Re: htslib_1.9-3_source.changes REJECTED

I really should finish that DD application. In the mean time, can I get someone to dcut dm --uid 724D609337113C710550D7473C26763F6C67E6E2 --allow htslib ? Thanks, În dum., 14 oct. 2018 la 20:19, Debian FTP Masters < ftpmas...@ftp-master.debian.org> a scris: > > > ACL dm: not allowed to upload

Re: htslib: FTBFS on i386: 2 tests fail

Andreas Tille, et al. I propose that we drop *-i386 for htslib, as it is blocking a lot of packages. On Sat, 04 Aug 2018 16:45:42 +0200 Andreas Beckmann wrote: > Source: htslib > Version: 1.9-1 > Severity: serious > Tags: ftbfs > Justification: fails to build from source (but built successfully

Re: DebianMed Sprint in Vilnius?

[sending without attachments, as no one seems to have received this?] În mar., 21 aug. 2018 la 15:24, Michael Crusoe a scris: > Howdy y'all, > > My co-working place has confirmed that we can have the common room and a > conference room for free any weekend plus one week d

Re: Delly is on salsa Re: bcbio is on salsa

CWL documents go in /use/share/commonwl/ As per https://www.commonwl.org/v1.0/CommandLineTool.html#Discovering_CWL_documents_on_a_local_filesystem mie., 11 iul. 2018, 10:27 Andreas Tille a scris: > On Tue, Jul 10, 2018 at 10:41:11PM +0200, Steffen Möller wrote: > > Delly is on the TODO list

Re: Digressions (Re: Bio-Linux 9)

2018-07-06 5:16 GMT+03:00 Charles Plessy : > Le Sun, Jun 24, 2018 at 11:26:32AM +0100, Tony Travis a écrit : > > On 24/06/18 01:21, Charles Plessy wrote: > > > > > > Very much agreed. I see how bioconda is slowly overtaking us, just by > > > providing an essential feature: the ability to install

Fwd: jellyfish_2.2.8-2_source.changes REJECTED

Hi hi, Can I be given permissions to upload new packages for Jellyfish? dcut dm --uid 724D609337113C710550D7473C26763F6C67E6E2 --allow jellyfish Thanks! -- Forwarded message -- From: "Debian FTP Masters" Date: Mar 12, 2018 14:54 Subject:

Re: sponsorship of galaxy-lib needed

Thank you, Andreas! 2018-03-05 17:29 GMT+02:00 Andreas Tille <andr...@an3as.eu>: > On Mon, Mar 05, 2018 at 03:52:00PM +0200, Michael Crusoe wrote: > > https://salsa.debian.org/med-team/galaxy-lib > > Done with some changes - please git pull, Andreas. > &g

sponsorship of galaxy-lib needed

https://salsa.debian.org/med-team/galaxy-lib Thanks! -- Michael R. Crusoe Co-founder & Lead, Common Workflow Language project Direktorius, VšĮ "Darbo eigos", Vilnius, Lithuania https://orcid.org/-0002-2961-9670

Uploading privileges requested for guzzle-sphinx-theme

dcut dm --uid 724D609337113C710550D7473C26763F6C67E6E2 --allow guzzle-sphinx-theme Thanks! -- Forwarded message -- From: "Debian FTP Masters" Date: Mar 2, 2018 18:34 Subject: guzzle-sphinx-theme_0.7.11-3_source.changes REJECTED To: "Michael R.

seqan2 FTBFS on jenkins.debian.net, but not buildd

Hello, I'm trying to troubleshoot https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/seqan2.html I see that the compilation succeeds, but the tests fail. The build daemons have no issue with seqan2: https://buildd.debian.org/status/package.php?p=seqan2 Any guidance? Locally

Fwd: ctdopts_1.2-3_source.changes REJECTED

May I have upload privileges for ctdopts? dcut dm --uid 724D609337113C710550D7473C26763F6C67E6E2 --allow ctdopts Thanks! -- Forwarded message -- From: Debian FTP Masters Date: 2018-02-25 19:49 GMT+02:00 Subject: ctdopts_1.2-3_source.changes

Fwd: [force11/force11-sciwg] Experience with Debian Science's Citations project? (#45)

