Re: RFS: r-bioc-geneplotter & r-bio-deseq2

I'll take it. On Tue, Jun 28, 2016 at 09:26:33PM -0400, Michael Crusoe wrote: > Thanks! > > -- > Michael R. Crusoe > Community Engineer & Co-founder > Common Workflow Language project > https://impactstory.org/u/-0002-2961-9670 > michael.cru...@gmail.com > +32 (0) 2 808 25 58 > +1 480 627 91

Re: Daily Report[28.06.16] [GSOC]

Hallo Canberk, thanks for your daily report. On Tue, Jun 28, 2016 at 08:01:29PM +0300, Canberk Koç wrote: > I write to maker of Muscle he give me a recipe as you see. I've seen this. May be we are lucky and upstream will respond. > I work on perlprimer and this program don't work from console

RFS: r-bioc-geneplotter & r-bio-deseq2

Thanks! -- Michael R. Crusoe Community Engineer & Co-founder Common Workflow Language project https://impactstory.org/u/-0002-2961-9670 michael.cru...@gmail.com +32 (0) 2 808 25 58 +1 480 627 9108

Re: RRID: a namespace for research software

I'm a big fan of the duecredit project, but I am a bit unclear as to what role Debian can play here. Pe 28 iun. 2016 16:36, "Yaroslav Halchenko" a scris: > Related (although we yet to "support" RRIDs) - have a look at > http://duecredit.org , might be of interest if you are looking into > sitting

Re: RRID: a namespace for research software

Related (although we yet to "support" RRIDs) - have a look at http://duecredit.org , might be of interest if you are looking into sitting surviving methods and contributions, not only entire package On June 28, 2016 5:57:00 PM GMT+02:00, Michael Crusoe wrote: >On Tue, Jun 28, 2016 at 9:10 AM,

Daily Report[28.06.16] [GSOC]

Hello Andreas, I admit that some programs can make people insane :-) I write to maker of Muscle he give me a recipe as you see. I work on perlprimer and this program don't work from console or interface it gives an error inself about array bug report

Muscle Tests

Hello, I'm contacting you on behalf of the Debian Med team. I work on a Google Summer of Code project in Debian Med here is the link of project Debian Med CI project due to this program i must produce autopkgtests for muscle. At thi

Re: request for sponsorship: r-cran-r.cache r-cran-future r-cran-globals r-cran-listev r-bioc-dnacopy

On Tue, Jun 28, 2016 at 3:31 AM, Andreas Tille wrote: > On Mon, Jun 27, 2016 at 08:14:39AM -0400, Michael Crusoe wrote: > > > does *not* resolve package dependencies (which sucks, I know, but > nobody > > > feels obliged to write a proper R packaging support). So you always > need > > > to repea

Re: RRID: a namespace for research software

On Tue, Jun 28, 2016 at 9:10 AM, Steffen Möller wrote: > > On 27/06/16 16:22, Andreas Tille wrote: > > On Mon, Jun 27, 2016 at 10:04:40AM -0400, Michael Crusoe wrote: > >> http://identifiers.org/rrid/ > >> > >> Example: http://identifiers.org/rrid/RRID:SCR_001156 > >> > >> Where would be the best

Re: Galaxy project producing their own Debian packages

On 06/28/2016 04:34 PM, Olivier Sallou wrote: > by the way, as they are all python packages, should we handle them in > DebianMed or Python team ? > > On 06/28/2016 03:20 PM, Steffen Möller wrote: >> This is great! That custom fokr of pysam reads as if one wants to avoid >> that and rather give t

Re: Orthanc 1.1.0

Hi, In complement to yesterday's update of the main "orthanc" package, I have just updated two of its companion plugins: - orthanc-webviewer 2.2 [1] - orthanc-dicomweb 0.3 [2] Would it be possible to upload them as well? TIA, Sébastien- [1] http://anonscm.debian.org/viewvc/debian-med?view=

Re: Galaxy project producing their own Debian packages

by the way, as they are all python packages, should we handle them in DebianMed or Python team ? On 06/28/2016 03:20 PM, Steffen Möller wrote: > This is great! That custom fokr of pysam reads as if one wants to avoid > that and rather give those extra features back to everyone via upstream. > > I'

Re: Galaxy project producing their own Debian packages

On 06/28/2016 03:20 PM, Steffen Möller wrote: > This is great! That custom fokr of pysam reads as if one wants to avoid > that and rather give those extra features back to everyone via upstream. > > I'll do bioblend and svgwrite - now. > > Anybody else chiming in? > > > bx-python > wchartype > di

