Re: canu

> I'm just undecided because slurm itself needs a bit more than just install the client package and you have immediate advantage without more administration. if I may: maybe gnu parallel would be a good suggestion, as well? On Thu, Nov 2, 2023 at 7:21 AM Andreas Tille wrote: > Hi Tony, > >

Re: removing tophat from Debian

that also means there is a need for the maintainers of packages such as galaxy or taverna to be notified and/or make sure when used in a pipeline tophat throws a yuge error. On Sat, Dec 16, 2017 at 8:00 PM, Fabian Klötzl wrote: > Hi, > > On 16.12.2017 15:40,

Re: Researcher and technician positions open at RIKEN in Japan.

Wow. Do they need sysadmins, as well? On Fri, Dec 14, 2012 at 7:38 AM, Charles Plessy ple...@debian.org wrote: Hello everybody, As you may know I am working at RIKEN in Japan where I analyse the expression of genes and the mechanism of their regulation using molecular biology and

Re: Debian quotes? (Was: sponsor upload 1.1.13-1)

Debian; I'm just sayin' http://www.youtube.com/watch?v=4bhrSqBgrHI 'Support Contract' is a nice way of describing that our sysadmins are not technically inclined oh, wait, you said nice :D PS: Wanted: Sysadmins and programmers with neck-beard and jeans to re-shoot the original (cuz i got a heavy

Confused - question about NCBI Tools++

Hey guys, I am confused: I am trying to find out to which Debian package do the NCBI Tools++ software map to; a bit of googling did not come up with anything consistent. Any clues, please? Thank you. George Marselis -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org

Re: Confused - question about NCBI Tools++

Sorry, I should have included the URL: ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools++/ does that ring a bell? On Fri, Aug 3, 2012 at 2:37 PM, Olivier Sallou olivier.sal...@irisa.fr wrote: Le 8/3/12 1:25 PM, George Marselis a écrit : Hey guys, I am confused: I am trying to find out

proposed patch libbam-dev due to cufflinks configure script not picking up bam.h

into libbam-dev be an acceptable solution till i finally finish the autotools book and submit a patch to upsteam? thank you, george marselis -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http

Re: blast+ packaging

since we are on the subject, i have been trying to compile ncbi-blast on my own, for my own use. i would like to enable ever single one of it's features; eg, UUIDs . or xalan. I cannot find any info on how to activate UUIDs (it's not an option in ./configure --help) and I cannot find the proper

Re: blast+ packaging

- De: George Marselis geo...@marsel.is À: Debian Med Project List debian-med@lists.debian.org Envoyé: Dimanche 29 Mai 2011 13:57:28 Objet: Re: blast+ packaging since we are on the subject, i have been trying to compile ncbi-blast on my own, for my own use. i would like to enable ever single one

Re: Is there a wiki I can keep notes for applications I install/package?

I fixed some mistakes - you might like to read my commit logs. just svn updated, will read them after work. SNAP, repeatmasker, trf, augustus, mugsy, apollo, chado, eHive, ECHO, ANNOVAR, CMap, GBrowse_syn, JBrowse, Trupal I wonder why you added trf if   License: binary only (non-free)

Re: Is there a wiki I can keep notes for applications I install/package?

is now packaged and available in Debian unstable. Kind regards      Andreas. On Tue, Apr 19, 2011 at 01:45:48PM +0300, George Marselis wrote: Hey guys, I am working on GMOD ( http://gmod.org/wiki/Main_Page ).  As you can see for yourselves, that page was not created with a technical guy

Re: genome annotation program to add to list

Fri, Apr 15, 2011 at 08:26:48PM +0100, George Marselis a écrit : http://www.yandell-lab.org/software/maker.html with how-to here: http://gmod.org/wiki/MAKER_Tutorial#Installation how are you guys doing? :D just came back from london. i have to say: god bless the Queen for allowing her

Is there a wiki I can keep notes for applications I install/package?

