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examples/running_scipion_tutorials.md
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1 | +## SCIPION: running tutorials without write privileges |
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2 | +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. |
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3 | + |
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4 | +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. |
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5 | + |
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6 | +The configuration file is located at ~/.config/scipion/scipion.conf and should look similar to this: |
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7 | +``` |
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8 | +[DIRS_LOCAL] |
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9 | +SCIPION_USER_DATA = ~/ScipionUserData |
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10 | +SCIPION_LOGS = %(SCIPION_USER_DATA)s/logs |
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11 | +SCIPION_TMP = %(SCIPION_USER_DATA)s/tmp |
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12 | + |
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13 | +[PACKAGES] |
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14 | +EM_ROOT = software/em |
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15 | +XMIPP_HOME = %(EM_ROOT)s/xmipp |
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16 | +CHIMERA_HOME = %(EM_ROOT)s/chimera-1.13.1 |
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17 | +CHIMERA_HEADLESS_HOME = %(EM_ROOT)s/chimera_headless |
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18 | +VMD_HOME = %(EM_ROOT)s/vmd |
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19 | + |
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20 | +[VARIABLES] |
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21 | +SCIPION_NOTES_PROGRAM = |
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22 | +SCIPION_NOTES_ARGS = |
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23 | +SCIPION_NOTES_FILE = notes.txt |
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24 | +SCIPION_NOTIFY = False |
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25 | +VIEWERS = {"Volume":["pyworkflow.em.viewers.viewers_data.DataViewer"]} |
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26 | +``` |
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27 | + |
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28 | +Open the file in your favourite editor, and add a line |
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29 | + |
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30 | +SCIPION_TESTS = ~/scipion/tests |
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31 | + |
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32 | +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. |
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33 | + |
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34 | +Your modified ~/.config/scipion/scipion.conf file should now look similar to this: |
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35 | +``` |
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36 | +[DIRS_LOCAL] |
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37 | +SCIPION_USER_DATA = ~/ScipionUserData |
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38 | +SCIPION_LOGS = %(SCIPION_USER_DATA)s/logs |
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39 | +SCIPION_TMP = %(SCIPION_USER_DATA)s/tmp |
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40 | +SCIPION_TESTS = ~/scipion/tests |
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41 | + |
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42 | +[PACKAGES] |
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43 | +EM_ROOT = software/em |
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44 | +XMIPP_HOME = %(EM_ROOT)s/xmipp |
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45 | +CHIMERA_HOME = %(EM_ROOT)s/chimera-1.13.1 |
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46 | +CHIMERA_HEADLESS_HOME = %(EM_ROOT)s/chimera_headless |
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47 | +VMD_HOME = %(EM_ROOT)s/vmd |
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48 | + |
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49 | +[VARIABLES] |
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50 | +SCIPION_NOTES_PROGRAM = |
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51 | +SCIPION_NOTES_ARGS = |
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52 | +SCIPION_NOTES_FILE = notes.txt |
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53 | +SCIPION_NOTIFY = False |
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54 | +VIEWERS = {"Volume":["pyworkflow.em.viewers.viewers_data.DataViewer"]} |
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55 | +``` |
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56 | + |
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57 | +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. |
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58 | + |