Bug#828850: ITP: r-bioc-deseq2 -- R package for RNA-Seq Differential Expression Analysis

Package: wnpp Severity: wishlist Owner: Debian Med team * Package name: r-bioc-deseq2 Version : 1.12.3 Upstream Author : Michael Love * URL : https://bioconductor.org/packages/DESeq2 * License : LGPL-3+ Programming Lang: R Description : R package for R

Re: Galaxy project producing their own Debian packages

This is great! That custom fokr of pysam reads as if one wants to avoid that and rather give those extra features back to everyone via upstream. I'll do bioblend and svgwrite - now. Anybody else chiming in? bx-python wchartype dictobj bioblendSteffen requests-toolbelt pulsar-galaxy-

Re: RRID: a namespace for research software

On 27/06/16 16:22, Andreas Tille wrote: > On Mon, Jun 27, 2016 at 10:04:40AM -0400, Michael Crusoe wrote: >> http://identifiers.org/rrid/ >> >> Example: http://identifiers.org/rrid/RRID:SCR_001156 >> >> Where would be the best place to incorporate this into Debian? We are >> adding support for thi

Re: Galaxy project producing their own Debian packages

On Tuesday, June 28, 2016, Afif Elghraoui wrote: > Hello, > > على الإثنين 27 حزيران 2016 ‫12:04، كتب Michael Crusoe: > > Python packages that need packaging: > > > > bx-python > [...] > > I had started some packaging work on bx-python as a dependency for > pbtranscript, but that seems not to be a

Re: Primer3

Hello Canberk, On Tue, Jun 28, 2016 at 10:55:46AM +0300, Canberk Koç wrote: > I am working on perlprimer but it is a visual tool so it might be tricky i > tried it and saw a solution about test i think. OK. > Looking for ffindex again > and muscle situation.I think i manage them in this week. T

Bug#828690: marked as done (ITP: r-cran-pscbs -- R package: Analysis of Parent-Specific DNA Copy Numbers)

Your message dated Tue, 28 Jun 2016 08:00:21 + with message-id and subject line Bug#828690: fixed in r-cran-pscbs 0.61.0-1 has caused the Debian Bug report #828690, regarding ITP: r-cran-pscbs -- R package: Analysis of Parent-Specific DNA Copy Numbers to be marked as done. This means that yo

Re: Primer3

Hello Andreas, I am working on perlprimer but it is a visual tool so it might be tricky i tried it and saw a solution about test i think. Looking for ffindex again and muscle situation.I think i manage them in this week. I could give you daily report every day at evening is it okay ? Best Regards

Re: Suspicious output in test (Was: [ffindex] 01/01: Autopkgtest suite added with allocation error])

Hello Andreas, It is remain unsolved it gives same error at build time also.I relook at it and give you a feedback by evening. Best Regards Canberk Koç [image: https://]about.me/canberkkoc

Re: Primer3

Hi Canberk, On Mon, Jun 27, 2016 at 10:25:40AM +0300, Canberk Koç wrote: > Thanks for trusting me,guidance and give pass. Please make sure that you try to commit daily some resultsof your work even if not finished or at least give a daily report about your work and potential showstoppers. > I'm

Re: Suspicious output in test (Was: [ffindex] 01/01: Autopkgtest suite added with allocation error])

Hi Canberk, what's the status of this test? Kind regards Andreas. On Fri, Jun 24, 2016 at 10:44:35AM +0300, Canberk Koç wrote: > Hi Andreas, > > I forget to use -s parameter for ffindex_build i'll fix it today. İt gives > allocation error as i said before in my testbed. > > Best Regards

Re: request for sponsorship: r-cran-r.cache r-cran-future r-cran-globals r-cran-listev r-bioc-dnacopy

On Mon, Jun 27, 2016 at 08:14:39AM -0400, Michael Crusoe wrote: > > does *not* resolve package dependencies (which sucks, I know, but nobody > > feels obliged to write a proper R packaging support). So you always need > > to repeat the Build-Depends inside Depends. > > Oof, sorry for forgetting t

Re: Galaxy project producing their own Debian packages

Hello, على الإثنين 27 حزيران 2016 ‫12:04، كتب Michael Crusoe: > Python packages that need packaging: > > bx-python [...] I had started some packaging work on bx-python as a dependency for pbtranscript, but that seems not to be a dependency anymore, so I didn't pursue it. In any case, bx-python d