Re: Fixed all upstream metadata in Debian Med (Was: RRID update on salsa on packages starting with A+B)

This was still open on my desk - sorry for the late reply. On 4/10/18 6:09 PM, Andreas Tille wrote: On Tue, Apr 10, 2018 at 05:25:52PM +0200, Steffen Möller wrote: An immediate concern of mine is that we have no visibility of our task page with Google. A strategic mistake apparently

Helping tracker.d.o to show research identifiers of software?!?

Hello, on https://wiki.debian.org/UpstreamMetadata we describe how Research Resource Identifiers (RRIDs) can be used to further annotate a package and help to link a package of Debian with e.g. a scientific paper using that software. Also, workflow engines have adopted them as identifiers to

Re: Fixed all upstream metadata in Debian Med (Was: RRID update on salsa on packages starting with A+B)

On 4/9/18 10:34 PM, Andreas Tille wrote: On Mon, Apr 09, 2018 at 12:36:32AM +0200, Steffen Möller wrote: On 4/6/18 2:22 PM, Steffen Möller wrote: rate4site sambamba genometools maffilter I've now added an entry severity "error" in the UDD importer log if some unknown field n

Re: RRID update on salsa on packages starting with A+B

On 4/6/18 2:22 PM, Steffen Möller wrote: Hi Andreas, Whenever you find the moment, please review the presentation of rate4site sambamba genometools maffilter on the task page which do not show their references. Cheers, Steffen

scoary Re: spread-phy missing, was Re: pynast did not migrate to salsa?

On 4/6/18 6:31 PM, Steffen Möller wrote: On 4/6/18 5:10 PM, Andreas Tille wrote: On Fri, Apr 06, 2018 at 01:59:50PM +0200, Steffen Möller wrote: Hi again, please also check spread-phy ?? What about https://salsa.debian.org/med-team/spread-phy Ah, the forwarding does not work

Re: spread-phy missing, was Re: pynast did not migrate to salsa?

On 4/6/18 5:10 PM, Andreas Tille wrote: On Fri, Apr 06, 2018 at 01:59:50PM +0200, Steffen Möller wrote: Hi again, please also check spread-phy ?? What about https://salsa.debian.org/med-team/spread-phy Ah, the forwarding does not work. Thank you for the pointer, I have added

Re: RRID update on salsa on packages starting with A+B

Hi Andreas, Whenever you find the moment, please review the presentation of rate4site sambamba on the task page which do not show their references. Cheers, Steffen

spread-phy missing, was Re: pynast did not migrate to salsa?

Hi again, please also check spread-phy Cheers, Steffen On 4/3/18 10:34 AM, Sascha Steinbiss wrote: Hi Steffen and Andreas, I cannot find the pynast repository on salsa. Any ideas? The entry on  the med/bio task page points to its previous location on alioth and I cannot find it on salsa.

Re: RRID update on salsa on packages starting with A+B

Hi Tony, On 4/3/18 1:59 PM, Tony Travis wrote: On 03/04/18 11:27, Steffen Möller wrote: [...] This is a bit of a side-track from the core of this thread. Maybe we would have Tony describing our achievements one they are manifesting in Bio-Linux. And if we have a look at https

d/u/metadata for binary or source tree Re: RRID update on salsa on packages starting with A+B

On 4/3/18 5:09 PM, Andreas Tille wrote: On Tue, Apr 03, 2018 at 12:27:08PM +0200, Steffen Möller wrote: There is a daily cron job parsing Salsa directories. Fine. Somewhere there is (or should be :o) ) a documentation how this page is crafted. On our Wiki? Let us then have a link to that page

Re: RRID update on salsa on packages starting with A+B

On 4/3/18 10:30 AM, Andreas Tille wrote: On Tue, Apr 03, 2018 at 12:14:57AM +0200, Steffen Möller wrote: Registry: - Name: OMICtools Entry: NA - Name: RRID Entry: NA - Name: bio.tools Entry: NA That is an interesting one. Please kindly check https://salsa.debian.org

Re: RRID update on salsa on packages starting with A+B

On 4/2/18 11:32 PM, Andreas Tille wrote: Hi Steffen, thanks a lot for your continuous work on assembling registry data. On Sat, Mar 31, 2018 at 02:41:42AM +0200, Steffen Möller wrote: There are still packages that are not updated. Worthwhile candidates are autodock This has: Registry

Re: pynast did not migrate to salsa?

