Re: Packaging of software used at EMBL Grenoble
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Le 6/29/12 2:21 PM, Mickaël Canévet a écrit :
> Hello,
>
> I'm sysadmin at European Molecular Biology Laboratory (EMBL), Grenoble.
> After the "Debian for Scientific Facilities Days" that took place on
> June, 24-26 at ESRF where we met Andreas ; we decided to work with the
> Debian Med Blend to package and include in the offical Debian archive
> some electron microscopy softs that our users are using.
>
> Currently they use this list of software:
>
> - AMoRe (http://mem.ibs.fr/JORGE/index.html )
> - atsas (EMBL Hamburg, not sure we can re-distribute it)
> - blast (not sure if it's a former version of the package blast2 that
> already exists in debian)
blast and blast+ are both packaged in Debian.
>
> - bsoft (http://lsbr.niams.nih.gov/bsoft/ )
> - chimera (http://www.cgl.ucsf.edu/chimera/ )
> - coot (http://lmb.bioch.ox.ac.uk/coot/ )
> - ctfind3 and ctftilt (http://emlab.rose2.brandeis.edu/ctf ) (GPLv3)
> - eman2 (http://blake.bcm.edu/emanwiki/ )
> - embfactor (https://sites.google.com/site/3demimageprocessing/embfactor
> )
> - empft/em3dr
>
(http://bilbo.bio.purdue.edu/~viruswww/Rossmann_home/softwares/river_programs/para-pft-em3dr.php
)
> - flex-em (http://salilab.org/Flex-EM/ )
> - frealign (http://emlab.rose2.brandeis.edu/frealign ) (GPLv3)
> - image2000 (http://www2.mrc-lmb.cam.ac.uk/image2000.html )
> - imagic (http://www.imagescience.de/imagic.html )
> - imod (http://bio3d.colorado.edu/imod/ )
> - maloc (http://fetk.org/codes/maloc/ )
> - modeller (http://salilab.org/modeller/ )
> - naccess (http://www.bioinf.manchester.ac.uk/naccess/ )
> - nuccyl (http://www.biosci.ki.se/groups/ljo/software/nuccyl.html )
> - peet (http://bio3d.colorado.edu/PEET/ )
> - relion (http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page )
> - Rico (http://mem.ibs.fr/JORGE/index.html )
> - saxsview (http://saxsview.sourceforge.net/ )
> - spider (http://www.wadsworth.org/spider_doc/spider/docs/spider.html )
> - tiltpicker (http://www.ncbi.nlm.nih.gov/pubmed/19374019 )
> - uro (http://mem.ibs.fr/JORGE/index.html )
> - veda (http://mem.ibs.fr/GAEL/ )
> - vmd (http://www.ks.uiuc.edu/Research/vmd/ )
> - xmipp (http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/WebHome )
> - zdock (http://zlab.umassmed.edu/zdock/ )
>
> Most used at EMBL Grenoble are spider, xmipp and eman2.
>
> I already packaged Xmipp 3.0 on wheezy, but I can't compile it on
> squeeze as it needs python-numpy >= 1.6 which is not available even in
> squeeze-backports .
I think that you should target wheezy as it is next stable version. You
will whatever upload to unstable then testing. It will even not match
wheezy as freeze is in progress, but being wheezy compatible is a target
I think, even if backport is needed afterward because release will
already be delivered.
Being squeeze compatible is nice, but should not be a blocking point.
>
> I also made a package for spider, but it's not very clean yet... I
> worked with the developer to make it compile with gfortran and not only
> with PGI or ifort.
>
> My co-worker is currently working on ctfind and ctftilt.
>
> The main problem we encountered so far is that that kind of program
> often lack of clean Makefile and have non traditional install procedure
> (./configure && make && make install), so we have to write it first...
>
> We may not have a lot of time to dedicate to packaging in the next few
> weeks, but we'll try to get a few software in Debian Med before the end
> of the year.
>
> I'd like to know how we can start working with Debian Med (include list
> of software on this page:
> http://debian-med.alioth.debian.org/tasks/bio , upload unofficial
> packages for review, become a member of the debian med team...) and if
> some of you is using one of the softs we use.
I think a good point would be to join Debian Med on Alioth then ask for
review and once ok ask someone from Debian Med to upload the packages.
You could remain a Debian Maintainer of those packages if you wish to do so.
Olivier
>
>
> Regards,
> Mickaël
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