Monday, June 26, 2006

what to do if an update fails

ccp analysis has a very nice update feature. However, if it fails you can get in a state where you can't start analysis to get the updates. So here are two simple cures (one is from Tim and uses a python interface, the second is just how to get to the update site with a web browser to pull down raw files).

To run the update agent without analysis running

  1. initialise you analysis environment so the ccpn root directory is set e.g. setenv
    CCPN_HOME ... in csh syntax or export CCPN_HOME='...' in sh syntax
  2. if need be setup you pythonpath to include the ccpn directories
  3. python $CCPN_HOME/python/ccpnmr/update/ and proceed as usual

to use a web browser...

  2. this directory will contain files of the form where would be Util for for example
  3. download save and install

Monday, June 12, 2006

analysis on dapper drake & Edgy Eft

Installing analysis on ubuntu dapper drake (ubuntu 6.06LTS) is not a clean affair for various murky reasons (none of which are to do with the ccpn chaps by the way just life and code rot).

So here goes


  1. you need gcc and g++ installed (packages gcc and g++-4.0)
  2. you need glut installed (packages freeglut3, freeglut3-dev)
  3. you need the x development headers and extension installed (packages libext6 and libxext-dev libx11-dev; more on this later)
  4. you must have build-essential installed if you want to compile your own python

  1. don't try to use the installation of tcl/tk that comee from ubuntu they don't play well with the ccpn installation script (tcl/tk lib and include are not both under the same directory)
  2. don't use the tcl/tk 8.3 files that come with ccpnmr 1.0.10 tas hey have configure scripts that are broken under the latest versions of bash
  3. get tcl8.4.13-src.tar.gz and tk8.4.13-src.tar.gz
  4. mkdir tk8.4 and tcl8.4 in ccpnmr1.0
  5. place thetcl/tk tar files in their respective directories
  6. gunzip them
  7. remove the -src part of the name e.g. tk8.4.13-src.tar.gz -> tk8.4.13.tar.gz
now edit the installation script
  1. line 27 tcltk_version = '8.4' #was tcltk_version = '8.3'
  2. line 28 tcltk_release = '8.4.13' #was tcltk_release = '8.3...'
fiddle with the X extension libraries

  1. /usr/lib/ doesn't exists
  2. so become root
  3. ln -s
setup the environment variables changing tcl /tk 8.3 to 8.4

  1. setenv LD_LIBRARY_PATH\ ${CCPNMR_TOP_DIR}/tcl8.4/lib:${CCPNMR_TOP_DIR}/tk8.4/lib
  2. setenv TCL_LIBRARY {$CCPNMR_TOP_DIR}/tcl8.4/lib/tcl8.4
  3. setenv TK_LIBRARY {$CCPNMR_TOP_DIR}/tk8.4/lib/tk8.4

carry out your normal installation using

all done and here is the proof (and no I didn't fake it in photoshop ;-))

  1. all paths entered have to be absolute
  2. the X11 directory is /usr