Re: ensembl_57-7_amd64.changes ACCEPTED into experimental
I apologize for the delayed reply, but I just had a flood in my
apartment. I love living in KAUST <3
Right now, the apartment is flooded with water from the fire
extinguish valve and there is no electricity. it will take me an hour
to go to the kaust coffee shop and set up my laptop from there
>
> In Debian Med are missing on your list:
>
> - ssaha
> It is just ITPed by Charles:
> http://debian-med.alioth.debian.org/tasks/bio#ssaha
> Charles, any news about this package? The record in our tasks
> file says, that the source is not available.
> George, do you have some clue how to get the source? This would
> definitely help us packaging it ...
there does not seem to be any source here :
ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/
so I think I will have to write to sanger and ask them politely. we
got some sanger and ebi people over here at KAUST, let me see if they
are willing to help.
> - VCFtools
> I just added this to our tasks file.
>
> I have a question: On the Wiki pages you are listing VCFtools as
>
> Packaging status Ongoing
>
> what exactly does this mean. Perhaps it is a lack of understanding what
> bioinformatics.org is doing. Debian has 6 of 8 programs mentioned on
> your page packaged and getting VCFtools might be a matter of time until
> somebody might grab this. Could you please clarify the term packaging
> and your relation to the Debian Med project. We would be happy to help
> you for your project - but it seems those package we just have packaged
> do not really fit into your concept.
The description is not accurate. The packaging status on the wiki is
listed as "ongoing", because of the excitement of the moment: me and
my friend were all excited about something we could do: list all the
available tools used in bioinformatics.
the idea took off from there: we discussed the possibility of
examining each tool; see if source code is available. if there was, we
were talking about checking to see the quality of the code and see if
there is a configure script. the aim was to aid the end-user, to
easily install a tool. then, we thought about writing the list and
handling the end results to debian-medical.
my relationship to debian-med? I am just a simple sysadmin, frustrated
with {(my perceived), the} lack of disarray. I would like to be a
debian-med packager. I offered to package mira 7-8 months ago, but my
inexperience stood in front of me.
what happened with this list was a vent of my frustration out of my
lack of knowledge in the bioinformatics world: i can name you 10
window managers, but i only know 5-6 bioinformatics tools. I have also
googled for a "list of bioiformatics tools" but I have not come up
with satisfactory answers. so, i thought i would start exploring this
field, by making a list of the tools available. then, i compounded on
the idea, by adding my frustration over the quality of source code and
installation tools i have been seeing, with the tools i have installed
from source so far.
>
>> This is indented to be a list of all the bioinformatics tools we know.
>
> Could you please clarify this "all we know"? We now a bit more and I
> can not believe that you do not so I wonder about the context you are
> talking about.
we == my friend from irc, and myself. the number of tools my friend
from irc and myself know
> Kind regards
>
> Andreas.
>
> --
> http://fam-tille.de
>
ok, let me go to the caffee and set up shop.
Reply to: