Appion

h1. Program/module call alias name in Appion (myami-3.3, myami-beta branches, and trunk)

Appion scripts interact with external packages in one of the two ways: Executing a shell command, or through python call.  The name of the file in the call may not be the same as the standard installation as described by the package distributor.

If it is accessed from shell, you should either create soft link (preferred) or rename the file you downloaded (not best practice since you may get confused later. Test its accessibility from the environment you would run appion script.

For example, ctffin4 of whatever version would typically installed in /usr/local/bin.  The executable file in there is called ctffind4.exe.  You should do

<pre>

cd /usr/local/bin

ln -s ctffind64.exe ctffind4

</pre>

Next time, when you start a shell, try:

<pre>

which ctffind4

</pre>

It should be able to find the link and the actual executable file.ctffind64.exe

For files called through python, the file need to be in the environment variable PYTHONPATH  You can test it in the appion environment with an import test.

<pre>

python

python> import deProcessFrames

</pre>

Those not mentioned here uses the original names in the call.

|program package name|version|appion executable alias|Accessible|

|MotionCor2|10-19-2016|motioncor2|shell|

|motioncorr v2.0 from Purdue|2.0|dosefgpu_driftcorr|shell|

|DE_process_frames.py|2.7.1|deProcessFrames.py|pythonpath|

|ctffind4|4.1.5|ctffind4|shell|

|Gctf|1.06|gctfCurrent|shell|

|ctftilt|1.5|ctftilt.exe|shell|

|FindEM|20/10/01|findem64.exe|shell|

|Gautomatch|0.53|gautomatch|shell|

|Spider|18.10|spider|shell|

|frealign|9.11|frealign_v9.exe and frealign_v9_mp.exe|shell|

|xmipp2 cl2d*|2.4|xmipp_mpi_class_averages|shell|

|xmipp3 cl2d*|3.1|xmipp_classify_CL2D|shell|

|EMAN1 proc2d|1.9|proc2d|shell|

* default environment is xmipp2.  All other xmipp functions wraps around xmipp2.

* xmipp3 conflict with xmipp2 is resolved in appion/bin/runXmipp3CL2D.py with a line of code

<pre>

csh -c 'modulecmd python load xmipp/3.1'

</pre>

Change it if desired.