Re: Wham aligner package name - just wham? wham-align?

Hello, On May 30, 2019 5:51:05 AM EDT, Sascha Steinbiss wrote: > >Hi Steffen, > >> I have no exact idea why alignment tools are all given such short >names. >> We have http://last.cbrc.jp/ as last-align with is. Should I do the >same >> for wham and name the package wham-align? > >That's what I

Re: Co-mentors for Outreachy / GSoC urgently needed

Hi, Andreas On May 6, 2019 10:48:07 AM EDT, Andreas Tille wrote: >Hi folks, > >as you might have noticed I have registered > >https://wiki.debian.org/SummerOfCode2019/Projects#SummerOfCode2019.2FApprovedProjects.2FCIforDebianMed.Continuous_Integration_for_biological_applications_inside_Debian >

Re: Uploaders orphaning packages / Conda (Was: Bug#921382: kineticstools: autopkgtest needs update for new version of h5py)

Hello, على ٣٠‏/٥‏/١٤٤٠ هـ ‫٢:١٦ ص، كتب Andreas Tille: > Hi Afif, > > please lets move this to the list I guess it is fine to quote your > non-privat text here. Fine with me. > > On Tue, Feb 05, 2019 at 01:03:26AM -0500, Afif Elghraoui wrote: >> >> The >>

Re: Competing arrow tools in pbgenomicconsensus and unanimity

On October 11, 2018 11:14:35 AM EDT, Andreas Tille wrote: >Hi Afif, > >On Thu, Oct 11, 2018 at 09:27:16AM -0400, Afif Elghraoui wrote: >> > >> >#!/bin/sh >> >variantCaller --algorithm=arrow $* >> > >> >while unanimity installs a compiled bi

Re: Competing arrow tools in pbgenomicconsensus and unanimity

Hello, On October 11, 2018 8:06:26 AM EDT, Andreas Tille wrote: >Hi, > >package unanimity[1] now builds and creates the binary package >python-consensuscore2 which in turn is needed to build the latest >version of pbgenomicconsensus[2]. I realised that both packages are >installing a tool

Re: Please consider a free license for tRNAscan-SE

Hi, all There's still a problem with the bundled src/dbmalloc.h. I had emailed about this before--the summary is that I had tracked down the author of this file and he agreed to distribute it under the MIT license. I had forwarded the correspondence with to you privately (since I don't think

Re: Please clarify relation of code copy of daligner and dazzdb in package pbdagcon

Hi, Andreas On July 19, 2018 5:36:15 AM EDT, Andreas Tille wrote: >Hi Afif, > >in my attempt to fix Vcs-fields and other issues in packages that were >not uploaded a long time I stumbled upon pbdagcon[1]. In my latest >commit[2] I managed to convert d/watch to git mode. However, git mode >does

Please allow smalr to migrate to testing

Hello, We have one more case of an arch:all package held up in testing because of installability issues on i386 due to a dependency on bwa. Can smalr be allowed to migrate to Testing? https://qa.debian.org/excuses.php?package=smalr Thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي

Re: Removed duplicated / outdated repositories kmer-tools, falconkit

On April 2, 2018 5:19:36 PM EDT, Andreas Tille wrote: >Hi, > >when trying to fix UDD importer I stumbled upon duplicated repositories >on salsa. I removed the duplicates leaving the repository name >matching >the source package name. I deleted > > kmer-tools (and left the

Re: Ensembl-core and ensembl-tools repositories on Salsa are empty

On March 13, 2018 1:28:49 PM EDT, Andreas Tille <andr...@an3as.eu> wrote: >Hi Afif, > >On Tue, Mar 13, 2018 at 09:34:41AM -0400, Afif Elghraoui wrote: >> >It seems these can be deleted since they never had any purpose on >> >Alioth. However, if you think

Re: Ensembl-core and ensembl-tools repositories on Salsa are empty

Hi, Andreas, On March 13, 2018 4:20:23 AM EDT, Andreas Tille wrote: >Hi Afif, > >I'm currently busy to rewrite the Blends metadata gatherer to check the >repositories on Salsa. This seems to be a sensible check whether the >migration from Alioth went properly. So I have

Re: RFS: simpleitk/1.0.1-2

على الأحد 11 آذار 2018 ‫16:04، كتب Afif Elghraoui: > > > على الأحد 11 آذار 2018 ‫14:04، كتب Ghislain Vaillant: >> Could someone upload simpleitk/1.0.1-2 [1], please? > > I'll get it. > I'm getting this lintian error: E: simpleitk source: missing-notice-file-for-ap

Re: RFS: simpleitk/1.0.1-2

على الأحد 11 آذار 2018 ‫14:04، كتب Ghislain Vaillant: > Could someone upload simpleitk/1.0.1-2 [1], please? I'll get it. Thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Re: Fw: Bug#890112: ITP: porechop -- adapter trimmer for Oxford Nanopore reads

we use for the Maintainer field and then all the BTS interaction is with the same address. Not really a big deal in any case; Others have put debian-med@l.d.o in Owner in the past. Thanks for all your work regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Re: Salsa migration of Debian Med team packages

; Many thanks, Sascha! > Do we also want the automatic tag-pending assignment hook? I would say so. I think the only reason we didn't have them before was that nobody got around to adding it. Thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Re: [git...@salsa.debian.org: Access to the Debian Med group was granted]

Hi, Andreas On February 9, 2018 12:27:33 PM EST, Andreas Tille wrote: >Hi, > >I just createt the Debian Med team on Salsa to start the migration of >our packages. > >Kind regards > > Andreas. > >- Forwarded message from Debian GitLab >- >

Re: RFS: dcm2niix/1.0.20171215-1

ady pushed and tagged to the packaging repository and has been > validated on debomatic. > Done. Thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Re: removing tophat from Debian

he only reason we have a problem here is because upstream renamed the program. If hisat is the continuation of tophat and they just made tophat 3.x and 4.x, we'd right now have the latest in the archive and the older versions would be in snapshot.debian.org. This is a similar situation for wgs-as

Re: removing tophat from Debian

On December 20, 2017 5:17:20 AM EST, Michael Crusoe <michael.cru...@gmail.com> wrote: >2017-12-16 10:18 GMT+02:00 Afif Elghraoui <a...@debian.org>: > >> Hi, all, >> >> Given the statement from the website [1] >> >> > Please note that TopHat ha

Re: removing tophat from Debian

Hello, On December 17, 2017 8:35:21 PM EST, "Steffen Möller" <steffen_moel...@gmx.de> wrote: >Hello, > >On 16.12.17 22:15, Andreas Tille wrote: >> Hi Afif, >> >> On Sat, Dec 16, 2017 at 12:31:28PM -0800, Afif Elghraoui wrote: >>>> Sinc

Re: removing tophat from Debian

Hi, Andreas, On December 16, 2017 1:15:16 PM PST, Andreas Tille <andr...@an3as.eu> wrote: >Hi Afif, > >On Sat, Dec 16, 2017 at 12:31:28PM -0800, Afif Elghraoui wrote: >> >Since I'm not a user of all this software I do not have any >objections. >> >However, I w

Re: removing tophat from Debian

On December 16, 2017 1:31:01 AM PST, Andreas Tille <andr...@an3as.eu> wrote: >Hi Afif, > >On Sat, Dec 16, 2017 at 03:18:05AM -0500, Afif Elghraoui wrote: >> >> Are there any objections? > >Since I'm not a user of all this software I do not have any objectio

removing tophat from Debian

/ccb.jhu.edu/software/tophat/index.shtml 2. https://twitter.com/lpachter/status/937055346987712512 -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Re: Bug#879886: libhts2: libhts2 needs to handle ABI changes

On November 9, 2017 3:06:32 AM EST, Mattia Rizzolo wrote: >On Wed, Nov 08, 2017 at 04:58:49PM -0800, Diane Trout wrote: >> > > I was wondering if we should split the cram headers into a >> > > libhts-private-dev so we can at least track what is depending on >> > > the >> > >

Re: [Debian-med-packaging] Bug#879886: libhts2: libhts2 needs to handle ABI changes

On November 9, 2017 2:32:56 AM EST, Diane Trout <di...@ghic.org> wrote: >On Thu, 2017-11-09 at 02:03 -0500, Afif Elghraoui wrote: >> > - TODO Split private cram headers off into a new libhts-private-dev >> > package >> >> I'd rather be in favor of

Re: [Debian-med-packaging] Bug#879886: libhts2: libhts2 needs to handle ABI changes

Hi, Diane, Thanks for working on this. On November 8, 2017 7:58:49 PM EST, Diane Trout wrote: >One of the htslib developers filed a new bug, > >https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=881170 > >asking us to not make their private libraries public. His suggestions >are

Re: RFS: simpleitk/1.0.1-1 [ITP]

على الخميس 2 تشرين الثاني 2017 ‫04:59، كتب Ghislain Vaillant: > Hi Afif, thanks for taking care of the review (and uploading dcm2niix). > No problem. I'm sorry I couldn't do it sooner. > On 02/11/17 02:05, Afif Elghraoui wrote: >> Based on the Python policy, the python3-dev b

Re: RFS: simpleitk/1.0.1-1 [ITP]

k.git > 2. https://www.debian.org/doc/packaging-manuals/python-policy/build_dependencies.html 3. https://lists.debian.org/debian-devel/2017/11/msg3.html 4. https://anonscm.debian.org/cgit/debian-med/python-pysam.git/tree/debian/rules?id=5897693255ab6a36fb69cfc5bc096c65973f5f47#n25 -- Afif Elghraou

Preprint about bioconda/conda package manager

Hi, all, This just came out. It's about the bioconda project, which packages bioinformatics software for the cross-platform, user-managed conda package manager. https://www.biorxiv.org/content/early/2017/10/21/207092 regards Afif

Re: Sponsored upload (maybe): odil 0.8.0-4

s the policy > regarding the upload to unstable in this kind of case? > I would just merge the changes from the NMU into the git repository. If the packaging changes are the same as what you already have, then just include the changelog entry. Then make your new changes follow it. regards Afif

Re: Python-pysam 0.12 released, could someone please care?

Hi, Andreas, On September 3, 2017 11:50:05 PM PDT, Andreas Tille wrote: >Hi Afif, > >I noticed that you commited some promising changes. They are depending >from bcftools 1.5 which is only in experimental. From my point of view >it makes sense to move bcftools 1.5 to unstable

Re: Python-pysam 0.12 released, could someone please care?

On August 29, 2017 2:05:50 PM PDT, Andreas Tille wrote: > >Could someone please care since I'm a bit offline-ish this week. > I'll take a look maybe tonight or tomorrow. Thanks for the ping--I hadn't been watching the releases. regards Afif

Re: CI for bamtools [Outreachy]

ools. Will you take > over the sponsoring for the package? If not, please ping me. > No, I think that was Sascha who said that (or implied it). I said I was working on bcftools. I will go ahead and sponsor anyway. regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Re: [Help] Failed to upgrade bcftools to version 1.5

n. Thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Re: [Help] Failed to upgrade bcftools to version 1.5

may get auto-removed from > testing. Oh, my mistake. I misremembered the 1.4 transition as 1.5. regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Re: [Help] Failed to upgrade bcftools to version 1.5

through updating pysam since my time became scarce and the time I did spend on it was not so effecient with a slow laptop. regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Re: Getting user-space containers with Singularity - works

n example would make use of snapshot.debian.org as a mirror in the definition file in order to be able to regenerate exactly the same container at any time. regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Re: permission error

layout issue in the beginning of the MoM discussion and also gave detailed directions. If you are still having trouble at this point, please review those emails. Thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Re: Status of python-pysam

Many thanks for helping with this. At least for pbcore, there is a new release that hasn't been tagged upstream. Upstream's CI testing passes and I verified that it's using pysam 0.10.0. I previously looked at pysam 0.10.0's release notes and didn't see anything about API changes. Maybe if

