Re: ensembl_57-7_amd64.changes ACCEPTED into experimental
On 1 Apr 2011, at 11:07, Andreas Tille wrote:
> On Fri, Apr 01, 2011 at 12:38:41PM +0300, George Marselis wrote:
>> 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
>
> Good luck. :-)
>
>>> - 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.
>
> It would definitely interesting to have the source of ssaha2. Please
> go on asking them and report here.
Sadly SSAHA2 uses crossmatch, which is non-free, meaning SSAHA2 is not appropriate for debian-med. I can get you the source for ssaha, but it's so old now that I doubt anyone would still want to use it. The latest tool from the same group is called SMALT - this is probably worth perusing. I believe that it uses the same k-mer index table algorithm as SSAHA (and BLAT); i.e. is a different algorithm to the Burrows-Wheeler tools that are so popular in the short-read world.
http://www.sanger.ac.uk/resources/software/smalt/
Will
>
>> 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.
>
> Did you ever had a look at
>
> http://debian-med.alioth.debian.org/tasks/bio ???
>
>> 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.
>
> It is great if you want to help - but at first please check what is
> there. I somehow have the feeling that you underestimate drastically
> qhat is there yet.
>
>> 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.
>
> The mira issue was answered by Steffen.
>
>> 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.
>
> I'd be interested what exactly your Google query was and whether we
> might approach that you get the page I mentioned above as first hit.
> BTW, there are *a* *lot* lists of such software in the net. We try to
> distinguish from those other lists by having those packages ready to
> install instead of having a simple list.
>
> In any case before starting to package a biological software you should
> verify whether it is on this list and in what status it is. If
> packaging might not be completed it might be in SVN in some intermediate
> state.
>
>> we == my friend from irc, and myself. the number of tools my friend
>> from irc and myself know
>>
>> ok, let me go to the caffee and set up shop.
>
> Make sure you order a "coffee long" if you want to enjoy it while
> reading the list of packaged software.
>
> Kind regards
>
> Andreas.
>
> --
> http://fam-tille.de
>
>
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> Archive: [🔎] 20110401100707.GA22210@an3as.eu">http://lists.debian.org/[🔎] 20110401100707.GA22210@an3as.eu
>
--
William Spooner
whs@eaglegenomics.com
http://www.eaglegenomics.com
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