Re: Jon says "thanks" ...
On Tue, Feb 09, 2016 at 06:50:51PM +0100, Andreas Tille wrote: > Hi Jon, > > you are now faced with my habit to repost private mails to public > mailing list if there is no privat but rather publicly interesting > content in it. Please stick to the list since otherwise publicly > relevant information will be dumped to private mailboxes which sucks. > (And sorry for violating the netiquette.) > > On Tue, Feb 09, 2016 at 05:45:55PM +0100, ji...@cbs.dtu.dk wrote: > > ... for a real blast at the Sprint. I had a great time, and I think we did > > well. > > +1 > and thanks a lot for the support by DTU! > > > A quick question: how many biology packages in total does Debian Med hold? > > You can answer this question yourself: Run > >https://github.com/bio-tools/biotoolsConnect/blob/master/DebianMed/edam.sh > > and than > >$ grep -c "debian[ |]\+sid" edam.txt >476 > > > And how many did we (me and you Steffen, and > > others) annotate during the event - i.e. create an upstream edam.yaml (or > > whatever) for ? > > I need a fresh checkout but I think it is below 30. To give an update here is a list of currently existing edam files in the Debian Med repositories (Git+SVN): $ find . -name "*.edam" | sort ./a/abacas.edam ./a/aegean.edam ./a/ampliconnoise.edam ./a/andi.edam ./a/anfo.edam ./a/aragorn.edam ./a/arden.edam ./a/artemis.edam ./b/barrnap.edam ./b/bowtie.edam ./c/clustalo.edam ./c/codonw.edam ./d/dialign.edam ./f/fastaq.edam ./f/fastqc.edam ./f/fastx-toolkit.edam ./f/filo.edam ./h/htslib.tabix.edam ./i/indelible.edam ./k/kissplice.edam ./k/kmc.edam ./l/ltrsift.edam ./m/miniasm.edam ./m/minimap.edam ./m/mothur.edam ./m/mummer.edam ./m/muscle.edam ./p/pbsim.edam ./p/picard-tools.edam ./q/qiime.edam ./s/snpomatic.edam ./s/snp-sites.edam ./s/sra-sdk.edam ./s/ssake.edam ./t/tantan.edam ./t/trimmomatic.edam ./u/uc-echo.edam The exact number is 37 - so my estimation based on an older checkout was wrong. Thanks to all those who worked on this Andreas. -- http://fam-tille.de
Re: Mentioning EDAM files in DebianMed Policy
Hi Fabian, thanks for the very helpful and needed hint. I was waiting a bit since Michael intended to work on the structure of the policy a bit and I did not wanted to shot on a moving target. Michael, could you comment on this how and where you would like to see this information? Kind regards Andreas. On Sat, Feb 06, 2016 at 04:36:34PM +0100, Fabian Klötzl wrote: > Hi all, > > The new edam files should also be mentioned in our team policy. Below is > a quick mock up; But we might also need to write a proper spec. > > Best, > Fabian > > > > > ## debian/upstream/edam > > This is a machine-readable file to categorize where in life-science this > package has its application. The categories themselves come from EDAM > and are arranged in YAML format. Check the [EDAM Ontology > Browser](http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=EDAM) > for terms that might fit the package. > > -- http://fam-tille.de
Re: Mentioning EDAM files in DebianMed Policy
Folks The link to OLS was to a deprecated ontology browser running an ancient version of EDAM. Please use this one instead (it's in beta, so go steady): http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=EDAM Alternatively you can use this: http://bioportal.bioontology.org/ontologies/EDAM/ ps. both now include EDAM_1.13 just released post-hackathon. Thanks for the hard work ! Cheers Jon > Hi Fabian, > > thanks for the very helpful and needed hint. I was waiting a bit since > Michael intended to work on the structure of the policy a bit and I did > not wanted to shot on a moving target. Michael, could you comment on > this how and where you would like to see this information? > > Kind regards > > Andreas. > > On Sat, Feb 06, 2016 at 04:36:34PM +0100, Fabian Kl�tzl wrote: >> Hi all, >> >> The new edam files should also be mentioned in our team policy. Below is >> a quick mock up; But we might also need to write a proper spec. >> >> Best, >> Fabian >> >> >> >> >> ## debian/upstream/edam >> >> This is a machine-readable file to categorize where in life-science this >> package has its application. The categories themselves come from EDAM >> and are arranged in YAML format. Check the [EDAM Ontology >> Browser](http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=EDAM) >> for terms that might fit the package. >> >> > > -- > http://fam-tille.de > >
Re: Jon says "thanks" ...
