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SPHIRE (SPARX for High-Resolution Electron Microscopy) is an open-source, user-friendly software suite for the semi-automated processing of single particle electron cryo-microscopy (cryo-EM) data. It allows fast and reproducible structure determination from cryo-EM images.

References:

• T.Moriya, M.Saur, M.Stabrin, F.Merino, H.Voicu, Z.Huang, P.A.Penczek, S.Raunser, C.Gatsogiannis
  High-resolution Single Particle Analysis from Electron Cryo-microscopy Images Using SPHIRE
  J. Vis Exp., 2017, 123(21), p.55448; doi:10.3791/55448.

• SPHIRE Wiki page

• Module Name: SPHIRE (see the modules page for more information)
• Unusual environment variables set
  • SPHIRE_HOME  installation directory
  • SPHIRE_BIN       executable directory
  • SPHIRE_TEST  test scripts

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive --mem=16g --gres=gpu:v100:1
[user@@cn4471 ~]$ module load SPHIRE
[+] Loading SPHIRE  1.1

Run basic commands for the spire executable:

[user@cn4471 SPHIRE]sphire -h
Usage: sphire 
	The main SPHIRE GUI application. It is designed as the command generator for the SPHIRE single particle analysis pipeline.

Options:
  --version   show program's version number and exit
  -h, --help  show this help message and exit

[user@cn4471 SPHIRE]sphire
Python 2.7.14 | packaged by conda-forge | (default, Dec  9 2017, 16:18:43) 
Type "copyright", "credits" or "license" for more information.

IPython 5.8.0 -- An enhanced Interactive Python.
?         -> Introduction and overview of IPython's features.
%quickref -> Quick reference.
help      -> Python's own help system.
object?   -> Details about 'object', use 'object??' for extra details.
Welcome to the interactive SPARX-NoGUI Python interface, provided by ipython
   SPARX v4.0 (GITHUB: 2018-08-20 20:32)

 In [1]: import mpi

 In [2]: Util.version() 
   Source modification date: August 2018 release 

In [3]: quit 
[user@cn4471 SPHIRE]$ e2version.py 
EMAN 2.22 final (GITHUB: 2018-08-20 20:32 - commit: f4f3952 )
Your EMAN2 is running on: Linux-3.10.0-862.14.4.el7.x86_64-x86_64-with-centos-7.5.1804-Core 3.10.0-862.14.4.el7.x86_64
Your Python version is: 2.7.14

Copy test scripts to your current folder:

[user@@cn4471 ~]$ cp -r $SPHIRE_TEST/* .

Run a test:

[user@@cn4471 ~]$ ./test_cmp.py 
test_DotCmp (__main__.TestCmp)
test DotCmp ...................................... ... ok
test_FRCCmp (__main__.TestCmp)
test FRCCmp ...................................... ... ok
test_OptVarianceCmp (__main__.TestCmp)
test OptVarianceCmp .............................. ... ok
test_PhaseCmp (__main__.TestCmp)
test PhaseCmp .................................... ... ok
test_QuadMinDotCmp (__main__.TestCmp)
test QuadMinDotCmp ............................... ... ok
test_SqEuclideanCmp (__main__.TestCmp)
test SqEuclideanCmp .............................. ... ok
test_basic_cmp (__main__.TestCmp)
test basic cmp ................................... ... ok
test_variance (__main__.TestCmp)
test variance .................................... ... ok

----------------------------------------------------------------------
Ran 8 tests in 0.041s

OK
[user@cn4471 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$