Re: Please check med-bio-ngs, med-bio-phylo and med-cloud

Hi, Andreas, على الثلاثاء 24 كانون الثاني 2017 ‫00:59، كتب Andreas Tille: > Hi Afif, > > On Sat, Jan 07, 2017 at 02:38:32PM -0800, Afif Elghraoui wrote: >> >> Ok, so I will plan to move things out of med-bio into the more specific ones >> in the next few days. >

Re: Status of python-pysam

override is in order. I think the rpath is only needed for the private library module it builds (libchtslib). Otherwise, I think I can get to this tomorrow. Thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Re: test mismatches expected output in signalp 4.1c

Hello, I didn't get any response to this message of mine from last May. There are two points there: one is the output of the test suite and the other is the request to consider less restrictive licensing. Thanks and regards Afif على الخميس 5 أيار 2016 ‫15:25، كتب Afif Elghraoui: > Hello,

Re: support for software liberation

على الأحد 22 كانون الثاني 2017 ‫13:22، كتب Andreas Tille: > Hi, > > On Sun, Jan 22, 2017 at 12:34:52PM -0800, Afif Elghraoui wrote: >>> Is there any public record of this we couly add to the Wiki page? >>> I could add another mail. >> >> No, this was just

Re: support for software liberation

على الأحد 22 كانون الثاني 2017 ‫09:13، كتب Andreas Tille: >> I've tried before with signalp or rnammer and got no response. > Is there any public record of this we couly add to the Wiki page? > I could add another mail. > No, this was just a direct email to the authors. regards

Re: support for software liberation (was: New version of fast5 does not build)

Hi, Andreas, على الجمعـة 20 كانون الثاني 2017 ‫00:30، كتب Andreas Tille: > Hi Afif, > > On Thu, Jan 19, 2017 at 09:13:20PM -0800, Afif Elghraoui wrote: >> >> See https://github.com/thegenemyers/DALIGNER/issues/35 > > I've added a comment. > Thanks &g

Re: Autopkgtest for falcon

Hi, Andreas, على الخميس 19 كانون الثاني 2017 ‫05:08، كتب Andreas Tille: > On Thu, Jan 19, 2017 at 12:44:31AM -0800, Afif Elghraoui wrote: [...] >> >> I'm fine with the idea, but it's not something I would do. This seems to >> me like something that is better implemented with

Re: New version of fast5 does not build

على الخميس 19 كانون الثاني 2017 ‫05:14، كتب Andreas Tille: > On Wed, Jan 18, 2017 at 11:59:36PM -0800, Afif Elghraoui wrote: >>> >>>> daligner/dazzdb/dascrubber probably have new upstream snapshots that need >>>> to >>>> be packaged. >>>

Re: Autopkgtest for falcon

Hi, Andreas, على الأربعاء 18 كانون الثاني 2017 ‫05:33، كتب Andreas Tille: > Hi again, > > On Wed, Jan 18, 2017 at 11:34:44AM +0100, Andreas Tille wrote: >> Hi Afif, >> >> On Wed, Jan 18, 2017 at 01:33:55AM -0800, Afif Elghraoui wrote: >>> >>> falcon'

Re: New version of fast5 does not build

Hi, Andreas, On الأربعاء 18 كانون الثاني 2017 02:34, Andreas Tille wrote: Hi Afif, On Wed, Jan 18, 2017 at 01:33:55AM -0800, Afif Elghraoui wrote: I guess it should be not to hard to fix the clean target but I'm wondering whether you might intend to continue on this. This new version, if I

Re: New version of fast5 does not build

to work on the onces I consider worth uploading this weekend. I was considering working on sprai a little earlier tonight, but that didn't happen. [1] https://udd.debian.org/dmd/?email1=debian-med-packag...@lists.alioth.debian.org=html regards Afif -- Afif Elghraoui | عفيف الغراوي

Re: pbcommand new upstream

(and thank you and Andreas for working on it). I mostly wanted to fix the issue with the package version and make sure some other touch-ups made it into the upload. Thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Re: pbcommand new upstream