Hey guys, I am working on GMOD ( http://gmod.org/wiki/Main_Page ). As you can see for yourselves, that page was not created with a technical guy in mind. I need to make a summary of that page. I was wondering where I should put it. Is the Debian Wiki an acceptable solution? Thank you, George

Re: question about packaging nonfree software

On Sat, Apr 16, 2011 at 5:59 AM, Yaroslav Halchenko deb...@onerussian.com wrote: Hi George, Hello! To upload into Debian non-free, someone would need to be really interested in having it there.  Otherwise, if it is not even satisfying requirements for Debian non-free, I guess there is

Re: please add genemark in task list

of your questions about this. Kind regards     Andreas. On Sat, Apr 16, 2011 at 12:54:13AM +0100, George Marselis wrote: http://exon.biology.gatech.edu/ for general description http://exon.biology.gatech.edu/license_download.cgi to download the binaries -- To UNSUBSCRIBE, email to debian

genome annotation program to add to list

http://www.yandell-lab.org/software/maker.html with how-to here: http://gmod.org/wiki/MAKER_Tutorial#Installation how are you guys doing? :D just came back from london. i have to say: god bless the Queen for allowing her subjects to create such a diverse line of beers! -- To UNSUBSCRIBE,

Re: genome annotation program to add to list

Fine.  I hope you as well.  You did not answered my question whether you need help with arachne and I have not noticed any commit. Kind regards My apologies, I was in vacation and I was not reading my emails. No, I have not done anything with arachne. I came back last night and I just woke

question about packaging nonfree software

Hey guys, As you all know, a lot of bioinformatics programs come in nonfree packaging. Newbler comes easily to mind. What is the policy for including software in debian-med? I mean, free software uber alles, yes, but some people will just not release the software under the gpl. what then? For

please add this Nucleic Acid Parser to the list

It is off the page of Dr ian Korf at UC Davis Genome Center. http://homepage.mac.com/iankorf/ He is one of the Authors of the O'Reilly BLAST book http://homepage.mac.com/iankorf/snap-2010-07-28.tar.gz the program is under GPL 2 -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org

Question about packages requiring slightly modified versions of programs.

Hey guys, Apparently, repeat masker comes with its own version of Blast: http://www.repeatmasker.org/RMBlast.html they say that RMBlast is a RepeatMasker compatible version of the standard NCBI BLAST suite. The primary difference between this distribution and the NCBI distribution is the

one gene prediction program for the task list

http://augustus.gobics.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/banlktim0fu5b+acu9to87cq+z0pe0w4...@mail.gmail.com

please add genemark in task list

http://exon.biology.gatech.edu/ for general description http://exon.biology.gatech.edu/license_download.cgi to download the binaries -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive:

can you please put ARACHNE on the task list

http://www.broadinstitute.org/crd/wiki/index.php/Arachne#Download_Arachne can you list this program, as wel, please? -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive:

Re: can you please put ARACHNE on the task list

i thought i already did have permissions, from my attempt with Mira. Let me check again. On Tue, Apr 5, 2011 at 6:29 PM, Andreas Tille andr...@an3as.eu wrote: On Tue, Apr 05, 2011 at 05:30:42PM +0300, George Marselis wrote: http://www.broadinstitute.org/crd/wiki/index.php/Arachne

Re: can you please put ARACHNE on the task list

Oh. right :) yes, you are correct. never committed anything to git. On Tue, Apr 5, 2011 at 9:53 PM, Andreas Tille andr...@an3as.eu wrote: On Tue, Apr 05, 2011 at 09:47:39PM +0300, George Marselis wrote: i thought i already did have permissions, from my attempt with Mira. Let me check again

*groan* Amos assembler

hey guys, i am trying to compile amos from source. it apparently requires qt3. will the latest version of qt will do? anybody got a clue? or rather, i will report myself as well, as soon as i finish compiling oy! -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a

