Re: libjung-free-java_2.0.1-1_amd64.changes REJECTED

I've uploaded an amended package without the offending code and I've deleted the previous debian/2.0.1-1 tag Andreas, could you review & upload? On Thu, Jan 14, 2016 at 10:44 AM Michael R. Crusoe wrote: > According to their sourceforge page a new release is imminent & they are > moving to GitHu

trinityrnaseq ready for review!!

Now that libjung-free-java has been accepted I've updated the trinityrnaseq package The tests again pass, this has been tested in a debci virtual machine. All that is left is two spelling corrections and a mysterious hardening warning from Lintian. Given that this package is quite complex I thou

Re: Doc package in seqan remains empty

I'll email the team; am trying to build a partnership with them for other reasons. Vin, 22 ian. 2016, 16:45, Andreas Tille a scris: > Hi Kevin, > > I worked a bit on seqan and injected the latest upstream version > (2.0.1). I have no idea whether the seqan-doc package that was injected > by you

Re: [Debian-med-packaging] Bug#812376: snap-aligner: FTBFS on non-x86: unrecognized command line option '-msse'

I've fixed this. Can someone upload the -2 package for me? On Sat, Jan 23, 2016 at 12:39 AM Aaron M. Ucko wrote: > Source: snap-aligner > Version: 0.18~1.0~beta.18+dfsg1-1 > Severity: important > Justification: fails to build from source > > Builds of snap-aligner for non-x86 architectures all f

Re: Bug#810842: [a...@debian.org: Bug#810842: igv: libsam-java is gone]

You need to change the invocation in /usr/bin/tracer to be java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" -classpath /usr/share/java/itext1.jar:$BEAST_LIB/tracer.jar dr.app.tracer.application.TracerApp On Wed, Jan 27, 2016 at 7:50 PM, Andreas Tille wrote: > On Wed, Jan 27, 2016 at 04:2

Re: Bug#810842: [a...@debian.org: Bug#810842: igv: libsam-java is gone]

and libhmsbeagle-java is missing a dependency on libhmsbeagle1v5 which is also causing a problem. Looks like this was fixed in git but unreleased. On Wed, Jan 27, 2016 at 9:28 PM, Michael Crusoe wrote: > You need to change the invocation in /usr/bin/tracer to be > > java -Xms64m

Re: Bug#810842: [a...@debian.org: Bug#810842: igv: libsam-java is gone]

On Thu, Jan 28, 2016 at 12:09 PM Andreas Tille wrote: > Hi Michael, > > On Wed, Jan 27, 2016 at 10:06:49PM +0200, Michael Crusoe wrote: > > and libhmsbeagle-java is missing a dependency on libhmsbeagle1v5 which is > > also causing a problem. Looks like this was fixed in git

Re: trinityrnaseq ready for review!!

On Sat, Jan 16, 2016 at 2:36 PM Andreas Tille wrote: > Hi Michael, > > On Fri, Jan 15, 2016 at 11:00:05PM +, Michael Crusoe wrote: > > All that is left is two spelling corrections > > Sometimes I just report this upstream and ignore it for the package ... > Don

Re: trinityrnaseq ready for review!!

PM +0000, Michael Crusoe wrote: > > On Sat, Jan 16, 2016 at 2:36 PM Andreas Tille wrote: > > > > > Hi Michael, > > > > > > On Fri, Jan 15, 2016 at 11:00:05PM +, Michael Crusoe wrote: > > > > > > All that is left is two spelling correctio

new version of libspdlog-dev ready for sponsoring

git+ssh://git.debian.org/git/debian-med/spdlog.git Thanks! -- Michael R. Crusoe CWL Community Engineer cru...@ucdavis.edu Common Workflow Language projectUniversity of California, Davis https://impactstory.org/MichaelRCrusoe http://twitter.com/biocrusoe

Re: new version of libspdlog-dev ready for sponsoring

Sorry, was testing all the way through with salmon & transrate; should be available now. On Sat, Jan 30, 2016 at 7:38 PM Andreas Tille wrote: > On Sat, Jan 30, 2016 at 05:26:11PM +, Michael Crusoe wrote: > > git+ssh://git.debian.org/git/debian-med/spdlog.git >

Request for review & upload: salmon

The Lintian warning is due to the eigen3 library; I've filed a bug about that. Thanks! -- Michael R. Crusoe CWL Community Engineer cru...@ucdavis.edu Common Workflow Language projectUniversity of California, Davis https://impactstory.org/MichaelRCrusoe http://twitter.com/biocrusoe

Re: Request for review & upload: salmon

On Sat, Jan 30, 2016 at 8:10 PM Andreas Tille wrote: > On Sat, Jan 30, 2016 at 05:51:59PM +0000, Michael Crusoe wrote: > > The Lintian warning is due to the eigen3 library; I've filed a bug about > > that. > > Probably a lintian check for an empty debian/upstream/me

Re: Request for review & upload: salmon

Thank you! Sâm, 30 ian. 2016, 22:56, Andreas Tille a scris: > On Sat, Jan 30, 2016 at 06:32:54PM +0000, Michael Crusoe wrote: > > > > Heh, a timely mistake. Fixed. > > So its uploaded now (after fixing yaml syntax). > > Thanks for your work on this > >

Re: [Debian-med-packaging] mira is marked for autoremoval from testing

I have a fix for this; am converting the repo to Git first. On Tue, Feb 2, 2016 at 6:39 AM Debian testing autoremoval watch < nore...@release.debian.org> wrote: > mira 4.9.5-2 is marked for autoremoval from testing on 2016-02-23 > > It is affected by these RC bugs: > 812681: mira: FTBFS with flex

python-screed package with autopkgtests avail for uploading

git+ssh://git.debian.org/debian-med/python-screed.git Thanks! -- Michael R. Crusoe CWL Community Engineer cru...@ucdavis.edu Common Workflow Language projectUniversity of California, Davis https://impactstory.org/MichaelRCrusoe http://twitter.com/biocrusoe

Re: [Debian-med-packaging] mira is marked for autoremoval from testing

Interestingly there is already a git repo for mira; last commit is from 2010. I'm moving it from /git/debian-med/mira.git to /git/debian-med/mira-old.git On Tue, Feb 2, 2016 at 3:31 PM Michael Crusoe wrote: > I have a fix for this; am converting the repo to Git first. > > > On

Re: [Debian-med-packaging] mira is marked for autoremoval from testing

On Tue, Feb 2, 2016 at 5:41 PM Andreas Tille wrote: > On Tue, Feb 02, 2016 at 03:25:37PM +0000, Michael Crusoe wrote: > > Interestingly there is already a git repo for mira; last commit is from > > 2010. I'm moving it from /git/debian-med/mira.git > > to /git/debian-m

macs, libcereal, mira need review and sponsored upload

Thanks! -- Michael R. Crusoe CWL Community Engineer cru...@ucdavis.edu Common Workflow Language projectUniversity of California, Davis https://impactstory.org/MichaelRCrusoe http://twitter.com/biocrusoe

Re: macs, libcereal, mira need review and sponsored upload

real.git are up to date.. > On Wed, Feb 03, 2016 at 06:43:16AM +, Michael Crusoe wrote: > > Thanks! > > -- > > Michael R. Crusoe CWL Community Engineer cru...@ucdavis.edu > > > > Common Workflow Language projectUniversity of California, Davis >

python-rdflib-jsonld is ready for review & sponsoring

Thanks! git+ssh://git.debian.org/git/debian-med/python-rdflib-jsonld.git -- Michael R. Crusoe CWL Community Engineer cru...@ucdavis.edu Common Workflow Language projectUniversity of California, Davis https://impactstory.org/MichaelRCrusoe http://twitter.com/biocrusoe

Debian-med in three sentences

The Debian Med group is dedicated to maintaining software packages of medical and biological interest within the larger volunteer framework that is the Debian Linux distribution. The focus is on the user of the software: to ensure that the applications and software libraries are easy to install, th

RFS: python-schema-salad & cwltool

git+ssh://git.debian.org/git/debian-med/python-schema-salad.git -- Michael R. Crusoe CWL Community Engineer cru...@ucdavis.edu Common Workflow Language projectUniversity of California, Davis https://impactstory.org/MichaelRCrusoe http://twitter.com/biocrusoe

Re: macs, libcereal, mira need review and sponsored upload

, Feb 03, 2016 at 06:43:16AM +0000, Michael Crusoe wrote: > > Thanks! > > -- > > Michael R. Crusoe CWL Community Engineer cru...@ucdavis.edu > > > > Common Workflow Language projectUniversity of California, Davis > > https://impactstory.org/MichaelRCr

Re: Associating packages with file types using appstream succeeded

On Wed, Feb 10, 2016 at 7:15 PM Petter Reinholdtsen wrote: > > I am happy to report that the experiment we conducted during the Debian > Med meeting in Denmark was successful, after fixing a bug in the > appstream import system. > Fantastic! Thank you for following up on this and the patch. >

Re: Associating packages with file types using appstream succeeded

Yep! That effort is being organized via https://osf.io/a6kvu/ & https://groups.google.com/forum/#!forum/bioinformatics-formats On Thu, Feb 11, 2016 at 1:19 PM Petter Reinholdtsen wrote: > [Michael Crusoe] > > Fantastic! Thank you for following up on this and the patch. > &

libcereal updated with patch to increase arch support from upstream

Can I get a sponsorship? Thanks! -- Michael R. Crusoe CWL Community Engineer cru...@ucdavis.edu Common Workflow Language projectUniversity of California, Davis https://impactstory.org/MichaelRCrusoe http://twitter.com/biocrusoe

Re: cwl - ok for me to document my progress on wiki.d.o?

Thanks for the reminder :-) Go for it! The draft package is at git+ssh://git.debian.org/git/debian-med/cwltool.git [ I just pushed it ] On Fri, Feb 12, 2016 at 2:00 PM Steffen Möller wrote: > @Michael in particular, > > I need to run a yet not completely defined NGS workflow on some ~30 > nuc

Re: libcereal updated with patch to increase arch support from upstream

ork on this > Andreas. > > On Thu, Feb 11, 2016 at 10:13:03PM +, Michael Crusoe wrote: > > Can I get a sponsorship? > > > > Thanks! > > -- > > Michael R. Crusoe CWL Community Engineer cru...@ucdavis.edu > > > > Common Workflow

Re: cwl - ok for me to document my progress on wiki.d.o?

While the Common Workflow Language grew out of the bioinformatics community it has seen uptake in the neuroimaging community and is theoretically useful in other fields and outside science. Sâm, 13 feb. 2016, 07:53, Andreas Tille a scris: > On Sat, Feb 13, 2016 at 12:39:39AM +0000, Mich

Re: cwl - ok for me to document my progress on wiki.d.o?

Sure! Sâm, 13 feb. 2016, 08:49, Andreas Tille a scris: > On Sat, Feb 13, 2016 at 07:36:40AM +0000, Michael Crusoe wrote: > > While the Common Workflow Language grew out of the bioinformatics > community > > it has seen uptake in the neuroimaging community and is theoretic

detecting the presence of new files / licenses / copyrights

http://sources.debian.net/src/amtterm/1.4-1/debian/rules/?hl=4#L4 Has anyone used this technique in practice? -- Michael R. Crusoe CWL Community Engineer cru...@ucdavis.edu Common Workflow Language projectUniversity of California, Davis https://impactstory.org/MichaelRCrusoe http://t

Re: detecting the presence of new files / licenses / copyrights

On Mon, Feb 15, 2016 at 10:32 PM Sascha Steinbiss wrote: > Hi, > > > http://sources.debian.net/src/amtterm/1.4-1/debian/rules/?hl=4#L4 > > > > Has anyone used this technique in practice? > > Not yet, but it looks useful in case things change. Unfortunately doesn’t > help with getting the licenses

Re: cwltool - upload?

Thank you Steffen, I made a few tweaks to enable building in pbuilder & bumped the version. Let's do it! On Mon, Feb 22, 2016 at 9:34 PM Steffen Möller wrote: > Hi Michael, hi all, > > the cwltool is now lintian clean (I autogenerated man pages for it) > which renders it a prime candidate for a

upload permissions for new DMs

Hello, Can I get upload permissions for the packages I contribute to? https://qa.debian.org/developer.php?login=crusoe%40ucdavis.edu Thanks!

Re: upload permissions for new DMs

Thank you, Afif! On Wed, Feb 24, 2016 at 4:48 PM Afif Elghraoui wrote: > Hi, Michael, > > على الأربعاء 24 شباط 2016 ‫07:04، كتب Michael Crusoe: > > Can I get upload permissions for the packages I contribute to? > > > > I believe I've taken care of this. > >

Re: RFS: reapr

Sascha, care to share your reproducibility test setup? Joi, 25 feb. 2016, 19:51, Sascha Steinbiss a scris: > Hey, > > > [...] > >> and builds reproducibly. > > > > Actually, I just noticed it doesn't! I do get slightly different > > binaries (though no timestamps involved) and I can't track it d

Re: bamtools_2.4.0+dfsg-4_amd64.changes REJECTED

My apologies; I've updated Git On Sun, Mar 6, 2016 at 10:50 AM, Afif Elghraoui wrote: > Hi, Michael, > > On السبت 5 آذار 2016 11:22, Michael R. Crusoe wrote: > >> Can I get bamtools 2.4.0+dfsg-4 sponsored? I split the library >> documentation into a separate package so I can't upload on my own.

Re: bamtools_2.4.0+dfsg-4_amd64.changes REJECTED

Thanks! On Mon, Mar 7, 2016 at 8:26 AM Mattia Rizzolo wrote: > uploaded. > > On Mon, Mar 7, 2016 at 6:55 AM Michael Crusoe > wrote: > >> My apologies; I've updated Git >> >> On Sun, Mar 6, 2016 at 10:50 AM, Afif Elghraoui >> wrote: >> &g

RFS: python-typing

Thanks! git+ssh://git.debian.org/git/debian-med/python-typing.git -- Michael R. Crusoe

Re: RFS: python-typing

Yeah, I've decided to switch python-schema-salad to Py3 only (and likewise for cwltool). I'll close the ITP. On Mon, Mar 7, 2016 at 10:44 PM, Mattia Rizzolo wrote: > On Mon, Mar 07, 2016 at 06:33:24PM +0100, Michael Crusoe wrote: > > Thanks! > > > > git+ssh:

Jellyfish 2.2.5 fixes dataloss error, packaging in progress

Details at https://github.com/gmarcais/Jellyfish/issues/55

Re: Jellyfish 2.2.5 fixes dataloss error, packaging in progress

2.2.5 is ready for review & upload: git+ssh://git.debian.org/git/debian-med/jellyfish.git On Sat, Mar 12, 2016 at 1:55 PM, Michael Crusoe wrote: > Details at https://github.com/gmarcais/Jellyfish/issues/55 > >

Invitation to CWL hackathon, May 18-20th in Paris

Hello friends, Our colleague, Hervé Ménager is hosting a "Tools, Workflows and Workbenches" hackathon with a significant CWL theme on May 18th-20th at Institut Pasteur, Paris, France. Sign ups are at https://www.eventbrite.fr/e/technical-hackathon-tools-workflows-and-workbenches-tickets-227975250

Re: Bug#823512: ITP: mypy -- Optional static typing for Python

This is ready for sponsoring, thanks! git+ssh://git.debian.org/git/debian-med/mypy.git On Thu, May 5, 2016 at 3:53 PM, Michael R. Crusoe wrote: > Package: wnpp > Severity: wishlist > Owner: Debian Med team > > * Package name: mypy > Version : 0.3.1 > Upstream Author : Jukka Leh

Re: mypy_0.4-1_source.changes REJECTED

Andreas, or someone else, may I have permission to upload updates of this package? FYI, I responded to the activity poll for me Debian Developer application on April 25th but I haven't heard any reply. On Fri, May 6, 2016 at 2:19 PM, Debian FTP Masters < ftpmas...@ftp-master.debian.org> wrote:

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: Cc: Log of processing your commands file /dcut.M

Re: Processing of dcut.Michael_R__Crusoe__michael_crusoe_gmail_com_.1462615038.28130.commands

Okay, thanks! On Sat, May 7, 2016 at 12:31 PM, Mattia Rizzolo wrote: > If the package has been rejected you just need to upload it again (after > having fixed whatever problem leaded to the reject). You don't have to > dcut anything. > > On Sat, 7 May 2016, 12:00 p.m. Mich

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 should

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 ke

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 wi

Re: NETTAB 2016 abstract deadline extended to June 30th

On Wed, Jun 8, 2016 at 3:53 PM, Andreas Tille 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 think a presentation on what

Galaxy project producing their own Debian packages

Vezi Tweetul lui @natefoo: https://twitter.com/natefoo/status/743306923026440194 https://depot.galaxyproject.org/nate/dpkg/

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 next (which to my > recollec

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 wrote: > > > On 16/06/16 09:56, Michael Crusoe wrote: > > On Tue, Jun 14, 2016 at 1:12 AM, Steffen Möller > > mailto:steffen_moel...@gmx.de>> wrote: > > > > I was peeking into the one or other scie

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

These are all dependencies of cnvkit http://cnvkit.readthedocs.io/ -- 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: request for sponsorship: r-cran-r.cache r-cran-future r-cran-globals r-cran-listev r-bioc-dnacopy

ble 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 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 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-listenv. > > Uploa

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 Build-Depends > > r-

RRID: a namespace for research software

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 this into the CWL spec so it would be nice to have a resolver that give a Debian package name for a given RRID. -- Michael R

Re: Galaxy project producing their own Debian packages

/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 many things at run time from > r

Re: Galaxy project producing their own Debian packages

, Michael Crusoe wrote: > Hoopla, > > I'm at the Galaxy Community Conference sitting next to Nate Coraor. > > Nate is enthusiastic about Galaxy becoming properly packaged for Debian. > He is well aware of how hacky his current package is :-) > > On Thu, Jun 16, 201

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:

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 yo

Re: RRID: a namespace for research software

nterest 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, Steffen Möller >>

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: Galaxy project producing their own Debian packages

hu, Jun 16, 2016 at 11:07 AM, Olivier Sallou 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/ > > &g

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: https://cpan

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:(python-dev

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

Pe 11 iul. 2016 11:17, "Andreas Tille" 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 unstable. > > > &g

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: 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). I didn't think it

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

You may be interested in the http://nucleotid.es/ & http://bioboxes.org/ efforts. Bonus, the harmonized interface can be described using the Common Workflow Language (whose 1.0 release just occurred); it is likely that you could represent the conversion using CWL itself. On Wed, Jul 13, 2016 at 11

MEGAN finally released under the GPL!

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

Re: Status of seqan

Are the upstreams using 2.0, 2.1, or 2.2? We may need to package each separately.. On Wed, Jul 20, 2016 at 10:54 AM, Andreas Tille wrote: > Hi folks, > > upstreams are moving to seqan 2.x (I just received a mail from the > flexbar author). Could someone please give a status update. We > *real

Re: Status of seqan

Agreed On Wed, Jul 20, 2016 at 11:16 AM, Andreas Tille 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 > latest seqan upstream a

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 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 unstable but > still

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: RFS: python3-typed-ast, hisat2

27;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 >

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 descr

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 wrote: > Hello everyone, > > I'm at the H3Abionet Cloud computing hackathon this week in Pretoria, > South Africa. > > http://www.h3abionet.org/training-and-educ

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 Steffen > > The plan* i

Re: Packaging wishlist for this week's H3Africa workshop

Thanks! Pe 27 aug. 2016 9:46 a.m., "Andreas Tille" 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/debian-med/trunk/pack

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 beagle-lib which for instanc

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 https://github.com/bcgsc/btl_bloomfilter/blob/master/COPY

Re: FYI: New Abyss 2.0 contains undistributable components

72453454499840 https://twitter.com/biocrusoe/status/772874936012664832 On Mon, Sep 5, 2016 at 10:12 PM, Andreas Tille wrote: > Hi Michael, > > On Mon, Sep 05, 2016 at 07:17:10PM +0300, Michael Crusoe wrote: > > Just to save you all some time. > > > > https://github.com/bcgsc/

Re: Packaging wishlist for this week's H3Africa workshop

On Tue, Sep 13, 2016 at 10:26 AM, Andreas Tille 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. > > > > > &g

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: 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 thi

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 l

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 Debian Med. Unfor

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 +1 480 627 910

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

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

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 attend.

Re: Next sprint

https://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 : > Hello Oliver, > > Thank you for the reminder. I've waiting to he

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

Likewise r-bioc-geneplotter 2016-11-10 13:23 GMT+02:00 Michael Crusoe : > dcut dm --uid 724D609337113C710550D7473C26763F6C67E6E2 > --allow r-cran-future > > Thanks, > > -- > Michael R. Crusoe > Community Engineer & Co-founder > Common Workflow Language project <

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 t

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