على السبت 14 كانون الثاني 2017 ‫21:42، كتب Sascha Steinbiss: > OK, thanks for the confirmation. I’ll update to the latest version of > pbcommand then. Many thanks for updating pbcommand--but don't forget to push the final changes and tag. :) regards Afif -- Afif Elghraoui | عفيف ا

Re: pbcommand new upstream

ons of the different PacBio tools together. If it breaks anything, then that just points out something else that should be updated. Thanks and regards Afif > > [1] https://github.com/PacificBiosciences/pbcommand/issues/116 > [2] > https://github.com/PacificBiosciences/pbcommand/commits/mast

Re: Please check med-bio-ngs, med-bio-phylo and med-cloud

On السبت 7 كانون الثاني 2017 03:48, Andreas Tille wrote: Hi Afif, On Sat, Jan 07, 2017 at 12:51:26AM -0800, Afif Elghraoui wrote: Metapackages are an exception here anyway. While we should not try to move too much around the Blends metapackages are re-uploaded short before the final

Re: Please check med-bio-ngs, med-bio-phylo and med-cloud

على السبت 7 كانون الثاني 2017 ‫00:45، كتب Afif Elghraoui: > The > problem here is making the leap to actually releasing a bio-ngs > metapackage (which is too late now anyway). Maybe it's not too late [1]. I think new binary packages are still allowed into testing--just not new source

Re: Please check med-bio-ngs, med-bio-phylo and med-cloud

e do that? Thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Re: cme tickets filed (was: cme and stylistic changes in team uploads)

For whoever's interested: على الأحد 25 كانون الأول 2016 ‫15:51، كتب Afif Elghraoui: >> IMHO we should consider two things: >> >> 1. File bug to not mess up comments https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=849500 > >> 2. File wishlist bug "plea

Re: cme and stylistic changes in team uploads

On الإثنين 26 كانون الأول 2016 06:50, Ghislain Vaillant wrote: On 25/12/16 23:51, Afif Elghraoui wrote: I think it's enough consistency that people are either using dh_make, debmake, or the debian-med packaging template and just adding to that. If people were writing these packaging files

Re: cme and stylistic changes in team uploads

Hello, على السبت 24 كانون الأول 2016 ‫22:51، كتب Andreas Tille: > Hi, > > On Sat, Dec 24, 2016 at 10:00:07PM -0800, Afif Elghraoui wrote: >>> On 24/12/16 15:41, Afif Elghraoui wrote: >>>> I'm admittedly no fan of cme's styling. While I have my own style that I &

Re: cme and stylistic changes in team uploads

Hi, Ghislain, على السبت 24 كانون الأول 2016 ‫08:12، كتب Ghislain Vaillant: > On 24/12/16 15:41, Afif Elghraoui wrote: >> Hi, all, >> >> I'm admittedly no fan of cme's styling. While I have my own style that I >> prefer to use in d/control, I don't impose this on a

Re: [MoM] deepnano getting info from maintainer

> created with empty package. I dont want to change the way this package > builded. Didn't find any useful example for python split packaging. Any > ideas? I just made this change and will upload poretools with a data package shortly. regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Re: Bug#832391: consensuscore2: Any news?

Whoa, wait a minute. Consensuscore2 hasn't been deprecated yet--it's just been bundled with other things in the unanimity suite. The reason I don't support removal of this source package is that we might find the best solution to be extracting consensuscore2 from unanimity and using that for

Re: RFS: qtltools -- Tool set for molecular QTL discovery and analysis

he License, or (at your option) any later > version...". > > Ah, you're right. I thought I did this particular check yesterday and so made the comment from memrory, but I must have been looking at another package or something. Thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Re: RFS: qtltools -- Tool set for molecular QTL discovery and analysis

d you clarify this in README.source or use a more intuitive name? the build is taking a bit too long on the computer I'm using now, so I would have to try on a more resourceful machine to fully test it out. Thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Re: New upstream version available type bugs for advent calendar use

whether its a hard one. I think the "newcomer" BTS tag would be appropriate for the easy ones, so I wanted to advertise the use of that. :) Many thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Re: pyBigWig

the situation here. Thanks and regards Afif 1. https://www.debian.org/doc/debian-policy/ch-source.html#s-embeddedfiles -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Re: [MoM] Bug#843022: ITP: emperor -- analysis and visualization of large microbial ecology datasets

e source before, it looks like you manually copied the tarball contents over the existing source. You should do it using the instructions in the Debian Med policy: http://debian-med.alioth.debian.org/docs/policy.html#updating-git-package Thanks and regards Afif -- Afif Elghraoui | عف

