Dear Stefan,
On 10/10/2018 14:27, Dr. Stefan Harfst wrote:
Dear EasyBuilders,
the easyconfig for AUGUSTUS includes a setting for the
AUGUSTUS_CONFIG_PATH which is located in the installation directory.
However, it seems that workflows using AUGUSTUS frequently require write
permission on this path. We solved this now (after a manual fix to the
module file) by adding the modluafooter below to the eb-file. It is not
pretty but it seems to do the trick.
I am just wondering if this is abusing the footer too much (i.e. can it
lead to unexpected side-effects) and if there is a better way dealing
with this problem?
I'd say this is a bit much to shove into modluafooter (especially with
the auto-copying to the home directory), but on the other hand it's your
call.
My approach would be to somehow document that people need to copy the
contents of where $AUGUSTUS_CONFIG_PATH points to, and then redefine
$AUGUSTUS_CONFIG_PATH after loading the module.
That's expecting more from the user though, of course.
A cleaner solution would be a fix in AUGUSTUS: if it doesn't have write
permissions, it should fall back to writing to a location like
$HOME/.config/AUGUSTUS or something like that, while providing an option
to specify a different location, perhaps via $AUGUSTUS_USER_CONFIG_PATH?
regards,
Kenneth
Best wishes
Stefan
#modextravars = {'AUGUSTUS_CONFIG_PATH': '%(installdir)s/config'}
modluafooter = (
'local global_config = "%(installdir)s/config"\n'
'local local_config = pathJoin(os.getenv("HOME"), "augustus_config")\n\n'
'setenv("AUGUSTUS_CONFIG_PATH", local_config)\n\n'
'if mode() == "load" then\n'
' if (isDir(local_config)) then\n'
' LmodMessage("setting AUGUSTUS_CONFIG_PATH to " .. local_config)\n'
' else\n'
' LmodMessage("creating a copy of EBROOTAUGUSTUS/config in your
$HOME and ")\n'
' execute {cmd="cp -r " .. global_config .. " " .. local_config,
modeA={"load"}}\n'
' LmodMessage("setting AUGUSTUS_CONFIG_PATH to " .. local_config)\n'
' end\n'
'end\n'
)
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