On Thu, Jun 10, 2021 at 08:19:01AM -0700, James Holton wrote:
> I'm afraid the only bash command I know is: "tcsh"
I'm using the exact opposite direction ;-)
<begin_geeky_sidetrack>
To everyone using "echo" (interactively and/or in scripts): be careful
which command is picked up at any given point. There are shell
built-in versions of "echo" and then there is /bin/echo. Some
recognize "\n" and some don't. Some support "-e" flag and some
don't. A better command might be
printf "THREshold RMS 5.0\n" | peakmax MAPIN "myfile.ccp4" XYZOUT
"myfiles_omit_atom.pdb"
or (if no cards are to be used)
peakmax MAPIN "myfile.ccp4" XYZOUT "myfiles_omit_atom.pdb" < /dev/null
or
printf "\n" | peakmax MAPIN "myfile.ccp4" XYZOUT "myfiles_omit_atom.pdb"
(not all CCP4 programs support the "END" card").
If you want to write instantly portable scripts, it might be best to
have "#!/bin/sh": not all systems will have /bin/bash, /bin/csh or
/bin/tcsh installed. Of course, /bin/sh might point to /bin/bash, but
it could also point to /bin/dash (another variant) ... or something
else entirely (MacOS is known to replace "standard" Linux/UNIX
commands from time to time, often going from GNU versions to BSD based
ones - or something else again). With /bin/sh you /should/ be within a
POSIX sh environment: maybe more limited to other shells, but
standardized and therefore much more portable since every UNIX-like
system so far will always have /bin/sh available.
<end_geeky_sidetrack>
Cheers
Clemens
*--------------------------------------------------------------
* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
* Global Phasing Ltd., Sheraton House, Castle Park
* Cambridge CB3 0AX, UK www.globalphasing.com
*--------------------------------------------------------------
########################################################################
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/
