Dear Oliver and others,
an alternative way of installing system-wide third party software is
with a non-root account that is in the same group as all the users. Use
that account to install software centrally and initialize in each user's
.bashrc. (Root is used only for administrative tasks on the local
machines and installation of RPMs.) Users can use all the software but
have no permission to tinker with it and potentially screw it up.
Still, with this setup, there's a problem with ccp4 6.2.
ccp4-6.2.0/src/phaser/bin/machine_type needs to be made executable for
the group.
Andreas
On 19/07/2011 11:25, Weiergräber, Oliver H. wrote:
Hello,
version 6.2.0 of ccp4 has strange permissions set to several
setup/configuration scripts which are read while sourcing ccp4.setup.
For a long time, ccp4 packages have been distributed with some arbitrary file
and directory ownerships which users are obviously supposed to edit to meet
their needs. On unix/linux workstations, we usually install under /usr/local
and change all ownerships to root.root (default practice for third-party
software).
Up to now, this has not caused any problems.
In version 6.2.0, however, ccp4.setup has permissions rwx r-- --- which makes
it unreadable (and un-sourcable) for ordinary users! Strangely,
ccp4-others.setup has the usual permissions rwx r-x r-x (although rw- r-- r--
should be sufficient for sourcing).
After rectifying the permissions of ccp4.setup, additional errors appear,
concerning permissions of several scripts in the xia2 and phaser trees:
ccp4-6.2.0/share/xia2/setup.csh
ccp4-6.2.0/share/xia2/xia2core/setup.csh
ccp4-6.2.0/share/xia2/xia2/setup.csh
ccp4-6.2.0/src/phaser/bin/machine_type
ccp4-6.2.0/src/phaser/conf/version.csh
All these files have the same problematic permissions as ccp4.setup. After
fixing them, ccp4.setup can be sourced without errors.
The bad thing is that there may be many more issues of this kind, which will
only surface when trying to run a specific ccp4 program...
Maybe the developers or packagers could comment on this issue. It looks like
this ccp4 version is supposed to be installed in a user's home directory, so
that he/she can take ownership of all the files.
While in general there is nothing wrong with this type of installation, it
should _NOT_ be considered the default on unix-type (i.e. multi-user) operating
systems.
Best regards,
Oliver
================================================
PD Dr. Oliver H. Weiergräber
Institute of Complex Systems
ICS-6: Structural Biochemistry
Tel.: +49 2461 61-2028
Fax: +49 2461 61-1448
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Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher
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Andreas Förster, Research Associate
Paul Freemont & Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
http://www.msf.bio.ic.ac.uk
