Re: [COOT] problem in coot installation in ubuntu

[Mark Brooks]

Hi,

It may be useful to have a 'contrib' section for the Coot binary download
web page (or even some unofficial web page), so that we have more options of
binaries to test. For example, upon upgrading to Ubuntu Hardy Heron, Coot
stopped working, for reasons beyond my understanding, but worked when
recompiled. (Which was very easy using the build-it-gtk2-simple script BTW).
To have a central repository of tested binaries could be very handy, to
avoid having to do this.

The Coot developers and yourself (Bill) have done an enormous amount to
furnish us with working, tested programs,  but perhaps one or two more
updated binaries contributed by users  would be useful, especially for newer
releases of the myriad Linux flavours.

I think for the Coot developers to start providing .deb, .rpm and Gentoo
packages for every update is too onerous, especially when .tar.gz files work
OK. Just my opinion.

Which Ubuntu are you on Bill, and which binary are you using? Are these on
your debian web site? I guess I may be able to give a Hardy Heron binary if
need be.

Thanks for your .debs though, I use them all the time.

Mark

2008/11/12 William G. Scott <[EMAIL PROTECTED]>

> Since Ubuntu has gotten to be popular (for good reason, IMO), it might be
> useful to have an official (or at least semi-official) debian package whose
> installation would guarantee all the dependencies also get installed.  I've
> tried to do it in a half-arsed sort of way, but lately have dropped the ball
> (sorry).
>
> On Wed, Nov 12, 2008 at 1:03 AM, Kevin Cowtan <[EMAIL PROTECTED]>wrote:
>
>> Hi!
>>
>> Firstly, do you need to build coot at all? There are binary packages which
>> work just fine on Gutsy. You can install them wherever you want on your
>> system, and they should just work.
>>
>> Secondly, if for some reason you do want to build your own (you want to
>> make changes to the code???), then are you using the build-it-gtk2-simple
>> script?
>>
>> http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/COOT#Installation_from_source_code
>> Building coot without this script requires days or weeks of messing around
>> with dependencies. With this script it is usually pretty easy.
>>
>> Kevin
>>
>>
>> Rimi wrote:
>>
>>> Hi all,
>>>  I am new to coot. Recently I tried to install coot in my ubuntu
>>> gutsy. But it can not find mmdb library somehow. Below is the message
>>>
>>
>
>
> --
> -
>
>
> William G. Scott
>
> contact info:  
> http://chemistry.ucsc.edu/~wgscott
>
> Please reply to:  [EMAIL PROTECTED]
>
>
>
>


-- 
Mark BROOKS
Telephone: 0169157968
Fax: 0169853715
Institut de Biochmie et de Biophysique Moleculaire et Cellulaire
UMR8619 - Bât 430 - Université de Paris-Sud
91405 Orsay CEDEX
Skype: markabrooks

Re: [COOT] problem in coot installation in ubuntu

[William G. Scott]

Hi Mark et al:

The last coot I compiled on Ubuntu Hardy was coot-0.5-pre-1- 
revision-1003.  I've been a bit distracted with other obligations. The  
last one I made into a debian package and put on our server was a
0.4-pre-2release, so I apologize. I keep the OS X fink debian  
packages much more up to date and have tried to maintain those,  
officially (via fink), to a much higher standard.


I don't fully understand the linux debian packaging requirements  
nearly well enough, but should probably take the time to do so, and to  
create standard-compliant debian packages for coot and its  
dependencies and then figure out how to get these things into the  
official distribution system.  I guess if someone else out there with  
the competence and time can do for Debian/Ubuntu what Donnie Berkholz  
has done for Gentoo, it would be helpful.  What is needed are properly  
created debian packages for clipper, mmdb, gpp4, ssm, coot, and a few  
of the other misc dependencies that aren't present in a standard linux  
distribution.


Once you have that, you can use the program alien to convert to rpm,  
etc.


My main limitations are knowledge, time, only one PC running only one  
version of ubuntu, and more specifically getting a complete listing of  
dependencies so that package installation for the end-user is truly  
seamless.  This has been my goal with OSX/fink, and I've invested most  
of my time and effort into that. Linux should actually be much easier,  
but I don't know it nearly as well. I've also now just been put into a  
tailspin by our main funding agency, so I will now have to prioritize  
further, or find something else to do for a living.


Peace and joy,

Bill




On Nov 15, 2008, at 3:32 AM, Mark Brooks wrote:


Hi,

It may be useful to have a 'contrib' section for the Coot binary  
download
web page (or even some unofficial web page), so that we have more  
options of
binaries to test. For example, upon upgrading to Ubuntu Hardy Heron,  
Coot

stopped working, for reasons beyond my understanding, but worked when
recompiled. (Which was very easy using the build-it-gtk2-simple  
script BTW).
To have a central repository of tested binaries could be very handy,  
to

avoid having to do this.