On 4/2/18 11:19 PM, Andreas Tille wrote: On Mon, Apr 02, 2018 at 10:56:56PM +0200, Steffen Möller wrote: ... Thanks for checking I hope there will not be to many of similar cases. The package is now on Salsa That was darn quick. Many thanks! Best, Steffen

pynast did not migrate to salsa?

Hi Andreas, hi Sascha, I cannot find the pynast repository on salsa. Any ideas? The entry on  the med/bio task page points to its previous location on alioth and I cannot find it on salsa. Many thanks for your help Steffen

Re: RRID update on salsa on packages starting with A+B

Hi Andreas, On 3/30/18 3:14 PM, Andreas Tille wrote: Hi Steffen, On Fri, Mar 30, 2018 at 01:11:28AM +0200, Andreas Tille wrote: Please kindly have a look at clonalframe - it has a ref for SciCrunch, is yamllint clean but nothing shows up. H, good catch. clonalframe | SciCrunch |

Re: RRID update on salsa on packages starting with A+B

On 3/29/18 8:48 PM, Steffen Möller wrote: On 3/28/18 1:14 PM, Andreas Tille wrote: On Wed, Mar 28, 2018 at 12:03:54PM +0200, Steffen Möller wrote: But I found artemis (https://salsa.debian.org/med-team/artemis/tree/master/debian/upstream) which was not touched for a while and looks

Re: RRID update on salsa on packages starting with A+B

On 3/28/18 1:14 PM, Andreas Tille wrote: On Wed, Mar 28, 2018 at 12:03:54PM +0200, Steffen Möller wrote: But I found artemis (https://salsa.debian.org/med-team/artemis/tree/master/debian/upstream) which was not touched for a while and looks syntactically just fine but has its RRIDs not shown

Re: RRID update on salsa on packages starting with A+B

Hi Andreas, I'll get to the other points of your fine reply a bit later. The easy ones first On 3/27/18 9:04 AM, Andreas Tille wrote: Anyway. I came across  * one or two entries Which ones? I had thought this would be dead easy to answer and then I added quite a few more references

Debian has RRID SCR_006638

Hello all, I just tripped over https://scicrunch.org/scicrunch/Resources/search?q=SCR_006638=SCR_006638 and, well, we should probably start adding that reference on our web site and papers. Best, Steffen

RRID update on salsa on packages starting with A+B

Hello, I just procrastinated a bit into using the comfort of salsa to update debian/upstream/metadata and here the references to SciCrunch, OMICtools and bio.tools registries. All three registries have improved their coverage enormously over the past few months. I am deeply impressed.

Re: cwltool removed from unstable, new uploads are being ignored

Hi Michael, On 3/5/18 3:07 PM, Michael Crusoe wrote: https://packages.debian.org/search?keywords=cwltool Hey all, I just noticed that cwltool is no longer in unstable. Any hints as to why this happened? I can't find any bug report requesting its removal either:

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

Hi Michael, hi Andreas, On 15.02.18 07:32, Andreas Tille wrote: Hi Michael, if you intend to mentor this simply add it to https://wiki.debian.org/SummerOfCode2018/Projects Kind regards Andreas. On Wed, Feb 14, 2018 at 05:46:38PM +0100, Michael Crusoe wrote: Steps: 1. Collect

Hotel for Debian Med Sprint

Hello, our local contact is not available as it seems - skiing? Anyway - I found the hotel http://www.hotel-barcelonahouse.com/ which seems to be just fine for our purpose since it seems modern enough, low budget (~50 EUR) and in walking distance. They have 12 rooms still available, I just

Re: debianmed sprint hosting location?