FYI -- Forwarded message -- From: Katrin Leinweber Date: 2018-02-17 23:11 GMT+02:00 Subject: [force11/force11-sciwg] Experience with Debian Science's Citations project? (#45) To: force11/force11-sciwg Cc: Subscribed

two packages available for sponsorship: ctdops, ctdconverter

g...@salsa.debian.org:med-team/ctdopts.git g...@salsa.debian.org:med-team/ctdconverter.git Thanks! -- Michael R. Crusoe Co-founder & Lead, Common Workflow Language project Direktorius, VšĮ "Darbo eigos", Vilnius, Lithuania https://orcid.org/-0002-2961-9670

Re: GSoC idea: recognize Debian-Med contributions via ORCID

org/SummerOfCode2018/Projects >> >> Kind regards >> >> Andreas. >> >> On Wed, Feb 14, 2018 at 05:46:38PM +0100, Michael Crusoe wrote: >> >>> Steps: >>> 1. Collect ORCIDs using the public API >>> 2. On a monthly, quarterly, or yearly

GSoC idea: recognize Debian-Med contributions via ORCID

Steps: 1. Collect ORCIDs using the public API 2. On a monthly, quarterly, or yearly basis: generate a report of all contributions during that period and publish on Zenodo with correct metadata 3. The contribution is listed on the researchers' profiles alongside their other outputs. -- Michael R.

Re: removing tophat from Debian

2017-12-16 10:18 GMT+02:00 Afif Elghraoui : > Hi, all, > > Given the statement from the website [1] > > > Please note that TopHat has entered a low maintenance, low support > > stage as it is now largely superseded by HISAT2 which provides the > > same core functionality (i.e.

Fwd: [registry-core] heads-up! : bio.tools API / serialisation format changing

As bio.tools now has both full length URIs https://bio.tools/signalp and compact URIs (CURIES) bio.tools/signalp via https://identifiers.org/ biotools/signalp I think the https://wiki.debian.org/UpstreamMetadata Registry should stick to URIs. -- Forwarded message -- From: Jon Ison

Re: RRID -> SciCrunch

2017-10-25 20:47 GMT+03:00 Steffen Möller <steffen_moel...@gmx.de>: > > On 25.10.17 18:52, Michael Crusoe wrote: > > > > > > 2017-10-25 19:21 GMT+03:00 Steffen Möller <steffen_moel...@gmx.de > > <mailto:steffen_moel...@gmx.de>>: > &g

Re: RRID -> SciCrunch

2017-10-25 19:21 GMT+03:00 Steffen Möller <steffen_moel...@gmx.de>: > > On 25.10.17 17:49, Michael Crusoe wrote: > > > > > > 2017-10-25 18:19 GMT+03:00 Matus Kalas <matus.ka...@uib.no > > <mailto:matus.ka...@uib.no>>: > > > > On 201

Re: RRID -> SciCrunch

2017-10-25 18:54 GMT+03:00 Steffen Möller <steffen_moel...@gmx.de>: > > On 25.10.17 17:19, Matus Kalas wrote: > > On 2017-10-25 15:12, Michael Crusoe wrote: > >> 2017-10-25 16:04 GMT+03:00 Steffen Möller <steffen_moel...@gmx.de>: > >> >

Re: RRID -> SciCrunch

2017-10-25 18:19 GMT+03:00 Matus Kalas <matus.ka...@uib.no>: > On 2017-10-25 15:12, Michael Crusoe wrote: > >> 2017-10-25 16:04 GMT+03:00 Steffen Möller <steffen_moel...@gmx.de>: >> >> On 25.10.17 13:47, Michael Crusoe wrote: >>> >>>

Re: RRID -> SciCrunch (Was: [libtfbs-perl] 01/01: Update metadata; add SciCrunch ID.)

2017-10-25 16:04 GMT+03:00 Steffen Möller <steffen_moel...@gmx.de>: > > On 25.10.17 13:47, Michael Crusoe wrote: > > > > > > 2017-10-25 14:34 GMT+03:00 Steffen Möller <steffen_moel...@gmx.de > > <mailto:steffen_moel...@gmx.de>>: > &g

Re: RRID -> SciCrunch (Was: [libtfbs-perl] 01/01: Update metadata; add SciCrunch ID.)

2017-10-25 14:34 GMT+03:00 Steffen Möller <steffen_moel...@gmx.de>: > > On 25.10.17 10:56, Michael Crusoe wrote: > > Sorry, I missed the bit where we are deprecating RRID. Can someone > > explain? > > Because of https://arxiv.org/ftp/arxiv/papers/1707/1707.03659.pd

Re: RRID -> SciCrunch (Was: [libtfbs-perl] 01/01: Update metadata; add SciCrunch ID.)

Sorry, I missed the bit where we are deprecating RRID. Can someone explain? 2017-10-22 14:34 GMT+03:00 Steffen Möller : > Args, I have only now updated > > https://wiki.debian.org/UpstreamMetadata > > to reference SciCrunch by their name. > > Many thanks and sorry > >

Re: Fwd: Lack of license for pal2nal

nt, I don't have an access permission to the download site of PAL2NAL on the web, so I attached a tar.gz file that contains the modified script with the license declaration. best regards, Mikita On 2017/10/10 18:48, Michael Crusoe wrote: Hello Mikita, This is wonderful news -- thank you very

Re: Auto creation of docker images from Debian (Med) packages?

2017-10-12 10:59 GMT+03:00 Olivier Sallou <olivier.sal...@irisa.fr>: > > > On 10/11/2017 05:26 PM, Michael Crusoe wrote: > > Hello, > > A quick internet search failed me, so my apologies if the answer to this > is well known. > > Is there a service that auto

Auto creation of docker images from Debian (Med) packages?

Hello, A quick internet search failed me, so my apologies if the answer to this is well known. Is there a service that automatically builds software containers for each Debian Med application* package? As discussed at this week's biocontainers workshop, while they themselves won't be building

Re: Fwd: Lack of license for pal2nal

Hello Mikita, This is wonderful news -- thank you very much! We really appreciate it. Have a safe trip, 2017-10-10 11:46 GMT+02:00 Mikita Suyama : > Hi Peer, > > Thank you for forwarding the message. > > > Hello Michael, > > I will set GPL license to PAL2NAL to

Re: CWL workflow as Debian package

Hey Fabian, Thank you for your enthusiasm, I agree! FYI: the easiest way to find a CWL description is to do a Google **and** GitHub search for the tool name along with "cwlVersion" (which is required in all CWL v1+ documents). Cheers, Pe 15 aug. 2017 1:10 p.m., "Fabian Klötzl"

Re: CWL workflow as Debian package

GATK4 is DFSG compatible, GATK3 still has a non-DFSG core https://github.com/ProteinsWebTeam/ebi-metagenomics-cwl is entirely based upon free software, but the reference libraries are quite large 2017-08-11 18:57 GMT+03:00 Steffen Möller : > Hello, > > I had

Re: please push the last upload of python-schema-salad

Pushed, thanks for the reminder! I'll make another release with that fix. 2017-08-08 17:32 GMT+03:00 Mattia Rizzolo : > Hi, > I noticed you didn't push the last upload, could you please push it. > > FWIW, I wanted to upload the fix for https://bugs.debian.org/851336 - > which

Re: RRIDs for debian/upstream/metadata

Here's the equivalent "cool URI" for Bowtie: https://identifiers.org/rrid/RRID:SCR_005476 Pe 8 iun. 2017 19:33, "Steffen Möller" a scris: > Hello, > > We had a quick exchange on RRIDs on this list before, if I am not > erroneous. Michael is particularly supportive of

Re: Fwd: [WSSSPE] WSSSPE5.1 & WSSSPE5.2

WSSSPE4 (last year's edition) so feel free to ask questions! > Ghis > > > On Sat, 2017-06-03 at 16:00 +0300, Michael Crusoe wrote: > > The WSSSPE 5.1 conference on Sept 6th in Manchester, UK would be a good > opportunity to present our thoughts on a role for De

Fwd: [WSSSPE] WSSSPE5.1 & WSSSPE5.2

The WSSSPE 5.1 conference on Sept 6th in Manchester, UK would be a good opportunity to present our thoughts on a role for Debian in the pursuit of sustainable research software. -- Forwarded message -- From: Daniel S. Katz Date: 2017-05-31 18:11 GMT+03:00

Re: Bug#860746: ITP: easel -- a library of C functions for biological sequence analysis

You are welcome! git+ssh://git.debian.org/git/debian-med/easel.git is ready for review 2017-04-19 20:11 GMT+03:00 Andreas Tille : > Very sensible! Thanks for working on this > Andreas. > > On Wed, Apr 19, 2017 at 10:06:57AM -0700, Michael R. Crusoe wrote: > > Package:

spades updated to 3.10.1 in git

It will need sponsoring once sketch has been released -- Michael R. Crusoe Community Engineer & Co-founder Common Workflow Language project https://impactstory.org/u/-0002-2961-9670 michael.cru...@gmail.com +1 480 627 9108 +32 2 808 25 58

Re: paragraph for DPN and/or blogpost about the sprint

Pe 1 feb. 2017 18:30, "Laura Arjona Reina" a scris: Hi friends of the Debian Med team (Please CC me or -publicity, since I'm not subscribed) I just noticed that you sprinted last January in Bucharest. Reading the wiki page of the sprint and the report that Andreas Tille

Re: `internal compiler error: Segmentation fault` & `internal compiler error` w/ Seqan2

Thanks for the update. I'll disregard further errors of that type. Cheers, Pe 25 ian. 2017 10:17, "Michael Cree" <mc...@orcon.net.nz> a scris: > On Fri, Jan 13, 2017 at 02:34:36PM +0200, Michael Crusoe wrote: > > Can you help diagnose the errors I get at > > h

Second Conference of Research Software Engineers: Sep 07-08, 2017

Hello all, As you all probably know, there is a huge need for sustainable community maintenance of research software; and I think Debian is the logical foundation for such efforts due to its distributed nature and extensive technical & social infrastructure** To help make this a reality I urge

`internal compiler error: Segmentation fault` & `internal compiler error` w/ Seqan2

Hello Alpha team, Can you help diagnose the errors I get at https://buildd.debian.org/status/fetch.php?pkg=seqan2=alpha=2.3.0~1.20161019~af07bc1%2Bdfsg-4=148010 ? Thanks! -- Michael R. Crusoe Community Engineer & Co-founder Common Workflow Language project

Re: Sprint organisation

> > On 2017-01-09 16:38, Michael Crusoe wrote: > >> 2017-01-09 17:35 GMT+02:00 Olivier Sallou <olivier.sal...@irisa.fr>: >> >> On 01/09/2017 11:34 AM, Michael Crusoe wrote: >>> >>> I did a walk through of the space today, a snowy 10 minute walk >&

Re: Sprint organisation

2017-01-09 17:35 GMT+02:00 Olivier Sallou <olivier.sal...@irisa.fr>: > > > On 01/09/2017 11:34 AM, Michael Crusoe wrote: > > I did a walk through of the space today, a snowy 10 minute walk from the > hotel. > > Good news on the Wi-Fi! > > http://www.speedtes

Re: Sprint organisation

I did a walk through of the space today, a snowy 10 minute walk from the hotel. Good news on the Wi-Fi! http://www.speedtest.net/my-result/a/2527663676 Pe 8 ian. 2017 8:25 p.m., "Andreas Tille" <andr...@an3as.eu> a scris: > Hi, > > On Sun, Jan 08, 2017 at 11:13:24AM -0

Re: Sprint organisation

Hello Olivier, I will be at the Sprint site starting from Thursday, and I can either meet people at the hotel and walk them over or give them directions on the phone. To reach me, please use my Belgian or US numbers: +32 2 808 25 58 or +1 480 627 9108 I can receive SMS via my US number, and it

Re: Sprint

Happy to alert when the DPL sends approval -- I haven't had any reply to my request of three days ago. 2016-12-19 19:25 GMT+02:00 olivier sallou : > Hi mickael, > Can you ping us when you have approval from dpl for the sprint? I will > check fir plane tickets right

Application for approval of the Debian Med Sprint 2017

The DebianMed team is planning to hold a Sprint meeting in Bucharest, Romania from January 12th to January 16th, 2017.. This is the 7th sprint event of the team. More info will come on the wiki page: https://wiki.debian.org/Sprints/2017/DebianMed2017 The goals of this sprint is to progress on

Sprint will be Jan 12th-16th in Bucharest

Thank you all for your responses to the many polls, and for your patience. I will start collecting quotes from hotels and meetings spaces. Feel free to book transportation now.

Re: Versioning of snap-aligner

Go for it :-) Pe 2 dec. 2016 19:42, "Andreas Tille" <andr...@an3as.eu> a scris: > Hi Michael, > > On Fri, Dec 02, 2016 at 04:52:39PM +0200, Michael Crusoe wrote: > > 2016-12-02 15:22 GMT+02:00 Andreas Tille <andr...@an3as.eu>: > > > I'd be m

Re: Versioning of snap-aligner

2016-12-02 15:22 GMT+02:00 Andreas Tille <andr...@an3as.eu>: > Hi Michael, > > On Fri, Dec 02, 2016 at 03:00:26PM +0200, Michael Crusoe wrote: > > This issue may not provide much value for effort. Upstream never > responded > > to my request for clarification: htt

Two weekends to consider in detail: Jan 14th, Feb 4th

Andreas Tille can't make the weekend of February 11th I am re-evaluating two different weekends: January 14th and February 4th. Please respond with which days you'd attend in this new poll so we can finalize the dates and I can pick a venue.

Re: Versioning of snap-aligner

This issue may not provide much value for effort. Upstream never responded to my request for clarification: https://github.com/amplab/snap/issues/57 2016-12-02 13:39 GMT+02:00 Ghislain Vaillant : > On 02/12/16 10:38, Andreas Tille wrote: > >> Hi Michael, >> >> when browsing

Re: Sprint

Hello Olivier, After discussing with the locals we came to the conclusion that a Bucharest location will increase involvement people living in Romania. I've updated the wiki to reflect this. Pe 19 nov. 2016 10:08 a.m., "olivier sallou" a scris: > Hi mickael, > Wiki sprint

Re: DebianMed Sprint

No worries Olivier, the more the merrier! What's the procedure for getting a budget from Debian? Switching focus to the weekend of February 11th, the follow up poll is at at https://dudle.inf.tu-dresden.de/DebianMed2017Specifics2/ to narrow down the official start and end dates. If anyone wants

Re: request: dm upload rights for r-cran-future

Likewise r-bioc-geneplotter 2016-11-10 13:23 GMT+02:00 Michael Crusoe <michael.cru...@gmail.com>: > dcut dm --uid 724D609337113C710550D7473C26763F6C67E6E2 > --allow r-cran-future > > Thanks, > > -- > Michael R. Crusoe > Community Engineer & Co-founder > C

request: dm upload rights for r-cran-future

dcut dm --uid 724D609337113C710550D7473C26763F6C67E6E2 --allow r-cran-future Thanks, -- Michael R. Crusoe Community Engineer & Co-founder Common Workflow Language project https://impactstory.org/u/-0002-2961-9670 michael.cru...@gmail.com +40 720 781 765 +1 480 627

Re: Next sprint

://dudle.inf.tu-dresden.de/DebianMed2016/ ** and I'll send out a new specific dates poll if the overall consensus shifts. ** Yes, I got the year wrong on this one :-) 2016-11-07 12:56 GMT+02:00 Michael Crusoe <michael.cru...@gmail.com>: > Hello Oliver, > > Thank you for the reminde

Re: Next sprint

Hello Oliver, Thank you for the reminder. I've waiting to hear back from a local who wants to co-host. In the meantime, we should pick the weekend to meet up. I've made a poll at https://dudle.inf.tu-dresden.de/DebianMed2016/ Everyone: please indicate which weekends you would be able to

Advice sought for fixing seqan2 OOM build errors

Hello kfreebsd-*, The seqan2 builds are running out of memory even with "-j2" Do we need to add logic to turn off parallel builds ourselves in d/rules or is there a better way? Cheers, -- Michael R. Crusoe Community Engineer & Co-founder Common Workflow Language project

RFS r-hms-dbmi-spp

git+ssh://git.debian.org/git/debian-med/r-hms-dbmi-spp.git Thanks! -- Michael R. Crusoe Community Engineer & Co-founder Common Workflow Language project https://impactstory.org/u/-0002-2961-9670 michael.cru...@gmail.com +40 720 781 765 +1 480 627 9108

r-cran-knitr not up to date in git?

I have a fix for the failing tests, it needs the r-cran-codetools dependency added -- Michael R. Crusoe Community Engineer & Co-founder Common Workflow Language project https://impactstory.org/u/-0002-2961-9670 michael.cru...@gmail.com +40 720 781 765 +1 480 627

Re: Anybody able to have a 20min talk at 3rd Swiss Galaxy Workshop, Thursday, October 20th, Freiburg (Germany)?

That's unfortunate to hear. I would volunteer, except that I'll be in Barcelona for the BioExcel workflows workshop. 2016-10-12 12:24 GMT+03:00 Andreas Tille : > Hi, > > I was invited to > >https://wiki.galaxyproject.org/Events/Switzerland2016 > > to have a short talk about

Re: seqan2_2.2.0+dfsg-4~test_source.changes ACCEPTED into unstable

Whoops, this was only meant for experimental, mea culpa! If it works I'll make a new release within the five day window that skips armel due to https://github.com/seqan/seqan/issues/1861#issuecomment-252641362 Is there a simpler syntax to skip a specific architecture yet? Last I knew one had to

Re: seqan2_2.2.0+dfsg-3_source.changes REJECTED

Dear friends, can I get a dcut dm --uid 724D609337113C710550D7473C26763F6C67E6E2 --allow seqan2 ? Thanks, 2016-10-09 16:54 GMT+03:00 Debian FTP Masters < ftpmas...@ftp-master.debian.org>: > > > ACL dm: not allowed to upload source package 'seqan2' > > === > > Please feel free to respond to

upload rights request for python3-typed-ast

Thanks! -- Michael R. Crusoe Community Engineer & Co-founder Common Workflow Language project https://impactstory.org/u/-0002-2961-9670 michael.cru...@gmail.com +40 720 781 765 +1 480 627 9108

Re: Packaging wishlist for this week's H3Africa workshop

On Tue, Sep 13, 2016 at 10:26 AM, Andreas Tille <andr...@an3as.eu> wrote: > Status update. > > On Mon, Aug 22, 2016 at 05:42:26PM +0200, Michael Crusoe wrote: > > > I'm at the H3Abionet Cloud computing hackathon this week in Pretoria, > > > South Africa. >

Re: FYI: New Abyss 2.0 contains undistributable components

9840 https://twitter.com/biocrusoe/status/772874936012664832 On Mon, Sep 5, 2016 at 10:12 PM, Andreas Tille <andr...@an3as.eu> wrote: > Hi Michael, > > On Mon, Sep 05, 2016 at 07:17:10PM +0300, Michael Crusoe wrote: > > Just to save you all some time. > > > > https://git

FYI: New Abyss 2.0 contains undistributable components

Just to save you all some time. https://github.com/bcgsc/abyss/tree/master/lib/rolling-hash which is from https://github.com/bcgsc/ntHash/blob/master/COPYING Likewise https://github.com/bcgsc/abyss/tree/master/lib/bloomfilter which is from

Re: [Help] Could anybody provide a docker container to test POCL OpenCL interface for beagle lib

Just Debian or Debian plus extra software? For the former than can `docker pull debian:sid` for the later I'll need a list of package names or pointers to repositories to build from. Pe 1 sept. 2016 09:29, "Andreas Tille" a scris: > Hi, > > I have opened an issue on

Re: Packaging wishlist for this week's H3Africa workshop

Thanks! Pe 27 aug. 2016 9:46 a.m., "Andreas Tille" <andr...@an3as.eu> a scris: > On Mon, Aug 22, 2016 at 05:36:30PM +0200, Michael Crusoe wrote: > > phloseq https://github.com/joey711/phyloseq > > Packaging prepared in > > svn://anonscm.debian.org/

Re: EBI-ELIXIR and descriptional workflows

My understanding from talking with the TESS team is that these are abstract workflows and not meant to be directly executable, so no competition for CWL :-) One could imagine a model "finished" workflow created in CWL as a reference. Pe 21 aug. 2016 10:50, a scris: > Hey

Re: Packaging wishlist for this week's H3Africa workshop

One more: snpeff http://snpeff.sourceforge.net/download.html On Mon, Aug 22, 2016 at 5:36 PM, Michael Crusoe <michael.cru...@gmail.com> wrote: > Hello everyone, > > I'm at the H3Abionet Cloud computing hackathon this week in Pretoria, > South Africa. > > http://ww

Packaging wishlist for this week's H3Africa workshop

Hello everyone, I'm at the H3Abionet Cloud computing hackathon this week in Pretoria, South Africa. http://www.h3abionet.org/training-and-education/h3abionet-courses/17-h3abionet-courses/h3abionet-courses-upcoming/266-h3abionet-cloud-computing-hackathon The resulting CWL tools and workflow

Re: RFS: python3-typed-ast, hisat2

you think? > I'm not familiar with that team's norms. I'm happy to hand it over after it is accepted. > > Cheers and thanks for working on these > Sascha > > [1] https://wiki.debian.org/Teams/PythonModulesTeam > > > > On 17 Aug 2016, at 16:56, Michael Crusoe <michael.cru

RFS: python3-typed-ast, hisat2

Thanks! -- Michael R. Crusoe Community Engineer & Co-founder Common Workflow Language project https://impactstory.org/u/-0002-2961-9670 michael.cru...@gmail.com +40 720 781 765 +1 480 627 9108

Re: trinityrnaseq in Git

Done, sorry about that! [I forced pushed with your commit after mine] On Fri, Aug 5, 2016 at 6:40 PM, Sascha Steinbiss wrote: > Hi all, > > I was going to look at the last GCC 6 FTBFS and trinityrnaseq looks like > a good point to start. However, 2.2.0-dfsg-1 is already in

While we wait for Galaxy, two other F/OSS CWL implementations could be packaged

TOIL: https://github.com/BD2KGenomics/toil Arvados, from Curoverse: https://github.com/curoverse/arvados -- 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

Re: Status of seqan

Agreed On Wed, Jul 20, 2016 at 11:16 AM, Andreas Tille <ti...@debian.org> wrote: > On Wed, Jul 20, 2016 at 10:57:44AM +0200, Michael Crusoe wrote: > > Are the upstreams using 2.0, 2.1, or 2.2? > > Well, flexbar is using 2.1.1 - but if you ask me we should follow the &g

MEGAN finally released under the GPL!

Any volunteers? https://github.com/danielhuson/megan-ce/ (Found via https://twitter.com/koadman/status/755041609683574784 )

Re: A common test-data package for genome assemblers

This is a great idea! On Wed, Jul 13, 2016 at 11:24 AM, Afif Elghraoui wrote: > Hi, all, > > I've had a couple packages that indicate the availability of data > outside of the source distribution that can be used to try out the > software (and make sure that it actually runs).

List of software debuted at ISMB2016

https://github.com/bioconda/bioconda-recipes/pull/1951 URLs and availability helpfully consolidated by the BioConda community. I like their suggestion of a SVG badge (suitable for posters, slideshows, webpages, and handouts) to offer tool authors who get their software packaged.

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

Pe 11 iul. 2016 11:17, "Andreas Tille" <andr...@an3as.eu> a scris: > > On Mon, Jul 11, 2016 at 10:02:11AM -0500, Michael Crusoe wrote: > > Yeah, -dev is inappropriate; we aren't compiling a custom module. Something > > broke with the Python packages in unstabl

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

Yeah, -dev is inappropriate; we aren't compiling a custom module. Something broke with the Python packages in unstable. Using python*-dev leads to I: mypy source: build-depends-on-python-dev-with-no-arch-any N: N:The given package appears to have a Python development package N:

Heads up: bioperl release candidate

Hello from the Bioinformatics Open Source Conference codefest. I'm sitting here with Hilmar Lapp & Christopher Fields who are working on a new release of bioperl. If someone would like to try updating the Debian package with the release candidate and testing it that would be useful:

Re: Galaxy project producing their own Debian packages

, 2016 at 11:07 AM, Olivier Sallou <olivier.sal...@irisa.fr> wrote: > > > On 06/16/2016 08:43 AM, Michael Crusoe wrote: > > > > Vezi Tweetul lui @natefoo: > > https://twitter.com/natefoo/status/743306923026440194 > > > > https://depot.galaxyproject.org/nat

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

rg , 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 < > michael.cru...@gmail.com> wrote: >> >> >> >> On Tue, Jun 28, 2016 at 9:10 AM, S

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 <andr...@an3as.eu> 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 pack

Re: RRID: a namespace for research software

On Tue, Jun 28, 2016 at 9:10 AM, Steffen Möller <steffen_moel...@gmx.de> 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

Re: Galaxy project producing their own Debian packages

wrote: > > > On 06/16/2016 08:43 AM, Michael Crusoe wrote: > > > > Vezi Tweetul lui @natefoo: > > https://twitter.com/natefoo/status/743306923026440194 > > > > https://depot.galaxyproject.org/nate/dpkg/ > > > nice, but easy for them. Galaxy installs

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

Pe 27 iun. 2016 4:54 a.m., "Andreas Tille" a scris: > > On Sun, Jun 26, 2016 at 09:30:36PM +0200, Andreas Tille wrote: > > > Good catch; I've updated r-cran-r.cache, r-cran-future, r-cran-globals, and > > > r-cran-listenv. > > > > Uploaded with exception of r-cran-future which

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

On Sun, Jun 26, 2016 at 3:30 PM, Andreas Tille <andr...@an3as.eu> wrote: > Hi Michael, > > On Sun, Jun 26, 2016 at 11:08:57AM -0400, Michael Crusoe wrote: > > > > Good catch; I've updated r-cran-r.cache, r-cran-future, r-cran-globals, > and > > r-cran-liste

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

much as possible tested. > > I'll sponsor later if nobody else will beat me. > > Kind regards > > Andreas. > > On Sat, Jun 25, 2016 at 09:50:13PM -0400, Michael Crusoe wrote: > > These are all dependencies of cnvkit http://cnvkit.readthedocs.io/ > > --

Re: Request for discussion: Is our Sprint more of a Mini-DebConf? What to have next?

On Tue, Jun 21, 2016 at 7:49 PM, Steffen Möller <steffen_moel...@gmx.de> wrote: > > > On 16/06/16 09:56, Michael Crusoe wrote: > > On Tue, Jun 14, 2016 at 1:12 AM, Steffen Möller > > <steffen_moel...@gmx.de <mailto:steffen_moel...@gmx.de>> wrote: > >

Re: Request for discussion: Is our Sprint more of a Mini-DebConf? What to have next?

On Tue, Jun 14, 2016 at 1:12 AM, Steffen Möller wrote: > Hello, > > I was peeking into the one or other scientific collaboration of mine to > invite them to our next Debian Med sprint. But I could not really tell > much about it, yet. Besides deciding where to convene

Re: NETTAB 2016 abstract deadline extended to June 30th

On Wed, Jun 8, 2016 at 3:53 PM, Andreas Tille <andr...@an3as.eu> wrote: > Hi Michael, > > On Wed, Jun 08, 2016 at 02:58:34PM +0200, Michael Crusoe wrote: > > Solicited topics http://www.igst.it/nettab/2016/submissions/topics/ > > Sounds very good. > > > I thin

NETTAB 2016 abstract deadline extended to June 30th

Solicited topics http://www.igst.it/nettab/2016/submissions/topics/ I think a presentation on what Debian (Med) has to offer the community would be well received and I would be happy to co-author or advise such an abstract. The COST mechanism is also interesting: could fund a four year project

Re: Debian Med in CentOS HPC environment - how?

Reminder: you can make fake chroots without root privileges (can also be used to convert Docker images and run software within them): https://github.com/common-workflow-language/common-workflow-language/wiki/Userspace-Container-Review#getting-userspace-containers-working-on-ancient-rhel If your

Re: Please provide source code for Tandem Repeats Finder under a freely redistributable license

Dear Yozen, As a research software engineer who works with sequencing analysis researchers I join Andreas in asking you to release Tandem Repeat Finder under a free license. I see that you have been funded with NSF grants, that is great! However, to treat the public ethically, the software

Re: Processing of dcut.Michael_R__Crusoe__michael_crusoe_gmail_com_.1462615038.28130.commands

7 May 2016, 12:00 p.m. Michael Crusoe, <michael.cru...@gmail.com> > wrote: > >> Ugh, how do I re-upload a rejected package? >> -- Mesaj redirecționat -- >> De la: "Debian FTP Masters" <ftpmas...@ftp-master.d

Fwd: Processing of dcut.Michael_R__Crusoe__michael_crusoe_gmail_com_.1462615038.28130.commands

Ugh, how do I re-upload a rejected package? -- Mesaj redirecționat -- De la: "Debian FTP Masters" Dată: 7 mai 2016 11:59 a.m. Subiect: Processing of dcut.Michael_R__Crusoe__michael_crusoe_gmail_com_.1462615038.28130.commands Către:

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