL]
SCIPION_USER_DATA = ~/ScipionUserData
SCIPION_LOGS = %(SCIPION_USER_DATA)s/logs
SCIPION_TMP = %(SCIPION_USER_DATA)s/tmp
SCIPION_TESTS = ~/scipion/tests

[PACKAGES]
EM_ROOT = software/em
XMIPP_HOME = %(EM_ROOT)s/xmipp
CHIMERA_HOME = %(EM_ROOT)s/chimera-1.13.1
CHIMERA_HEADLESS_HOME = %(EM_ROOT)s/chimera_headless
VMD_HOME = %(EM_ROOT)s/vmd

[VARIABLES]
SCIPION_NOTES_PROGRAM =
SCIPION_NOTES_ARGS =
SCIPION_NOTES_FILE = notes.txt
SCIPION_NOTIFY = False
VIEWERS = {"Volume":["pyworkflow.em.viewers.viewers_data.DataViewer"]}

After saving the file, running scipion tutorial intro will save the tutorial project in the ~/scipion/tests directory, and you should be able to follow the tutorials as described.