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Bug #1555

closed

appionLoop2 has its own setupRunDir

Added by Anchi Cheng almost 13 years ago. Updated over 12 years ago.

Status:
Closed
Priority:
Normal
Assignee:
Dmitry Lyumkis
Category:
-
Target version:
Appion/Leginon 2.2.0
Start date:
02/16/2012
Due date:
% Done:

0%

Estimated time:
Affected Version:
Appion/Leginon 2.2.0 (trunk)
Show in known bugs:
No
Workaround:

Description

This should have been removed when r15208 was committed for issue #1098.

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 #1

Updated by Anchi Cheng almost 13 years ago

r16333 corrects this in appionLoop2.py
r16334 corrects this in appionTiltSeriesLoop.py

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 #2

Updated by Anchi Cheng almost 13 years ago

  • Status changed from Assigned to In Code Review
  • Assignee changed from Anchi Cheng to Dmitry Lyumkis

Testing:

1. Run any appionLoop python comment on terminal on a session which leginon images are not on /ami/data00, 2. remove --rundir option to check if the rundir print out at the end of script running come out on /ami/data00.

My example script was:

alignDefocalPairs.py --description="test" --projectid=333 --preset=gr --runname=test1 --no-rejects --no-wait --no-commit --limit=2 --no-continue --expId=9488 --jobtype=test

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 #3

Updated by Dmitry Lyumkis over 12 years ago

works for me.

My leginon directory is in /ami/data15. I removed --rundir option:

/home/dlyumkis/myami/appion/bin/appion makestack2.py --single=start.hed --selectionid=80 --invert --normalized --xmipp-normalize=4.5 --phaseflip --flip-type=ace2image --boxsize=256 --bin=2 --description="test" --projectid=224 --preset=en --session=11sep24a --runname=stack12 --no-rejects --no-wait --no-commit --limit=1 --continue --expId=9060 --jobtype=makestack2

and the stack was created in /ami/data15/appion/11sep24a/makestack2/stack12

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 #4

Updated by Dmitry Lyumkis over 12 years ago

  • Status changed from In Code Review to Closed
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