Re: Trying apt-get install through the list in bio-ngs
Hi Albert,
thanks for your interest in Debian Med.
On Wed, Feb 19, 2014 at 05:13:22PM +0000, Albert Vilella wrote:
> Hi all,
>
> My name is Albert Vilella, I recently joined the mailing list with the
> intention to learn more about debian-med to the point where I can
> start contributing some of my time to it. I am doing this out of my
> own interest in open-source, and it's not part of my day job.
:-) same for me.
> Since at the moment I don't feel I can contribute much by pushing new
> packages into debian-med, I just thought I would try something mildly
> useful with the list of existing packages in bio-ngs
> (http://blends.debian.org/med/tasks/bio-ngs).
That's really great since we do not only rely on the work of packagers
but we also need comments from a user perspective to make Debian (Med)
even better.
BTW, regarding the bio-ngs task: It presents just a section of all
biology relevant packages and as I recently wrote here on this list[1]
it is not really properly maintained. You might try to install the
metapackage med-bio which should install all available packages dealing
with tasks in biology on your computer.
Attention: I have never tested whether the metapackages are working
properly under Ubuntu. Since the metapackage source is created by
reflecting the *Debian* package pool at the creation time it might
contain or missing packages which are at this time in Ubuntu. The
correct way to release debian-med metapackages in Ubuntu would be to use
blends-dev to recreate this package source. I have no idea whether this
is really done and I also have no idea whom to contact to explain how
this should be done correctly.
> What I did is to try and install them in a docker container
> (https://www.docker.io/) based on Ubuntu Precise and report on the
> results:
Please note that we are talking here about Debian and not (primarily)
about Ubuntu. While we are trying to support Ubuntu as best as we can
there is no official Ubuntu developer on this list and since I never
used Ubuntu personally my anser can be simply wrong.
> kissplice, sra-toolkit, tophat, cufflinks, uc-echo were not found by apt-get.
Here you can see, that the packages above are available in Debian. The
command
$ apt-cache policy kissplice sra-toolkit tophat cufflinks uc-echo | grep -e ^[a-z] -e Packages$ | grep -v file:
kissplice:
501 http://ftp2.de.debian.org/debian/ testing/main amd64 Packages
50 http://ftp2.de.debian.org/debian/ unstable/main amd64 Packages
sra-toolkit:
501 http://ftp2.de.debian.org/debian/ testing/main amd64 Packages
50 http://ftp2.de.debian.org/debian/ unstable/main amd64 Packages
tophat:
50 http://ftp2.de.debian.org/debian/ unstable/main amd64 Packages
cufflinks:
501 http://ftp2.de.debian.org/debian/ testing/non-free amd64 Packages
50 http://ftp2.de.debian.org/debian/ unstable/non-free amd64 Packages
uc-echo:
50 http://ftp2.de.debian.org/debian/ unstable/main amd64 Packages
501 http://ftp2.de.debian.org/debian/ testing/main amd64 Packages
shows that the four packages are available in Debian testing and
unstable while I can confirm that only sra-toolkit is available in
Debian Wheezy 7 (=stable). The other packages were added later to the
Debian package pool but should work under stable as well (as under a
recent Ubuntu).
Your mileage may vary but you might like to try adding a line for a
Debian testing mirror to your sources.list. And if you really want to
make sure everything works as expected and you are using a virtual
maschine anyway I see no reason not to try vanilla Debian.
> Qiime is a monster of a package, that attempts to even install grub on
> the docker container. The installation worked, even though I chose
> "continue without installing grub".
I can not see any reason that grub is in the list of dependencies qiime.
Can you please give a verbose output of your try to "apt-get install qiime"?
> Everything else went through "apt-get install" correctly.
>
> These are my 2c so far. Hope to do some packaging in the future.
Hope my comments were helpful to you
Andreas.
[1] https://lists.debian.org/debian-med/2014/02/msg00135.html
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