Re: [MoM] Bug#843022: ITP: emperor -- new version

Hi, Kerim, Any update? This part should be really quick. Thanks and regards Afif على السبت 19 تشرين الثاني 2016 ‫20:40، كتب Afif Elghraoui: > > > على السبت 19 تشرين الثاني 2016 ‫05:07، كتب Kerim Ölçer: >> i'm unterstand, shall i do make itp again > > Don't file it i

Re: [MoM] Bug#843022: ITP: emperor -- new version

fif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Re: [MoM] deepnano getting info from maintainer

her those files are useful for you. If they are, we can arrange to get them packaged and you can pull it in as a dependency. regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Re: [MoM] Bug#843022: ITP: emperor -- new version

Description : Emperor is a next-generation tool for the analysis > and visualization of large microbial ecology datasets; amongst many > features Emperor provides a modern user interface that will rapidly > adjust to your daily workflow. > Looks good. regards Afif 1. https://www.debian.org/

Re: [MoM]-Emperor package issue

Hi, Kerim, Is there any news on this packaging? Let me know if you are stuck on anything. regards Afif على الثلاثاء 1 تشرين الثاني 2016 ‫23:55، كتب Afif Elghraoui: > Hi, Kerim, > > على الثلاثاء 1 تشرين الثاني 2016 ‫11:56، كتب Kerim Ölçer: >> >> I made an ITP give lists m

Re: python-bx, upload ok? Re: galaxy dependency - current state

ke that repository belongs to a DD, but it's a couple years old. She's listed as a Debian Med member according to <https://wiki.debian.org/DebianMed/Developers>, but I have never heard of her working in our team, so it was surely before my time. Thanks and regards Afif -- Afif Elghr

Re: [Mom] Varmatch package situation

على الأربعاء 2 تشرين الثاني 2016 ‫00:45، كتب Ghislain Vaillant: > On 02/11/16 07:18, Afif Elghraoui wrote: >> Varmatch is a pretty new software package and they haven't yet made >> their first official release. I saw the preprint article, thought it was >> interesting

Re: [Mom] Varmatch package situation

rt in packaging it as a result. Being unreleased yet, the major concern is for it to produce accurate results, so you should make sure that it can reproduce the results they claim that it can with their test data. Thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Re: [MoM]-Emperor package issue

matically send the report. You can instead have it print out the text to paste into an email and send it to sub...@bugs.debian.org. Thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Re: [MoM]-Emperor package issue

out first filing the intent to package (ITP) ticket in the Debian BTS and then pointed you to git-buildpackage, which is the primary tool we're using to manage the git packaging (and handles things like importing new releases into the packaging repository). Thanks and regards Afif -- Afif El

Re: [MoM]-Emperor package issue

y to connect to the server. Take a look at <https://wiki.debian.org/Alioth/SSH> if you haven't already. regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Re: [MoM]-Emperor package issue

p import-orig --pristine-tar` command from git-buildpackage. If you already did this, go ahead and push to alioth. Make sure to push all branches and tags. regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Re: Sponsoring request: plink and galileo

u proceed with uploading. Thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Re: [MoM] Emperor license

s there anything specific that confused you (I'm not sure what you mean by a copyright license) regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Re: [MoM] packaging emperor

Hello, على الخميس 13 تشرين الأول 2016 ‫00:15، كتب Andreas Tille: > Hi, > > On Wed, Oct 12, 2016 at 11:39:44PM -0700, Afif Elghraoui wrote: >> >> Thanks for pointing this out, Andreas. I went ahead and did this >> conversion. Even if Kerim is comfortable

