Hi Maggie,
I have CCP4 version 8.0 on my Mac and it does have the file
/Applications/ccp4-8.0/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/ccp4i2/bin/i2run
If I run it without arguments, it says
CCP4 /Applications/ccp4-8.0
ccp4i2 version 1.1.0
ccp4i2 source revision 6539
Failed with exception list index out of range
Traceback (most recent call last):
File
"/Applications/ccp4-8.0/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/ccp4i2/core/CCP4I2Runner.py",
line 721, in <module>
theRunner = CI2Runner(sys.argv)
File
"/Applications/ccp4-8.0/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/ccp4i2/core/CCP4I2Runner.py",
line 34, in __init__
self.add_arguments(theParser, cmdLineArgs)
File
"/Applications/ccp4-8.0/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/ccp4i2/core/CCP4I2Runner.py",
line 381, in add_arguments
taskName = cmdLineArgs[1]
IndexError: list index out of range
so it seems to work in principle. However, the directory where i2run lives is
not in the $PATH so one might want to
sudo ln -s
/Applications/ccp4-8.0/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/ccp4i2/bin/i2run
/Applications/ccp4-8.0/bin
in order to run it with just "i2run".
There is documentation in
/Applications/ccp4-8.0/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/ccp4i2/docs/sphinx/build/html/_sources/i2run/i2run.rst.txt
Hope this helps,
Kay
On Sat, 17 Feb 2024 19:21:21 -0500, Klureza, Maggie <mklur...@g.harvard.edu>
wrote:
>Hi all,
>
>I would very much like to make use of i2run's capacity for scripting,
>rather than pressing the same sequence of GUI buttons a few dozen times,
>but I'm having trouble actually calling it.
>
>The documentation <https://ccp4i2.gitlab.io/rstdocs/i2run/i2run.html> I
>found gives example code snippets structured as "i2run [function]
>[options]", but even immediately after sourcing ccp4, entering e.g. "i2run
>import_merged --help" returns an error saying "bash: i2run: command not
>found".
>
>I found only one reference to i2run on the ccp4bb archive
><https://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg56079.html>
>(actually from just 2 days ago!), which included a script that called i2run
>using the full path of
>"/ccp4-8.0/lib/python3.7/site-packages/ccp4i2/bin/i2run crank2". However, I
>was not able to find any equivalent path in either of the 2 ccp4
>installations I have access to.
>
>Ideally I'd like to use our lab's installation of ccp4 on our university
>computational cluster, which is currently ccp4-7.1. Attempting to follow
>the analogous path took me to "ccp4-7.1/lib/python2.7/site-packages", which
>did not contain a ccp4i2 directory. I'm wondering if perhaps i2run wasn't
>introduced until ccp4-8.0, and we would need an updated installation?
>Except, I also have ccp4 downloaded on my laptop (a Mac, if that's
>relevant), and going to "ccp4-8.0/lib/python3.7/site-packages" there still
>did not produce a ccp4i2 directory.
>
>Therefore, I'm wondering: Does ccp4-7.1 contain i2run, or would I need to
>update to 8.0 no matter what? And, almost regardless of the answer to that
>first question: What is the proper way to call i2run/where does it live
>within a ccp4 installation? I've been searching through the online
>documentation, but all the information I could find seemed to assume that
>i2run was readily accessible given the existence of a ccp4 installation, so
>I'm a bit stumped.
>
>Many thanks,
>Maggie
>
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