running_scipion_tutorials

SCIPION: 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.