I'll substitute email with phone now and get back to you all - with a hotel if lucky. Olivier, which is the one you have selected? If it is not too far from the venue then I suppose it is a prime candidate. Steffen On 08.01.18 13:22, Andreas Tille wrote: Hi, On Mon, Jan 08, 2018 at

Re: removing tophat from Debian

On 23.12.17 09:06, Afif Elghraoui wrote: على الخميس 21 كانون الأول 2017 ‫08:10، كتب Steffen Möller: So, what could justify a deprecated piece of software in Debian. To mind come:  * an API change  * a well-established tutorial that was not yet updated These two points can be summarized

https://salsa.debian.org and Debian Med as a group?

Hello, just a few minutes ago I received an invitation to the Debian group on https://salsa.debian.org . This finally gives us web-editing and pull requests. For Debian Med this is even more important than for the packages that are more to the core of our distribution, I tend to think. Is

Re: removing tophat from Debian

On 21.12.17 04:41, Afif Elghraoui wrote: On December 20, 2017 5:17:20 AM EST, Michael Crusoe wrote: 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

Re: removing tophat from Debian

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: Since I'm not a user of all this software I do not have any objections. However, I wonder whether we should provide kind of a sensible "migration path" and add "Replaces:

Re: Failed to find source code of gromacsgui

I propose to remove it from the archive. Cheers, Steffen On 08.12.17 14:44, Andreas Tille wrote: Hi, when trying to migrate unfinished packaging code from SVN to Git I check the availablity of the upstream source code (to add it as pristine-tar). Unfortunately I have not found any souce code

Re: SVN to Git migration status

On 01.12.17 11:23, Andreas Tille wrote: Hi, as you know we need to be prepared that when Alioth is moved to some new system SVN will not be available any more. So I was busy to migrate close to all our packages from SVN to Git. That was a tremendous effort. Many thanks, Andreas. I am

Comments on task list

Hello, I just added a June 2017 PLoS One paper to DeepNano's debian/upstream/metadata and was a bit surprised about the comment "*Remark of Debian Med team:* There is no intend to keep continue the existing packaging since the program nanocall seems to serve the intended purpose better" in the

Sprint-derived paper now out:

Dear all, this paper has now surfaced Möller, Steffen; Prescott, Stuart W.; Wirzenius, Lars; Reinholdtsen, Petter; Chapman, Brad; Prins, Pjotr; Soiland-Reyes, Stian; Klötzl, Fabian; Bagnacani, Andrea; Kalaš, Matúš; Tille, Andreas; Crusoe, Michael R. (2017): Robust cross-platform workflows: how

Re: Date shift: Sprint moving to 10-12/2/2018, was: Debian Med Sprint 26-28/1/2018 in Barcelona

Hello, On 17.11.17 11:50, Sascha Steinbiss wrote: > Hi all, > > [...] >>> I wonder whether it would be possible to have our Sprint *before* the >>> ELIXIR meeting. I do not question your point above but I have strong >>> private reasons to keep the weekend 10./11. February 2018 free. If >>>

Re: Date shift: Sprint moving to 10-12/2/2018, was: Debian Med Sprint 26-28/1/2018 in Barcelona

On 15.11.17 16:00, Andreas Tille wrote: > Hi, > > On Sat, Nov 11, 2017 at 12:24:43PM +0100, Steffen Möller wrote: >> Dear all, >> >> I hope there are not too many of you who have reserved fixed flights >> already: There is an ELIXIR meeting already scheduled in B

Date shift: Sprint moving to 10-12/2/2018, was: Debian Med Sprint 26-28/1/2018 in Barcelona

are interested to learn about us among them. After a quick chat with the local organisers we came to the conclusion that shifting our meeting to start right when that meeting stops would serve Debian Med the most. Sorry or the hassle this may cause you Best, Steffen On 04.11.17 00:53, Steffen Möller

Debian Med Sprint 26-28/1/2018 in Barcelona

Dear all, Good news: Friday the 26th to Sunday the 28th of January 2018, a room is reserved for us in BARCELONA (https://en.wikipedia.org/wiki/Barcelona) to accommodate the annual Debian Med Sprint. Our local host is Cedric Notredame who many of you know for his work on sequence alignments.  We