The Coot developers and yourself (Bill) have done an enormous amount  
to

furnish us with working, tested programs,  but perhaps one or two more
updated binaries contributed by users  would be useful, especially  
for newer

releases of the myriad Linux flavours.

I think for the Coot developers to start providing .deb, .rpm and  
Gentoo
packages for every update is too onerous, especially when .tar.gz  
files work

OK. Just my opinion.

Which Ubuntu are you on Bill, and which binary are you using? Are  
these on
your debian web site? I guess I may be able to give a Hardy Heron  
binary if

need be.

Thanks for your .debs though, I use them all the time.

Mark

2008/11/12 William G. Scott <[EMAIL PROTECTED]>

Since Ubuntu has gotten to be popular (for good reason, IMO), it  
might be
useful to have an official (or at least semi-official) debian  
package whose
installation would guarantee all the dependencies also get  
installed.  I've
tried to do it in a half-arsed sort of way, but lately have dropped  
the ball

(sorry).

On Wed, Nov 12, 2008 at 1:03 AM, Kevin Cowtan  
<[EMAIL PROTECTED]>wrote:



Hi!

Firstly, do you need to build coot at all? There are binary  
packages which
work just fine on Gutsy. You can install them wherever you want on  
your

system, and they should just work.

Secondly, if for some reason you do want to build your own (you  
want to
make changes to the code???), then are you using the build-it-gtk2- 
simple

script?

http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/COOT#Installation_from_source_code
Building coot without this script requires days or weeks of  
messing around

with dependencies. With this script it is usually pretty easy.

Kevin


Rimi wrote:


Hi all,
I am new to coot. Recently I tried to install coot in my  
ubuntu
gutsy. But it can not find mmdb library somehow. Below is the  
message







--
-


William G. Scott

contact info:  http://chemistry.ucsc.edu/~wgscott


Please reply to:  [EMAIL PROTECTED]







--
Mark BROOKS
Telephone: 0169157968
Fax: 0169853715
Institut de Biochmie et de Biophysique Moleculaire et Cellulaire
UMR8619 - Bât 430 - Université de Paris-Sud
91405 Orsay CEDEX
Skype: markabrooks

[COOT] Custom building Coot from source code - CCP4 wiki

[William Scott]

Hi Citizens:

http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Custom_building_Coot_from_source_code


I updated the coot wiki for those attempting to build coot and its  
dependencies (gpp4, ssm, mmdb, clipper, fftw, and a bunch of guile  
fragments) from source. I can't remember who asked, but I hope this  
will be of some use.  I am going to try to make some debian packages  
eventually.


This now also includes instructions for building fftw to play nice  
with coot and clipper...


Bill

PS:  The york server appears to be down again.  If you need access to  
source code when this happens, you can often find it here, eg:


http://distfiles.msn.wi.us.finkmirrors.net/mirrors/fink/distfiles/coot-0.5.tar.gz

Re: [COOT] Custom building Coot from source code - CCP4 wiki

[Kay Diederichs]

William Scott schrieb:
...


PS:  The york server appears to be down again.  If you need access to 
source code when this happens, you can often find it here, eg:


http://distfiles.msn.wi.us.finkmirrors.net/mirrors/fink/distfiles/coot-0.5.tar.gz



FWIW, the York server is mirrored here nightly:

ftp://turn5.biologie.uni-konstanz.de/coot/

HTH,

Kay
--
Kay Diederichs http://strucbio.biologie.uni-konstanz.de
email: [EMAIL PROTECTED] Tel +49 7531 88 4049 Fax 3183
Fachbereich Biologie, Universitaet Konstanz, Box M647, D-78457 Konstanz


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Description: S/MIME Cryptographic Signature

Re: [COOT] problem in coot installation in ubuntu

[Paul Emsley]

It was rhetorical - why not just use autoconf to do all the dirty work?


Like Lynn Ten Eyck says, autoconf configures dependences, it doesn't 
build them (AFAICS, anyway).



Also, is the idea to migrate all of the scripting away from guile and
towards python, 


No.


or update the guile dependencies (as it seems goosh is
part of the os process module now, 


OK, Noted.


guile-gtk is deprecated in favor of
guile-gnome, 


I've not heard that.


guile net-http and guile-gui look unsupported...)?


Yes, they are tiny packages that could easily subsumed into Coot itself 
for ease of packaging (as Bill Scott once suggested).  Not done, no-one 
complained enough.