Re: ensembl_57-7_amd64.changes ACCEPTED into experimental

I do not really get it. I find most of those tools already in Debian. bwa, mummer,samtools,velvet are in ... not sure about the state of the others. i am inexperienced in the field of bioinformatics. i thought i would gain more experience, by first making a list of all the tools used in the

Re: ensembl_57-7_amd64.changes ACCEPTED into experimental

I will ask about ssaha2 and i will follow with a letter similar to the soapdenovo one. as i said we got sanger and ebi people here. while we are suggesting packages, have you guys seen this tool? http://sourceforge.net/apps/mediawiki/denovoassembler/index.php?title=Main_Page NGE sequencer using

Re: ensembl_57-7_amd64.changes ACCEPTED into experimental

. Best regards, Steffen [1] http://www.eaglegenomics.com/2011/01/symposium2011/ On 03/30/2011 04:58 PM, George Marselis wrote: great job, man. this will def minimize my headaches ... On Wed, Mar 16, 2011 at 1:37 PM, Steffen Möller steffen_moel...@gmx.dewrote:  Dear all, we can be very

Re: ensembl_57-7_amd64.changes ACCEPTED into experimental

great job, man. this will def minimize my headaches ... On Wed, Mar 16, 2011 at 1:37 PM, Steffen Möller steffen_moel...@gmx.dewrote: Dear all, we can be very happy to now have Ensembl in our distribution. It is in experimental since it depends on other packages that are still in

Re: MIRA, BALL, or svn vs git

yeah, that was my doing, but i sorta abandoned the project, because I could not create a perfect package, and i shied away from asking on the list in fear of sounding like a fool. if i can help with anything, let me know Best Regards, George On Wed, Mar 9, 2011 at 3:01 PM, Steffen Möller

SOAPdenovo is GPL v3

hey guys, to make up for some past sins with mira, I thought i would check with the soapdenovo site. it is now under the GPLv3 http://soap.genomics.org.cn/soapdenovo.html Well done to the soapdenovo team and andreas for writing that email. Best Regards, George. -- To UNSUBSCRIBE, email

Re: [Soap] Source code for SOAPdenovo available?

acceptable Best! RuiBang Luo BGI-Shenzhen On 2011-2-12, at 上午4:14, George Marselis wrote: hey guys, I have to hand it to the soap denovo people. Ruibang Luo luoruib...@genomics.org.cn actually spent some of his precious time to help me out at KAUST, where we have a pretty peculiar

Re: Source code for SOAPdenovo available?

hey guys, I have to hand it to the soap denovo people. Ruibang Luo luoruib...@genomics.org.cn actually spent some of his precious time to help me out at KAUST, where we have a pretty peculiar setup: Power7 series with 512GB of RAm and ugh, RHEL 5.4. It would be godsend if they would publish the

Roadmap for packaging for mira

can build a package from source. the question now is how do i make it available for more machines than amd64 that's for now, i will bug you all later :) Regards, George Marselis -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact

Re: Hi! I am new, I would appreciate some direction

Hi George, please enjoy Git! I have added you to the debian-med Alioth project, so you can add repositories in ssh://git.debian.org/git/debian-med. I am sorry that I have not managed to add instruction in the Debian Med policy yet. But you can find a lot of hints on the Debian wiki:

Re: Hi! I am new, I would appreciate some direction

installation InterPro - Integrated Resource Of Protein Domains And Functional Sites Copyright (C) 2001 The InterPro Consortium. so, this is definitely possible, but the framework needs cleaning up and disentanglement. Best, Steffen Regards from Saudi Arabia, George Marselis

Hi! I am new, I would appreciate some direction

, George Marselis -- 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/aanlktimbvblmmrz8genntcq0hnrpyxt-huv92pnlg...@mail.gmail.com

Re: ITP: MIRA -- A whole genome shotgun and EST sequence assembler

hai hai! i am talking with Bastien, trying to convince him to release the source out of CVS, else I will make vendor branches out of his releases. have some sake for me, please :) thank you. Dear George, There is a preliminary package in our subversion repository: