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Missing s_prehip

Added by James Stroud over 9 years ago

I am trying to run prehip usign the runHIP web page.

Upon executing the command provided by "Just Show Command", the script fails complaining about the unavailability of the program s_prehip. I verified by inspecting the python source that this is indeed the missing program.

     apDisplay.printMsg("now running s_prehip to set up input files")
     apDisplay.printMsg("Make sure the layer line/bessel order assignment is correct. If it is not, you may need to adjust    some of the input variables.")
     cmd = "s_prehip" 
     proc = subprocess.Popen(cmd)
     proc.wait()

The program fails at the line "proc = subprocess.Popen(cmd)":

Traceback (most recent call last):
  File "/usr/local/bin/appion/HIP.py", line 597, in <module>
    hip.start()
  File "/usr/local/bin/appion/HIP.py", line 577, in start
    proc = subprocess.Popen(cmd)
  File "/usr/lib/python2.7/subprocess.py", line 710, in __init__
    errread, errwrite)
  File "/usr/lib/python2.7/subprocess.py", line 1327, in _execute_child
    raise child_exception
OSError: [Errno 2] No such file or directory

How can the s_prehip program be installed so that appion may use it?

I also have a similar situation with the missing program s_finealign.

Thank you!


Replies (4)

RE: Missing s_prehip - Added by Anchi Cheng over 9 years ago

Hi, James,

s_prehip and s_finealign are Phoelix commands. Unfortunately, there is no place to download this any more. It will take considerable effort to update and distribute it again. I discussed it with others yesterday and the decision is for us to retire all references to it.

One recommendation is to use the package developed by Carsten Sachse at the EMBL
http://www.sachse.embl.de/emspring/

I am sorry that you went through all the trouble installing Appion just to find out you can't use this.

Anchi

RE: Missing s_prehip - Added by James Stroud over 9 years ago

So to be clear, the recommendation is to not use Appion for helical reconstruction but to use Emspring instead?

Will support for Emspring be built into Appion in the future?

RE: Missing s_prehip - Added by Anchi Cheng over 9 years ago

To the first question: Yes

To the second: I do not know. Appion is driven by the projects we (those involved in the development) encounter. I am not aware of any helical projects that must use such approach now. Therefore, the chance for this to happen in short time frame is low.

RE: Missing s_prehip - Added by Anchi Cheng over 9 years ago

Another suggestion from Gabe Lander

http://grigoriefflab.janelia.org/frealix

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