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 > > > -- > To UNSUBSCRIBE, email to [email protected] > with a subject of "unsubscribe". Trouble? Contact [email protected] > Archive: http://lists.debian.org/[email protected] > -- William Spooner [email protected] http://www.eaglegenomics.com -- To UNSUBSCRIBE, email to [email protected] with a subject of "unsubscribe". Trouble? Contact [email protected] Archive: http://lists.debian.org/[email protected]