 I'd
like to begin preparing a rpm for fedora (now that most of the
dependencies are part of the distributions),


Good going!  MATSUURA Takanori and Adam Huffman said they'd like to do 
something similar.



but their peer review
process might screen out unsupported deps...


Hmm... Fingers crossed we'll get the mmdb license issues sorted soon.

Paul.

Re: [COOT] ssm superpose coot 0.5 on osx 10.5

[Paul Emsley]

Sue Roberts wrote:
 (That reminds me, I need to figure out how to get rid of 
the old coot time to upgrade message.)


comment out (with a ;) the (old-coot?) line in 
xxx/share/coot-scheme/coot-gui.scm

Re: [COOT] problem in coot installation in ubuntu

[Paul Emsley]

FYI, IIUC, Morten Kjeldgaard has become a MOTU and is working on 
crystallographic libs for Ubuntu, e.g.:


https://launchpad.net/ubuntu/+source/clipper
https://launchpad.net/ubuntu/+source/mmdb

When he gets round to Coot I'm keen to help make his life easier.

Regards,

Paul.


Mark Brooks wrote:

Hi,

It may be useful to have a 'contrib' section for the Coot binary 
download web page (or even some unofficial web page), so that we have 
more options of binaries to test. For example, upon upgrading to Ubuntu 
Hardy Heron, Coot stopped working, for reasons beyond my understanding, 
but worked when recompiled. (Which was very easy using the 
build-it-gtk2-simple script BTW). To have a central repository of tested 
binaries could be very handy, to avoid having to do this.


The Coot developers and yourself (Bill) have done an enormous amount to 
furnish us with working, tested programs,  but perhaps one or two more 
updated binaries contributed by users  would be useful, especially for 
newer releases of the myriad Linux flavours.


I think for the Coot developers to start providing .deb, .rpm and Gentoo 
packages for every update is too onerous, especially when .tar.gz files 
work OK. Just my opinion.


Which Ubuntu are you on Bill, and which binary are you using? Are these 
on your debian web site? I guess I may be able to give a Hardy Heron 
binary if need be.


Thanks for your .debs though, I use them all the time.

Mark

2008/11/12 William G. Scott <[EMAIL PROTECTED] 
>


Since Ubuntu has gotten to be popular (for good reason, IMO), it
might be useful to have an official (or at least semi-official)
debian package whose installation would guarantee all the
dependencies also get installed.  I've tried to do it in a
half-arsed sort of way, but lately have dropped the ball (sorry). 


On Wed, Nov 12, 2008 at 1:03 AM, Kevin Cowtan
<[EMAIL PROTECTED] > wrote:

Hi!

Firstly, do you need to build coot at all? There are binary
packages which work just fine on Gutsy. You can install them
wherever you want on your system, and they should just work.

Secondly, if for some reason you do want to build your own (you
want to make changes to the code???), then are you using the
build-it-gtk2-simple script?

http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/COOT#Installation_from_source_code
Building coot without this script requires days or weeks of
messing around with dependencies. With this script it is usually
pretty easy.

Kevin


Rimi wrote:

Hi all,
 I am new to coot. Recently I tried to install coot
in my ubuntu
gutsy. But it can not find mmdb library somehow. Below is
the message




-- 
-



William G. Scott

contact info:  http://chemistry.ucsc.edu/~wgscott


Please reply to:  [EMAIL PROTECTED]







--
Mark BROOKS
Telephone: 0169157968
Fax: 0169853715
Institut de Biochmie et de Biophysique Moleculaire et Cellulaire
UMR8619 - Bât 430 - Université de Paris-Sud
91405 Orsay CEDEX
Skype: markabrooks

Re: [COOT] problem in coot installation in ubuntu

[Donnie Berkholz]

On 02:16 Sun 16 Nov , Paul Emsley wrote:
>> It was rhetorical - why not just use autoconf to do all the dirty 
>> work?
>
> Like Lynn Ten Eyck says, autoconf configures dependences, it doesn't 
> build them (AFAICS, anyway).

Well, autoconf does have a command to kick off another configure script 
as a child, so this can be done.

The (superior, I think) approach that we're using for a similar 
situation is based on GARNOME, a way of getting bleeding-edge GNOME. 
Take a look at 
http://oregonstate.edu/~benisong/software/releases/burrow-installer-1.4.tar.gz 
-- it's basically an easy way of building any required dependencies. 
Certainly looks a lot simpler than the existing script.

In our case, it's a total of ~1300 lines, but around 1000 of those are 
taken directly from GARNOME.

-- 
Thanks,
Donnie

Donnie Berkholz
Developer, Gentoo Linux
Blog: http://dberkholz.wordpress.com


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