Re: RRID -> SciCrunch

On 26.10.17 08:26, Michael Crusoe wrote: > > > 2017-10-25 20:47 GMT+03:00 Steffen Möller <steffen_moel...@gmx.de > <mailto:steffen_moel...@gmx.de>>: > > > On 25.10.17 18:52, Michael Crusoe wrote: > > > > > > 2017-10-25 19:21 GMT

Re: Packaging BLAT for Debian

Hello, On 25.10.17 23:50, Afif Elghraoui wrote: > Hello, > > On October 25, 2017 5:03:23 PM EDT, Maximilian Haeussler > wrote: >> Andreas: If clustal, When I had asked Andreas in 2001 or so to update clustalw for me, this was what started my contributions to Debian. Maybe

Re: RRID -> SciCrunch

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>>: > > > On 25.10.17 17:49, Michael Crusoe wrote: > > > > > > 2017-10

Re: RRID -> SciCrunch

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 2017-10-25 15:12, Michael Crusoe wrote: > > 2017-10-25 16:04 GMT+03:00 Steffen Möller > <s

Re: RRID -> SciCrunch

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>: >> >>> On 25.10.17 13:47, Michael Crusoe wrote: >>>> >>>> >>>>

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

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>>: > > > On 25.10.17 10:56, Michael Crusoe wrote: > > Sorry, I missed the bit where we are deprec

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

, not publicly visible, so nobody should truly care and the use of SciCrunch imho serves us best on a technical level. The https://www.force2017.org/ starts today in Berlin which should gather people who know best - is anybody following this list attending? Steffen > > 2017-10-2

Re: Review, please ! e: [med-svn] [rapmap] branch upstream updated (5fb69ea -> b8057c0)

On 23.10.17 16:46, Andreas Tille wrote: > On Mon, Oct 23, 2017 at 04:17:37PM +0200, Steffen Möller wrote: >> I admit my motivation was mostly to make yet another "New Version >> Available" button on our tasks page go away ... and add another link to >> the registr

Re: Review, please ! e: [med-svn] [rapmap] branch upstream updated (5fb69ea -> b8057c0)

On 23.10.17 16:07, Andreas Tille wrote: > Hi Steffen, > > On Mon, Oct 23, 2017 at 02:08:36PM +0200, Steffen Möller wrote: >> I have updated the rapmap package that I do not use myself. >> If we have some user of this tool on this list, please kindly >> give it a test r

Review, please ! e: [med-svn] [rapmap] branch upstream updated (5fb69ea -> b8057c0)

Hello, I have updated the rapmap package that I do not use myself. If we have some user of this tool on this list, please kindly give it a test run. Best, Steffen On 22.10.17 21:28, Steffen Möller wrote: > This is an automated email from the git hooks/post-receive script. > > moell

Re: Should we package BioConductor TFBSTools? [Was [libtfbs-perl] 04/08: Add upstream's notice of deprecation to the package's description.]

Hello, On 21.10.17 10:11, Charles Plessy wrote: > Le Sat, Oct 21, 2017 at 08:08:49AM +0200, Andreas Tille a écrit : >> when reading this commit log: Should we package Bioconductor TFBSTools? >> >> This would need at least a hand full of Bioconductor depencencies but >> usually it is quite

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

Args, I have only now updated https://wiki.debian.org/UpstreamMetadata to reference SciCrunch by their name. Many thanks and sorry Steffen On 22.10.17 12:20, Andreas Tille wrote: > Hi Charles, > > wasn't Steffen just doing heaps of uploads with > > - - Name: RRID > + - Name: SciCrunch > > As

Re: What's next. Re: Please check implementation

On 20.10.17 21:03, Andreas Tille wrote: > On Fri, Oct 20, 2017 at 06:13:10PM +0200, Steffen Möller wrote: > > . >>>> * RRID|SciCrunch: identifiers.org don't guarantee anything. If there's no >>>> cool permanent URL, identifiers.org don't have it either. T

What's next. Re: Please check implementation

On 20.10.17 15:12, Andreas Tille wrote: > Hi, > > On Fri, Oct 20, 2017 at 02:18:13PM +0200, Matus Kalas wrote: >> This is super awesome to see Andreas & Steffen, you really made my day! > You could make my day in turn to add more of the data we need for the > packages not yet tagged. :-P @Matúš,

Re: Role of acedb-other-belvu and acedb-other-dotter versus belvu & dotter from seqtools

Hi Andreas, On 19.10.17 18:09, Andreas Tille wrote: > Hi, > > I started to check the list of external packages of possibly interesting > packages and stumbled upon blixem which is part of seqtools[1]. The > source also contains dotter and belvu and seems to be actively > maintained. However,

Re: Any volunteer for Sprint organisation (Was: Proposal for Registry-display on task pages)

I am in a skype meeting at the very moment .. did not reach our contact over there, yet. Let us find another place if I fail to establish a contact till Monday. Cheers, Steffen On 20.10.17 09:56, Andreas Tille wrote: > Hi folks, > > up to now nobody volunteered for Sprint organisation. I

Re: Proposal for Registry-display on task pages

On 19.10.17 08:32, Andreas Tille wrote: > On Thu, Oct 19, 2017 at 08:29:15AM +0200, Andreas Tille wrote: >> On Mon, Oct 09, 2017 at 04:10:59PM +0200, Steffen Möller wrote: >>> "OMICtools" => "https://duckduckgo.com/?q=\\; (a single backslash at the

Re: Proposal for Registry-display on task pages

On 19.10.17 08:04, Andreas Tille wrote: > Hi Steffen, > > I'm working on some test implementation Great! > On Mon, Oct 09, 2017 at 04:10:59PM +0200, Steffen Möller wrote: >> registry_prefix={ >> "bio.tools"=>"https://bio.tools/;, >&g

Re: Proposal for Registry-display on task pages

On 11.10.17 21:29, Andreas Tille wrote: > On Wed, Oct 11, 2017 at 06:20:59PM +0200, Steffen Möller wrote: >>> One question regarding the 'NA' values. I'd consider it more readable >>> if we would just print nothing if there is no entry available. Or am I >>> mi

Proposal for Registry-display on task pages

Hi Andreas, here some R/Python/PHP-mix pseudocode idea for getting the registry links displayed on the task page: registry_prefix={ "bio.tools"=>"https://bio.tools/;, "RRID" => "http://identifiers.org/rrid/RRID:;, "SciCrunch" => "http://identifiers.org/rrid/RRID:;, "OMICtools" =>

Re: task pages: Moved many NGS packages from bio to bio-ngs

>>> BTW, I added the references to the UDD query that is used in the tasks >>> pages generation code. So one further step is done to put them on the >>> tasks pages. Unfortunately I was running (again) on a strange encoding >>> problem with the UDD on my developer machine (luckily not on the

Re: task pages: Moved many NGS packages from bio to bio-ngs

Hi Andreas, On 24.09.17 14:06, Andreas Tille wrote: > Hi Steffen, > > On Sun, Sep 24, 2017 at 11:24:49AM +0200, Steffen Möller wrote: >> I had a bit of fun on that one: >> >> ...blend-med/tasks$ for i in bio bio-ngs; do egrep -v "^[ \t]*[X#]" $i | >>

Re: task pages: Moved many NGS packages from bio to bio-ngs

Hi again, On 22.09.17 16:54, Andreas Tille wrote: > Hi Steffen, > > On Fri, Sep 22, 2017 at 04:00:52PM +0200, Steffen Möller wrote: >>> I do not think that the effort is really moot since there is no code yet >>> (and nobody volunteered to code this - I for

Re: task pages: Moved many NGS packages from bio to bio-ngs

Hi Andreas, On 22.09.17 11:47, Andreas Tille wrote: > Hi Steffen, > > On Thu, Sep 21, 2017 at 07:29:47PM +0200, Steffen Möller wrote: >> This effort is a bit moot since we should likely follow one of the >> classifications that are already out there (like EDAM ontology t

Re: References to registries -> debian-med policy?

On 21.09.17 23:13, Dylan Aïssi wrote: > Hi Steffen, > > 2017-09-16 18:37 GMT+02:00 Steffen Möller <steffen_moel...@gmx.de>: >> I have added a sentence to the Debian Med policy and also pushed >> the "Registry:" entry for the UpstreamMetadata wiki page that our

Re: Next Debian Med Sprint?

On 22.09.17 08:46, Olivier Sallou wrote: > > On 09/21/2017 07:08 PM, Steffen Möller wrote: >> Hi Andreas, >> >> On 21.09.17 09:27, Andreas Tille wrote: >>> Hi folks, >>> >>> I have not yet heard about any volunteer to organise the next Debi

Re: Bowtie segfaults in pbuilder chroot at build time (Was: Issue with new version of Bowtie)

On 21.09.17 22:42, Andreas Tille wrote: > On Thu, Sep 21, 2017 at 07:00:27PM +0200, Steffen Möller wrote: >>> That looks pretty similar and no visible missing. >> You have cowdancer - but you are right. Hm. Just because it works for me >> without pbuilder - I know the bui

task pages: Moved many NGS packages from bio to bio-ngs

Hello, This effort is a bit moot since we should likely follow one of the classifications that are already out there (like EDAM ontology topics or OMICtools categories), but this will take some time. So, I finally got around to manually moving a series of NGS-centric packages over to the bio-ngs

Re: Next Debian Med Sprint?

Hi Andreas, On 21.09.17 09:27, Andreas Tille wrote: > Hi folks, > > I have not yet heard about any volunteer to organise the next Debian Med > Sprint. Is there anybody who would like to organise our next meeting? Marseille was once offered to us but did not yet get an answer - had asked while

Re: Bowtie segfaults in pbuilder chroot at build time (Was: Issue with new version of Bowtie)

Hi Andreas, On 21.09.17 08:27, Andreas Tille wrote: > Hi Steffen, > > On Wed, Sep 20, 2017 at 10:52:55PM +0200, Steffen Möller wrote: >>> ... >>> Error testing example >>> --- tests/example6.out 2017-09-20 13:07:01.0 + +++ example6.out >>&

Re: References to registries -> debian-med policy?

Hi Andreas, On 10.09.17 20:22, Andreas Tille wrote: > Hi Steffen, > > On Sun, Sep 10, 2017 at 01:18:46PM +0200, Steffen Möller wrote: >> this morning brought updates to references to research software >> catalogues (SciCruch RRIDs, OMICtools, bio.tools) to packages referenc

Re: References to registries -> debian-med policy?

On 10.09.17 20:22, Andreas Tille wrote: > Hi Steffen, > > On Sun, Sep 10, 2017 at 01:18:46PM +0200, Steffen Möller wrote: >> this morning brought updates to references to research software >> catalogues (SciCruch RRIDs, OMICtools, bio.tools) to packages referenced >>

References to registries -> debian-med policy?

Dear all, this morning brought updates to references to research software catalogues (SciCruch RRIDs, OMICtools, bio.tools) to packages referenced in Debian Med's "NGS" task. At some point we need to decide what packages should be in what task, but that is for another email. The other bio-tasks I

Re: debian/upstream/metadata: registry item for the Blends' task pages?

On 15.08.17 00:17, Dylan Aïssi wrote: > Hi, > > 2017-08-12 13:25 GMT+02:00 Steffen Möller <steffen_moel...@gmx.de>: >> On 12.08.17 11:31, Charles Plessy wrote: >>> I wonder if this metadata would be even more useful via AppStream. From >>> https://appstre

Re: debian/upstream/metadata: registry item for the Blends' task pages?

Hi Charles, On 12.08.17 11:31, Charles Plessy wrote: > Le Sat, Jul 29, 2017 at 07:45:23PM +0200, Steffen Möller a écrit : >> In a direct email to Charles (asking if "Registry" was OK after becoming >> aware of the reserved keyword "Registration" with a diff

CWL workflow as Debian package

Hello, I had an exchange with Stian yesterday about what CWL workflow of his database he would propose to use as an experience-gathering example. He proposed the GATK workflow by Farah Zaib Khan et al. for being good to cite about workflows and reproducibility.

debian/upstream/metadata: registry item for the Blends' task pages?

Dear Andreas, dear Charles, You know me adding references to RRID, bio.tools and OMICtools these days. I am doing this for what I see currently active on the list (usually too late for the upload) or for what is already checked out on my laptop's hard drive. That done it will be about completing

Re: References to registries on task pages - how?

Hi Andreas, On 22.07.17 16:38, Andreas Tille wrote: > On Sat, Jul 22, 2017 at 11:43:59AM +0200, Steffen Möller wrote: >> you may have seen me and Dylan (!) add references to software registries >> for computational biology. I admit to have lost oversight a bit which >>

Getting user-space containers with Singularity - works

Hello, Many (most) HPC administrators very much detest the idea to grant any sort of root privileges to their users. This consequently rules out the installation of our Debian packages and also the employment of Docker images for the execution of binaries. Ouch! After all, with this perpetual

References to registries on task pages - how?

Hi Andreas, you may have seen me and Dylan (!) add references to software registries for computational biology. I admit to have lost oversight a bit which packages already have these references and which should still be annotated. So, to  - help myself but also to  - promote the effort a bit more

Re: Please fix bugs

Hi Andreas, On 6/27/17 9:34 PM, Andreas Tille wrote: > as I stated on debian-private list I will not be able to fix bugs in the > next two weeks. I have the feeling we are currently receiving way more > than we are fixing. It would be really cool if you could run some kind > of inofficial

RRIDs for debian/upstream/metadata

Hello, We had a quick exchange on RRIDs on this list before, if I am not erroneous. Michael is particularly supportive of them and again, correct me if I am wrong and if you care, we had another not ultimately decisive discussion about them at the Debian Med Sprint this year. Once you are made

ISMB 2017 abstract

Hello, is anyone already preparing a poster for the ISMB that shows Debian? There have been tons of infrastructure posters at last year's ECCB that got me disappointed that we were not somehow present. I know, we wanted to have a booth for quite a while but never got around organizing it. I have

Re: About storing edam files in Debian packaging

Hi Andreas, On 07/02/2017 15:54, Andreas Tille wrote: > Hi Matus and Steffen, > > I was again stumbling upon totally broken edam yaml files (bowties and > bowtie2 was totally broken, I fixed freecontact and clustalo which had > "topics" instead of "topic" and were breaking UDD import due to

Testing of pan-package workflows - how?

Hello, I am interested in testing complete workflows based on packages in Debian. The emphasis would be more on "data out here is working fine as data in there" for a chain of commands, and on "this result is close to the expected" rather than working on single packages. Are there any proposals

Re: Debianmed sprint

Hello, Right, we need to get the DPL's approval, even though I never asked my expenses to be covered ;o/ I can prepare for that together with Michael. Please all just add your names on the Sprint page. Something else that came to mind, which is that we should think about lowering mental hurdles

Shall we develop a Debian Med Tutorial? Fwd: [BC2-conference] Call for workshop and tutorial proposals open now.

Hello, much like many of you I just received this invitation to come up with a tutorial and/or workshop for the Basel (Switzerland) conference. The ISMB (next time in Prague (CZ) if I recall correctly) I expect to send the same around any minute or I already missed it as they typically have

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

And yet another "hello", On 05/07/2016 17:11, Steffen Möller wrote: > Hello again, > > bx-python vacant in our git repository, not uploaded > wchartype in unstable > bioblend in unstable > svgwrite in unstable > re

Re: Tutorials? Portal? Shiny web presence?

s and have no exact idea about how soon I can come up with anything. Feel free nag^H^H^Hpinging me about it. Best, Steffen On 19/09/2016 14:19, Steffen Möller wrote: > Hello, > > I was at the ECCB earlier this month and in particular over the > tutorials I had asked about t

Tutorials? Portal? Shiny web presence?

Hello, I was at the ECCB earlier this month and in particular over the tutorials I had asked about the idea to synchronize their tutorial efforts with our packaging. I was a bit surprised, but all tutorials indeed requested to install a considerable amount of software, one was even a

Re: Request for increased awareness: Open Source FPGA acceleration

lso about > NoCs?) > Matus > > > On 2016-09-02 10:18, Steffen Möller wrote: >> Hi all, >> >> Those who participated in our past Sprint in Lyngby have met Ruben. He >> is the one who kindly packaged all that needed to be packaged for the >> first and yet on

Synchronisation with tutors and pointing to such from our website

Hello, I am writing from the ECCB, attending this tutorial http://nbviewer.jupyter.org/urls/www.mtholyoke.edu/courses/afoulkes/ECCB2016.ipynb which tells me how to do right what I have been doing for the last years :o) It is very clear and so I asked if it would be o.k. to point to it from

Request for increased awareness: Open Source FPGA acceleration

Hi all, Those who participated in our past Sprint in Lyngby have met Ruben. He is the one who kindly packaged all that needed to be packaged for the first and yet only completely Open Source toolchain for FPGA computing. Details are on http://wiki.debian.org/FPGA/Lattice . Ruben started that

Brainstorming about Debian Med paper, motivated by Nat Rev Gen paper "Crowdsourcing biomedical research" citing our Sprint paper

Hello, https://www.researchgate.net/publication/305342071_Crowdsourcing_biomedical_research_Leveraging_communities_as_innovation_engines cites our "Community-driven development for computational biology at Sprints, Hackathons and Codefests" paper

Re: linuxbrew with homebrew/science - works!

On 30/07/16 10:15, Afif Elghraoui wrote: > Hi, all, > > على الخميس 28 تـمـوز 2016 ‫03:54، كتب Sascha Steinbiss: >>> I do not know what this means for Debian Med. It is a competition. And, with some early brain wash from the homebrew on the Mac I am now using on my desk, it also feels

linuxbrew with homebrew/science - works!

Hello, this is about https://github.com/Homebrew/homebrew-science It features an astonishing array of bioinformatics software and kind of saves what is left of my sanity to get our local HPC environment going. Our admins are "its in your home directory" fine with it. I do not know what this

EBI-ELIXIR and descriptional workflows

https://tess.elixir-uk.org/workflows/structural-bioinformatics-workflow I like it. And I very much hope this gets interlinked nicely with bio.tools so the resources of Debian Med are also found that way. It is all a bit high-level/non-existing yet to name the effort a competition to what the CWL

galaxy dependency - current state

Hello again, bx-python vacant in our git repository, not uploaded wchartype in unstable bioblendin unstable svgwritein unstable requests-toolbelt in unstable dictobj in unstable pulsar-galaxy-lib vacant

Re: bx-python

Hello, On 30/06/16 10:41, Afif Elghraoui wrote: > Hi, all, > > على الثلاثاء 28 حزيران 2016 ‫06:20، كتب Steffen Möller: > [...] >> bx-python > I checked-in to Debian Med git what I had done on this package a few > months ago. I don't really have an interest in it anymore,

Re: Galaxy project producing their own Debian packages

Hello again, https://anonscm.debian.org/cgit/python-modules/wchartype.git has a similar problem for me. The version 3 packages are not placed in their debian directories. Many thanks Steffen On 29/06/16 19:16, Steffen Möller wrote: > Hello, > > > On 28/06/16 16:34, Olivier

Re: Galaxy project producing their own Debian packages

e some issues with it, i.e. there is no python3 module and the examples do not install. Someone please have a look and direct me a bit. Cheers, Steffen > > On 06/28/2016 03:20 PM, Steffen Möller wrote: >> This is great! That custom fokr of pysam reads as if one wants to avoid >&

Re: Galaxy project producing their own Debian packages

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

Re: RRID: a namespace for research software

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

Re: upstream/metadata with references to software catalogs^Wregistries?

Hello, On 22/06/16 15:06, Olivier Sallou wrote: > On 06/22/2016 02:12 PM, Andreas Tille wrote: >> [For readers of Blends list: We are discussing an additional field >> in debian/upstream/metadata ] >> >> On Wed, Jun 22, 2016 at 01:12:46PM +0200, Steffen Möller wrote:

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