Re: [MoM] packaging emperor

ss of the packaging, even if it does not get completed anytime soon. Once that is up, I can look for old discussion threads regarding Andreas' previous packaging effort and post them to the log for reference. regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Re: MoM Application

ling to step in and do a mentorship. This way, two people can start at the same time. Thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Re: If you need students for small bioinformatics projects

ight be interested next > term (or next year - or at least somewhen :)). Great! > > BTW, I was not precise in my previous letter - they are non-profit > organization and they don't charge any fees from students or mentors - > except time consumption :) > Understood. Thanks and

Re: If you need students for small bioinformatics projects

على السبت 10 أيلول 2016 ‫14:23، كتب Afif Elghraoui: > It is a very nice idea and I > hope we could take advantage of it. Too many vague pronouns-- The program looks like a very nice idea and I hope that Debian Med could take advantage of it sometime. apologies for the ambiguity Afif --

Re: If you need students for small bioinformatics projects

ide to mention it. Some of my > friends know about it and they are interested in bioinformatics-related > projects. Andreas, I hope you are reading and will use this knowledge > for a great good :) > P.-P. S. - I just thought that it might help some of you to accelerate > your work or research. That's why I finally decided to write this. -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Re: Updated gwama and plink1.9

be great. > Also uploaded, though I couldn't help you with the reproducibility issue. Maybe it can be resolved for the next upload. Thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Re: Updated galileo

على السبت 13 آب 2016 ‫15:18، كتب Dylan: > Hi Afif, > > Le 13 août 2016 7:08 AM, "Afif Elghraoui" <a...@debian.org> a écrit : >> >> Your d/watch file is not working properly with uscan. Is there a >> particular reason that you have it pointing to

Re: Updated galileo

? Thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Re: linuxbrew with homebrew/science - works!

Hello and apologies for the delay [adding Tim to Cc since he was addressed in Steffen's last message] على الأحد 31 تـمـوز 2016 ‫15:07، كتب Steffen Möller: > > > On 30/07/16 10:15, Afif Elghraoui wrote: >> Hi, all, >> >> على الخميس 28 تـمـوز 2016 ‫03:54، كتب Sascha St

Re: linuxbrew with homebrew/science - works!

cial packages that follow such relaxed requirements, we might keep up in this regard with some unofficial ([semi-]auto-generated? [1]) packages, but I think our main problem is lack of support for unprivileged installation. regards Afif 1. https://wiki.debian.org/AutomaticPackagingTools -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Re: source-only uploads to new (was: Sponsoring request: ITK-4.10 (addendum))

really sure about this. New binaries in source-only uploads are somehow detected because they get automatically rejected for this reason specifically. regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Re: A common test-data package for genome assemblers

ion and shared corner cases to test (for programs that serve similar purposes) is also a very worthy reason. Thanks and regards Afif 1. https://github.com/PacificBiosciences/PacBioTestData -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Re: A common test-data package for genome assemblers

er ! Thanks for the link. Looks like one more for the to-do list.. Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Re: using `alternatives` for aligners and assemblers and promoting common interfaces

ters, so I was thinking of pushing to standardize that interface. For example, PacBio's pbalign program defines such an interface and can wrap blasr, bowtie, or gmap. I do think it's probably too much effort for too little gain, though, so I probably won't pursue it. Thanks and regards Afif -- Afif

using `alternatives` for aligners and assemblers and promoting common interfaces

). On the other hand, besides better organization and potentially more intuitive interfaces, I'm not sure whether undertaking this is worth the effort. Are there any strong feelings about this? regards Afif 1. https://wiki.debian.org/DebianAlternatives -- Afif Elghraoui | عفيف الغراوي http

A common test-data package for genome assemblers

egards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Re: [ftpmas...@ftp-master.debian.org: mypy_0.4.1-2_amd64.changes REJECTED]

r building. """ The admins responsible for buildd's for a particular arch can be reached at a...@buildd.debian.org, for example i...@buildd.debian.org. """ https://www.debian.org/devel/buildd/ regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Re: Galaxy project producing their own Debian packages

d-releases-corresponding-to-those-on -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

  1   2   3   >