Hi Kay, I did find /Applications/ccp4-8.0/Frameworks/Python.framework/Versions/3.7/lib/site-packages/ccp4i2/bin/i2run on my Mac, and was able to use that to successfully bring up the import_merged help documentation, so I think that's working - thanks!
For general reference, thanks to an individual reply I got: Evidently i2run is located in 7.0/7.1 installations at ccp4-7.1/share/ccp4i2/bin/i2run (and I was able to produce the same import_merged help documentation via that approach as well). Thanks! Maggie On Mon, Feb 19, 2024 at 3:37 AM Kay Diederichs < [email protected]> wrote: > 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 < > [email protected]> 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/[email protected]/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 > > > >######################################################################## > > > >To unsubscribe from the CCP4BB list, click the following link: > >https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > > >This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are > available at https://www.jiscmail.ac.uk/policyandsecurity/ > > > > > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
