Re: [COOT] problem in coot installation in ubuntu
Hi, I just tested it on a freshly installed system for a student; it works very well on Ubuntu Hardy. I'm not sure why nxnode is a dependency of the Coot .deb though! (Although that doesn't bother me too much- I would advise anyone to use NX ). Thanks again, Mark 2008/11/16 William G. Scott [EMAIL PROTECTED] That's great. In the short term, highly unofficial/unauthorized/zeroth-order coot and dependencies for i386 linux: debians: http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Coot#Instalation_on_Debian.2FUbuntu_from_debian_archive_files rpms (made via alien from above): http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Coot#Converting_to_rpm_packages These include mmdb, ssm, gpp4, fftw (in the form required for clipper and coot), clipper, coot, which will install into /usr/local/xtal and then the various guile-type dependencies, which will install into /usr On Nov 15, 2008, at 6:15 PM, Paul Emsley wrote: 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] mailto: [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] mailto:[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/~wgscotthttp://chemistry.ucsc.edu/%7Ewgscott http://chemistry.ucsc.edu/%7Ewgscott Please reply to: [EMAIL PROTECTED] mailto:[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 -- 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
Oh, in case anyone is wondering how I did this (and how I screwed it
up), the correct command should have been:
dpkg -S $( ldd /usr/local/xtal/coot/bin/coot-real | awk '{print $3}'
| sort -u | grep -v \( )| cut -f 1 -d : | sort -u | perl -pi -e 's|
\n|\, |g' | dependencies.txt
whereas I first used
dpkg -S $( ldd /usr/local/xtal/coot/bin/coot-real | awk '{print $1}'
| sort -u | grep -v \( )| cut -f 1 -d : | sort -u | perl -pi -e 's|
\n|\, |g' | dependencies.txt
My bad. I needed the third column of the output of ldd to get the
full path of the dynamic library. The first column only reports the
name of the file, and then it wrongly assumed it was in my NX
directory (it wasn't). Coot was properly linked. The list of
dependencies in the debian file was wrong. Fixed now.
( coot_0.5-2_i386.deb ). Again, thanks for catching this.
Bill
On Nov 17, 2008, at 6:57 AM, William G. Scott wrote:
Woops. I didn't see that. I auto-generated the list of
dependencies from the output of ldd on the coot binary, upon which I
then used dpgk -S to find the corresponding packages. For some
reason it generated this falsely (the library is also present, but
ldd does not report coot linking anything with NX in the path).
Sorry, I will edit this out.
Thanks for testing.
Bill
On Nov 17, 2008, at 3:16 AM, Mark Brooks wrote:
Hi,
I just tested it on a freshly installed system for a student; it
works very
well on Ubuntu Hardy.
I'm not sure why nxnode is a dependency of the Coot .deb though!
(Although
that doesn't bother me too much- I would advise anyone to use NX ).
Thanks again,
Mark
2008/11/16 William G. Scott [EMAIL PROTECTED]
That's great. In the short term, highly
unofficial/unauthorized/zeroth-order coot and dependencies for
i386 linux:
debians:
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Coot#Instalation_on_Debian.2FUbuntu_from_debian_archive_files
rpms (made via alien from above):
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Coot#Converting_to_rpm_packages
These include mmdb, ssm, gpp4, fftw (in the form required for
clipper and
coot), clipper, coot, which will install into /usr/local/xtal
and then the various guile-type dependencies, which will install
into /usr
On Nov 15, 2008, at 6:15 PM, Paul Emsley wrote:
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] mailto:
[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] mailto:[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
Re: [COOT] problem in coot installation in ubuntu
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] mailto:[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] mailto:[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 http://chemistry.ucsc.edu/%7Ewgscott Please reply to: [EMAIL PROTECTED] mailto:[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
On Wed, 12 Nov 2008 09:03:34 + Kevin Cowtan [EMAIL PROTECTED] wrote: 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. Why does coot require a 3000 line hand written shell script to set up the build process? -Tim -- - Tim Fenn [EMAIL PROTECTED] Stanford University, School of Medicine James H. Clark Center 318 Campus Drive, Room E300 Stanford, CA 94305-5432 Phone: (650) 736-1714 FAX: (650) 736-1961 -
