Task #2723 (closed)
Opened 9 years ago
Closed 6 years ago
mage: EMAN2 + IMOD
| Reported by: | wmoore | Owned by: | wmoore |
|---|---|---|---|
| Priority: | minor | Milestone: | n.a. |
| Component: | General | Version: | 4.4.9 |
| Keywords: | n.a. | Cc: | cxallan |
| Resources: | n.a. | Referenced By: | n.a. |
| References: | n.a. | Remaining Time: | n.a. |
| Sprint: | n.a. |
Description (last modified by wmoore)
Install these on mage, so that they can be used by web-emdb scripts.
Need to edit EMAN2 so it doesn't fail on import.
IMOD:
http://bio3d.colorado.edu/imod/doc/guide.html#Installation
SPIDER:
http://www.wadsworth.org/spider_doc/spider/docs/spider-inst-linux.html
Change History (17)
comment:1 Changed 9 years ago by wmoore
- Status changed from new to assigned
comment:2 Changed 9 years ago by wmoore
comment:3 Changed 9 years ago by wmoore
- Cc cxallan added
- Description modified (diff)
Tried to install EMAN2 on mage as described. http://blake.bcm.edu/emanwiki/EMAN2/Install/BinaryInstall
But apparently you need to use the EMAN2 python interpreter (e.g. #!/home/gtang/EMAN2/python/Python-2.6.5-ucs4/bin/python ) and add that line to any script running EMAN2!
Doing $ python
from EMAN2 import *
gives me seg fault!
comment:4 Changed 9 years ago by wmoore
IMOD instructions... http://bio3d.colorado.edu/imod/doc/guide.html#InstallingLinuxSGI
Not sure what system mage is, or where to install /usr/local/ ?
comment:5 Changed 9 years ago by wmoore
comment:6 Changed 9 years ago by jburel
- Sprint changed from 2010-08-12 (14) to 2010-08-26 (15)
comment:7 Changed 9 years ago by wmoore
EMAN2 now also used for rendering projections, see r7866.
comment:8 Changed 9 years ago by wmoore
comment:9 Changed 9 years ago by wmoore
Scipy would handle some EMAN2 functionality (rendering numpy array as jpeg) but installing scipy requires root access to mage.
comment:10 Changed 9 years ago by wmoore
comment:11 Changed 9 years ago by wmoore
- Description modified (diff)
comment:12 Changed 9 years ago by wmoore
- Status changed from assigned to closed
comment:13 Changed 9 years ago by wmoore
- Status changed from closed to reopened
comment:14 Changed 9 years ago by jburel
- Sprint changed from 2010-08-26 (15) to 2010-09-09 (16)
comment:15 Changed 9 years ago by wmoore
- Milestone OMERO-Beta4.2.1 deleted
- Sprint 2010-09-09 (16) deleted
EMAN2 doesn't work for some commands. import OpenGL fails.
Made processing movie http://cvs.openmicroscopy.org.uk/snapshots/movies/omero-4-2/mov/EMDB-processing.mov on my laptop. Not sure how much of this functionality we want to expose for demo on mage anyway (kinda error-prone).
Pushing this ticket for now.
comment:16 Changed 6 years ago by jburel
Any reason to keep that ticket opened?
comment:17 Changed 6 years ago by wmoore
- Resolution set to wontfix
- Status changed from reopened to closed
- Version set to 4.4.9
No ;)
(In [7829]) EMAN2 import happens in 'main' thread (does not fail). See #2723