Re: Hi! I am new, I would appreciate some direction
On Sat, Sep 04, 2010 at 01:07:36AM +0300, George Marselis wrote:
> > Obligation is probably the wrong word. It just makes sense to subscribe
> > this mailing list. IMHO the best way to start in the Debian Med team is
> > to read the Debian Med policy document[1] first.
>
> done.
Great.
> speaking of the Debian Med policy:
> * http://ddtp.debian.org/ is down and the document is not updated to
> reflect the change.
Ahh, that is and was ddtp.debian.net.
> * "Developpers Reference" <--typo
> if i knew where the source for that document was, i think this would
> be a 2 second change.
Fixed. It is in
svn://svn.debian.org/svn/debian-med/trunk/community/website/docs
> > Could you please give some more information about InterPro (URL,
> > short description)) and especially why it needs to be forked. Are
> > you talking about[2]?
>
> Yes, I am talking about [2]. EBI is (literaly) across the Sanger
> institute in the UK.
>
> Interpro Scan is what bioinformaticians calls a "pipeline". In
> software engineering terms, it is called a toolkit.
>
> It consists of pre-compiled bioinformatics tools (mira, hmmr, thmmr,
> signalp, seqret, pfscan, ncbi blast) and a framework to chain those
> tools together, by running each tool in sequence and passing the
> output files from one tool as the input to the next. Framework is
> coded in Perl. It supports batch engines to parallelize its output:
> Platform LSF, officially 4.2 even though I have it running on 7.0c,
> OpenPBS and
>
> It is our bread and butter over there at KAUST. While it does its job
> very adequately once set up, it is a major pain to setup for anything
> more than a single machine. It is showing its age: Officially, it
> supports only rsh for remote execution of commands, though it is
> trivial to patch it to use ssh.
>
> It is also showing how it was not coded by someone with a software
> engineering/computer science background, but I will not go into that,
> because I have seen enough bioinformatics code to curse Larry Wall to
> the 7th Circle of Hell :D THE GOGGLES! THEY DO NOTHING!
>
> ( production code: close( FILEHANDLE ) && system( chmod 777 $file );
> can you guess what happens if you run that over a slow NFS link? )
>
> EBI has been working on a Java version of this framework but ETA is
> well, unknown. In the meantime half the planet from California to Hong
> Kong and Saudi Arabia are using interpro scan and poor sysadmins
> around the world cry instead of celebrating Sysadmin Day.
>
> Officially, EBI has stopped maintaining this framework, but it is
> going to be with us for a long long long long time.
>
> So, it is due for an overhaul, it needs to learn how to use the
> official perl logging facility( to syslog, to file, to nagios ), it
> needs to tell you on which host it encountered what error, it needs
> stop having cryptic error messages, it needs to reduce the amount of
> conf files it uses and it needs to be able to work with multiple
> versions of the same program (just try to make it use hmmr 3.0)
>
> on the other hand, i have time. and cigars. and no beer.
>
>
> > In Free Software there is no "have to use". Charles just wanted to help
> > your work. If it is not helpful you probably can ignore Charles' work -
> > however, Charles has proven in the past to create high quality packaging
> > stuff. COnsidering that you wrote you would be a newcomer having at
> > least a look onto this is strongly recommended and will give you a good
> > example. However, I have not yet looked at Charles' mira packaging,
> > thought.
>
> people are singing the praises of Mr Plessy :) I did take a look into
> the debian/* contents. and i borrowed stuff :)
The good thing of a team with same packaging policy is that borrowing is
a nice way to save time. ;-)
> > Please create an Alioth login.
>
> done. created the repo as well: http://git.debian.org/git/debian-med/mira.git/
>
> > The deadline for Squeeze can not be mat any more - we are in freeze
> > period. It has turned out tat targeting at a certain release is not
> > feasible - just do a proper packaging of the recent stable upstrean
> > version and we will se in what distribution it will go.
>
> okie-dokie!
>
> > Hope that my first batch of answers was helpful
> yes, sir, they were!
>
> Regards from Saudi Arabia,
Ahh, great. It is good if Debian Med also grows in this region of the
world! Welcome in the team.
Kind regards
Andreas.
--
http://fam-tille.de
Reply to: