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 -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20100904182859.ga20...@an3as.eu
