Tim & Eugene node066:/software/CCP4-6.3.0/ccp4-6.3.0/bin-58> which ccp4um ./ccp4um
node066:/software/CCP4-6.3.0/ccp4-6.3.0/bin-59> cd node066:~-60> which ccp4um ccp4um: Command not found. node066:~-61> echo $PATH /software/virtualenv/python2.7/64/cluster/bin: ... :/software/CCP4-6.3.0/ccp4-6.3.0/share/dbccp4i/bin:/software/CCP4-6.3.0/ccp4-6.3.0/share/ccp4i/bin:/software/CCP4-6.3.0/ccp4-6.3.0/bin:/software/CCP4-6.3.0/ccp4-6.3.0/etc:/software/compilers/linux/intel_v11.7.256/composer_xe_2011_sp1.7.256/bin/ia32:/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/usr/X11R6/bin:/software/CCP4-6.3.0/ccp4-6.3.0/share/xia2/xia2core/Test:/software/CCP4-6.3.0/ccp4-6.3.0/share/xia2/xia2/Applications # CBIN is in the path, so we need to rehash after the update: node066:~-62> rehash <<<<<<<<<<<<<<<<<< node066:~-63> which ccp4um /software/CCP4-6.3.0/ccp4-6.3.0/bin/ccp4um node066:~-64> ccp4um WORKS! So I just needed to rehash the PATH after the last update (or I could have logged out & in). Thanks to Tim & Eugene for suggestions. Cheers -- Ian On 17 January 2013 13:25, Tim Gruene <t...@shelx.uni-ac.gwdg.de> wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > Dear Ian, > > I am not sure, but maybe the error is caused by $PWD being part of > your path variable so that when you call 'ccp4um' while your cwd is > /software/CCP4-6.3.0/ccp4-6.3.0/bin, python make 'sys.argv[0]' (line > 10 in $CBIN/ccp4um) "./ccp4um". This would result in the error you > receive. > > Can you type 'which ccp4um' while being in > /software/CCP4-6.3.0/ccp4-6.3.0/bin and while being in some other > directory (e.g. $HOME)? > > Does the error occur if you call 'ccp4um' from e.g. $HOME? > > Tim > > On 01/17/2013 01:44 PM, Ian Tickle wrote: > > Dear Eugene > > > > ccp4um doesn't work for me at all (update worked fine up until > > #012). > > > > node066:/software/CCP4-6.3.0/ccp4-6.3.0/bin-45> ccp4um Traceback > > (most recent call last): File "ccp4um", line 17, in <module> > > shutil.copy2 ( fname,fname1 ) File > > "/software/python/python_v2.7.3_64/lib/python2.7/shutil.py", line > > 128, in copy2 copyfile(src, dst) File > > "/software/python/python_v2.7.3_64/lib/python2.7/shutil.py", line > > 82, in copyfile with open(src, 'rb') as fsrc: IOError: [Errno 2] No > > such file or directory: '/libexec/ccp4um' > > > > Did I do something wrong? Or is it just that there's nothing to > > update? > > > > Cheers > > > > -- Ian > > > > > > On 16 January 2013 15:11, <eugene.krissi...@stfc.ac.uk> wrote: > > > >> Dear Andreas, > >> > >> Sorry for late response to your post and confusion with the > >> updater. For technical reasons (Windows does not like names > >> containing "update" :)), the updater was renamed into ccp4um > >> (ccp4 update manager) and is found in $CCP4/bin. > >> > >> I hope this helps, > >> > >> Eugene > >> > >> > >> Dear CCP4 maintainers, > >> > >> I've come to appreciate the CCP4 update functionality, which, in > >> our multiuser network (RHEL 6.2), I used to invoke by calling > >> $CCP4/bin/update. > >> > >> Update 012 removed that script with no immediately obvious > >> replacement. Was that on purpose? Is there a way of updating > >> CCP4 from the command line without calling CCP4i? > >> > >> Thanks > >> > >> > >> Andreas > >> > >> > >> (from update.log: > >> > >> [Thu Jan 3 2013 11:00:21] Ready to make changes > >> > >> --- applying update 6.3.0-012 --- update header read --- creating > >> restore package, please wait ... --- done ... file > >> '/csb/soft/Linux64/share/ccp4-6.3.0/bin/update' removed ... file > >> '/csb/soft/Linux64/share/ccp4-6.3.0/lib_exec/update' removed ... > >> file '/csb/soft/Linux64/share/ccp4-6.3.0/lib_exec/_update' > >> removed ... directory > >> '/csb/soft/Linux64/share/ccp4-6.3.0/lib_exec' removed > >> > >> > >> some more blah blah) > >> > >> > >> -- Andreas Förster, Research Associate Paul Freemont & Xiaodong > >> Zhang Labs Department of Biochemistry, Imperial College London > >> > >> -- Scanned by iCritical. > >> > >> > > > > - -- > - -- > Dr Tim Gruene > Institut fuer anorganische Chemie > Tammannstr. 4 > D-37077 Goettingen > > GPG Key ID = A46BEE1A > > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.12 (GNU/Linux) > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ > > iD8DBQFQ9/vYUxlJ7aRr7hoRAqXlAJ9qkk3BBNTT6P8eR1HxP6ODEz2GfACgkkvR > hUlISdYdsr1v5dryb76tNLg= > =kESK > -----END PGP SIGNATURE----- >
