Appion

1. XMIPP not installed

--- Error installing Xmipp. Could not locate and parse the path to libmpi.so

2. ace2image ctf phase flipping does not work.

makestack2.py --single=start.hed --selectionid=1 --invert --phaseflip --flip-type=ace2image --boxsize=240 --bin=2 --description="test installation" --projectid=1 --preset=upload --session=sample --runname=stack1 --rundir=/myamiImages/appion/sample/stacks/stack1 --no-rejects --no-wait --commit --continue --expId=4 --jobtype=makestack2

  File "/usr/bin/makestack2.py", line 623, in phaseFlipAceTwo
    apDisplay.printError("ACE 2 failed to create image file:\n%s" % outfile)
  File "/usr/lib/python2.6/site-packages/appionlib/apDisplay.py", line 57, in printError
    raise Exception, colorString("\n *** FATAL ERROR ***\n"+text+"\n\a","red")
Exception: 
 *** FATAL ERROR ***
ACE 2 failed to create image file:
/myamiImages/appion/sample/stacks/stack1/sample_06jul12a_00015gr_00028sq_00004hl_00002en.mrc.corrected.mrc

3. redux does not give png image right scale
http://localhost/myamiweb/processing/loadimg.php?filename=/myamiImages/appion/sample/stacks/stack3/montage3.png
imageinfo.amin and imageinfo.amax are null.

4. some eman phase flip stack image look scrambled.

makestack2.py --single=start.hed --selectionid=1 --invert --normalized --phaseflip --flip-type=emanimage --boxsize=240 --bin=2 --description="teset stack making with eman ctf correction since ace2 failed" --projectid=1 --preset=upload --session=sample --runname=stack2 --rundir=/myamiImages/appion/sample/stacks/stack2 --no-rejects --no-wait --commit --continue --expId=4 --jobtype=makestack2

5. NOT A BUG: spider ReferenceFree Alignment/Coran Analysis and /Clustering worked well.

6. uploadtemplate wants to open new tab from stack viewing page.

7. findem.exe:
/usr/bin/findem64.exe: error while loading shared libraries: libgfortran.so.1: cannot o
pen shared object file: No such file or directory

item 2 is resolved. See #1525
item 3 is resolved. The particular image is a 16-bit png. Jim changed redux in r16243 that solved the problem.
item 4 is resolved. See #1524
item 5 nothing to do.
item 7 is resolved. See #1516

Can we close this out Anchi?

I won't. This is meant to the parent issue for all the other issue related to this. And should be closed when a true denovo 3.0 installation is successfully made free of these problems.