Upgrading SHARP/autoSHARP

From time to time we will announce upgrades (patch releases) to an existing SHARP/autoSHARP release (see release notes). Please follow the instructions very carefully.

Upgrading SUSHI 3.4.X to 3.8.0 (May 2009)
Upgrading SUSHI 3.2.X to 3.4.0 (Nov 9 2005)
Upgrading SUSHI 3.0.X to 3.2.0 (Nov 20 2004)
Upgrading SUSHI 3.0.X to 3.0.15 (Dec 20 2002)
Upgrading SUSHI 3.0.X to 3.0.14 (Nov 14 2002)
Upgrading SUSHI 3.0.0/3.0.1

Upgrading SUSHI 3.4.X to 3.8.0

It is not recommended to just upgrade your SUSHI 3.4.X to 3.8.0 - instead a fresh installation should be done, following the instructions here.

If you want to carry over some existing configurations, please check the Notes for users of old versions of SHARP.

Upgrading SUSHI 3.2.X to 3.4.0

The basic, underlying structure hasn't changed that much between 3.2.X and 3.4.0 - with two exceptions:

a new external program is being used (SHELXC/SHELXD for heavy atom detection in autoSHARP): this requires the correct configuration - using the administrative script $BDG_home/adm/bin/shelx-setup
the interface to the submission mechanism has been updated and slightly altered: if the administrator configured their own submission mechanims (rsh, DQS, LSF, etc), the local configuration in $BDG_home/submit.local needs to be updated
a new script for setting up connection to external helpers (like O, Xfit, Coot, Plotmtv etc) can simplify setting these up for the user. This is available in $BDG_home/bin/add2rdf.sh.

Therefore, the recommended upgrade procedure is the following:

get all new files from the download page into the SHARP/autoSHARP installation directory ($BDG_home).
if a local submission mechanism was configured: get the differences between the previously distributed mechanism and the locally configured ones:
```
% cd /where/ever/sharp
% diff -cr submit submit.local > submit.local.diff
  
```

unpack/install SHARP/autoSHARP:

% cd /where/ever/sharp
% ./installSHARP -u           # to just unpack new files
  - or -
% ./installSHARP -U           # to unpack new files and run through
                              # the whole configuration again (recommended)

update machine-specific configuration for each machine (i.e. each machine with its own subdirectory inside the $BDG_home/machines directory):
```
% cd /where/ever/sharp

% source ./setup.csh                                            # for csh/tcsh
% foreach m ( `find machines/ -type d | sed "s%machines/%%g"` )
    adm/bin/newmachine $m
  end

  - or -

% . ./setup.sh                                                  # for sh/bash/ksh
% for m in `find machines/ -type d | sed "s%machines/%%g"`
  do
    adm/bin/newmachine $m
  done
```
This will also check the machine-specific configurations for CCP4, ARP/wARP and MAPMAN (since these might have changed since the last installation). The relevant configuration files for .e.g CCP4 can always be found in $BDG_home/machines/*/ccp4.setup - but you should use the corresponding administrative scripts (e.g. $BDG_home/adm/bin/ccp4-setup) to update these if necessary!

let every user re-run the script useSHARP:

% /where/ever/sharp/useSHARP <SHARP account>

update your submission system: if you configured your own submission system (in $BDG_home/submit.local) you might need to adapt the files in $BDG_home/submit.local to follow the new format/requirements in $BDG_home/submit.
It is highly recommended to use the checkBDG.sh script afterwards to test the new installation/upgrade (and try to follow the recommendations it might give):
```
% cd /where/ever/sharp

% source ./setup.csh          # for csh/tcsh
  - or -
% . ./setup.sh                # for sh/bash/ksh

% adm/bin/checkBDG.sh
```

Upgrading SUSHI 3.0.X to 3.2.0

Since a lot of changes have occured between 3.0.15 and 3.2.0, you might want to do a fresh installation (following the installation instructions at the SHARP/autoSHARP installation pages.

