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Re: Someone prepared to package GAMGI (molecular visualisation and editing)



Steffen Moeller wrote:

Hi Carlos,

I admit I feel too pressed with time to bring the package forward too
much myself. I'll follow through your tutorial but presume that GAMGI is
too far from what I would want to use from a molecular modelling GUI.
you are probably right, if you are doing biologic studies. For example GAMGI cannot currently read PDB format. Anyway if you tell me more about your needs I might be able to help,

Nevertheless I am confident that the skeleton of a package that I have
provided is sufficiently useful for others to complete the work.
After the compilation, the executable "gamgi" should be running just
fine. However, to use all the resources, the following two environment
variables should be set:

1) GAMGI_HELP

GAMGI_HELP=~/gamgi/gamgi/doc; export GAMGI_HELP

To test that this is working fine,  just launch GAMGI and select (in
the top main menu) for example Text->Create (a dialog pops up), then
select Help->Current (a Help dialog pops up, explaining the parameters
in the Text->Create dialog). If the environment variable is not set,
Help files cannot be found and an error message is produced when
Help->Current (or other Help option) is selected. In that case the
only Help that works is Help->Start, which is hard-coded in GAMGI
source code (so no matter what, users have at least some basic Help
guidelines).
Amazingly, yesterday the help files have been found even without this
variable been set. I just tested it  again and they do not work, so I
possibly had executed gamgi in the the source root and that is why it
was found :) I should patch GAMGI to make it look for the help where it
usually is installed under Debian. I prepared a separate -doc package
for them.
2) GAMGI_TEXT

to indicate where are the TrueType fonts distributed with GAMGI. For
example, adding a line as this to the ".bashrc" file (pointing to the
fonts/ directory):

GAMGI_TEXT=~/gamgi/gamgi/src/io/fonts; export GAMGI_TEXT

These are the 10 Bitstream Vera fonts comissioned by the Gnome
project, that can be freely distributed. The fonts/ directory also
include the Bitstream license file. I am almost sure these 10 files
are probably on any Linux distribution these days, but the only safe
way to guarantee that indeed we find them is to distribute them with
GAMGI.
Well, the Debian folks think that
/usr/share/fonts/truetype/ttf-bitstream-vera should be used since it is
there in package ttf-bitstream-vera. It should not be distributed with
your sources. Actually, for the inclusion of GAMGI with Debian the
redundancy should probably be removed from your source distribution. It
works with the Debian-distributed fonts, btw.

I totally agree that Debian should not carry two versions of the same files.

The solution is just the Debian developer, after grabbing the tarball, 1) remove the Gamgi directory src/io/fonts/. 2) add a new dependency, the Debian package ttf-bitstream-vera. 3) set GAMGI_TEXT to /usr/share/fonts/truetype/ttf-bitstream-vera

If I remove this directory myself from the general distribution, non-Debain users will have a hard time finding these fonts...

A man page should list these variables and explain them. I have not
found any such man page with your sources . There is none, is there?
No, current documentation is all in html format, except the INSTALL file.

I
had extended the skeleton for a man page that Debian provides just a
bit, but more work needs to be done on it.

Thanks, I will improve the man page

So, we have Debian packages now that are just not sufficiently neat to
make it into the distribution and I really cannot spare the time to work
on these. It should not be overly much work left to do for a minimal
version, but I really do not feel to have a free part in my brain for it
at the moment. I am certain someone else will jump in. Let's give the
package another four-eight weeks and see what happens. If these do not
bring a volunteer then I might be prepared to go for it despite being
torn to many pieces already.

Thanks again,

Best,

Steffen



Cheers,
Carlos


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