It is also possible to upgrade your existing installation (which might be easier if you have a lot of users and machines or configured your own submission system). This can be done using

get all new files from the download page and unpack/install SHARP/autoSHARP:

% cd /where/ever/sharp
% ./installSHARP -u           # to just unpack new files
  - or -
% ./installSHARP -U           # to unpack new files and run through
                              # the whole configuration again

update machine-specific configuration for each machine (i.e. each machine with its own subdirectory inside the $BDG_home/machines directory):
```
% cd /where/ever/sharp

% source ./setup.csh                                            # for csh/tcsh
% foreach m ( `find machines/ -type d | sed "s%machines/%%g"` )
    adm/bin/newmachine $m
  end

  - or -

% . ./setup.sh                                                  # for sh/bash/ksh
% for m in `find machines/ -type d | sed "s%machines/%%g"`
  do
    adm/bin/newmachine $m
  done
```
This will also check the machine-specific configurations for CCP4, ARP/wARP and MAPMAN (since these might have changed since the last installation). The relevant configuration files for .e.g CCP4 can always be found in $BDG_home/machines/*/ccp4.setup - but you should use the corresponding administrative scripts (e.g. $BDG_home/adm/bin/ccp4-setup) to update these if necessary!
update your submission system: if you configured your own submission system (in $BDG_home/submit.local) you will need to adapt the files in $BDG_home/submit.local to follow the new format/requirements in $BDG_home/submit (since the various scripts for e.g. dqs, lsf, rsh etc have changed).
It is highly recommended to use the checkBDG.sh script afterwards to test the new installation/upgrade (and try to follow the recommendations it might give):
```
% cd /where/ever/sharp

% source ./setup.csh          # for csh/tcsh
  - or -
% . ./setup.sh                # for sh/bash/ksh

% adm/bin/checkBDG.sh
```

Upgrading SUSHI 3.0.X to 3.0.15

If you're running SUSHI 3.0.X and want to upgrade to the latest SUSHI 3.0.15:

download all necessary new files into your current $BDG_home directory (i.e. where you installed SHARP/autoSHARP in - it should contain a .licence and .bdgrc file). The files you need are usually
- architecture independent files: installSHARP, sushi.tar.gz, sharp_tutorials.tar.gz
- architecture dependent file(s): sharp.linux.tar.gz and/or sharp.irixn32.tar.gz and/or sharp.alpha.tar.gz

run the update procedure (see also the Sushi 3.0.15 Release notes on the download page)

      % cd $BDG_home
      % chmod +x installSHARP
      % ./installSHARP -U

that should be it
if you have trouble: please have a look at notes

Upgrading SUSHI 3.0.X to 3.0.14

If you're running SUSHI 3.0.X and want to upgrade to the latest SUSHI 3.0.14:

download all necessary new files into your current $BDG_home directory (i.e. where you installed SHARP/autoSHARP in - it should contain a .licence and .bdgrc file). The files you need are usually
- architecture independent files: installSHARP, sushi.tar.gz, sharp_tutorials.tar.gz
- architecture dependent file(s): sharp.linux.tar.gz and/or sharp.irixn32.tar.gz and/or sharp.alpha.tar.gz

run the update procedure (see also the Sushi 3.0.14 Release notes on the download page)

      % cd $BDG_home
      % chmod +x installSHARP
      % ./installSHARP -u

that should be it
if you have trouble: please have a look at notes

Upgrading SUSHI 3.0.0/3.0.1

If you're running SUSHI 3.0.0 or 3.0.1 you should upgrade to the latest bug fix release. You can find your SUSHI version at the top of the "SHARP Control Panel" or in the file $BDG_home/sushi/.version.

Note : this procedure will overwrite any changes that you've done in directory $BDG_home/submit. If you've followed the recommendations in the "BDG Installation manual" (Chapter 5 : Submission mechanisms and queuing systems) you will have all your local configuration in directory $BDG_home/submit.local and nothing will get overwritten.

Here are the steps that should get your SUSHI version up-to-date

Download the latest versions of the following files to your existing SHARP/autoSHARP installation directory ($BDG_home):
```
      installSHARP
      sushi.tar.gz
      sharp_tutorials.tar.gz
      
```
Note : you can of course also download additional files (but these are the necessary ones).
Then run the following commands:
```
      % adm/bin/kill_server
      % chmod +x installSHARP
      % ./installSHARP -f
      
```
When asked about "Copy configuration from previous SHARP installation" you should answer "no".
The sample files contain two new SHARP input files (samples/sharp/cardfiles/IF3-C.1.sin and samples/sharp/cardfiles/KrEl.1.sin) that users might want to fetch.

Last modified: 20.07.2009