This is absolutely amazing Andreas! Thank you very much to everybody who contributed! Cheers, Matus To give an update here is a list of currently existing edam files in the Debian Med repositories (Git+SVN): $ find . -name "*.edam" | sort ./a/abacas.edam ./a/aegean.edam ./a/ampliconnoise.edam ./a/andi.edam ./a/anfo.edam ./a/aragorn.edam ./a/arden.edam ./a/artemis.edam ./b/barrnap.edam ./b/bowtie.edam ./c/clustalo.edam ./c/codonw.edam ./d/dialign.edam ./f/fastaq.edam ./f/fastqc.edam ./f/fastx-toolkit.edam ./f/filo.edam ./h/htslib.tabix.edam ./i/indelible.edam ./k/kissplice.edam ./k/kmc.edam ./l/ltrsift.edam ./m/miniasm.edam ./m/minimap.edam ./m/mothur.edam ./m/mummer.edam ./m/muscle.edam ./p/pbsim.edam ./p/picard-tools.edam ./q/qiime.edam ./s/snpomatic.edam ./s/snp-sites.edam ./s/sra-sdk.edam ./s/ssake.edam ./t/tantan.edam ./t/trimmomatic.edam ./u/uc-echo.edam The exact number is 37 - so my estimation based on an older checkout was wrong. Thanks to all those who worked on this Andreas. -- http://fam-tille.de
Associating packages with file types using appstream succeeded
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. The goal was to use appstream to announce file format support in a non-GUI package (aka one without a .desktop file), and we used the khmer package as an example. It is now listed as a package supporting the application/vnd.oxli.countgraph MIME type: % appstreamcli what-provides mimetype application/vnd.oxli.countgraph Identifier: oxli [generic] Name: khmer Summary: in-memory DNA sequence kmer counting, filtering & graph traversal Package: khmer % To do this, we added debian/khmer.metainfo.xml with the following content and installed it in /usr/share/appdata/: oxli MIT khmer in-memory DNA sequence kmer counting, filtering & graph traversal khmer is a library and suite of command line tools for working with DNA sequence. It is primarily aimed at short-read sequencing data such as that produced by the Illumina platform. khmer takes a k-mer-centric approach to sequence analysis, hence the name. application/vnd.oxli.countgraph -- Happy hacking Petter Reinholdtsen
Re: Jon says "thanks" ...
On Wed, Feb 10, 2016 at 11:14:00PM +0700, Matus Kalas wrote: > This is absolutely amazing Andreas! Thank you very much to everybody who > contributed! I admit I would sleep even better if somebody would confirm that you can effectively use this script: https://github.com/bio-tools/biotoolsConnect/blob/master/DebianMed/edam.sh Can any of you edam people confirm: [ ] Yes, I can use the script to query UDD. [ ] No, I use further help to run the script. My plan was to teach you how to get the data and I wonder whether this plan succeeded. Kind regards Andreas, -- http://fam-tille.de
Re: Associating packages with file types using appstream succeeded
Hi Petter, On Wed, Feb 10, 2016 at 07:15:02PM +0100, 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. Very cool. Thanks a lot for this very important information. I'm really happy to have you seen again as a goof friend on one hand and on the other hand as a very helpful contributor. > The goal was to use appstream to announce file format support in a > non-GUI package (aka one without a .desktop file), and we used the khmer > package as an example. It is now listed as a package supporting the > application/vnd.oxli.countgraph MIME type: > > % appstreamcli what-provides mimetype application/vnd.oxli.countgraph > Identifier: oxli [generic] > Name: khmer > Summary: in-memory DNA sequence kmer counting, filtering & graph traversal > Package: khmer > > % > > To do this, we added debian/khmer.metainfo.xml with the following > content and installed it in /usr/share/appdata/: > > > > oxli > MIT > khmer > in-memory DNA sequence kmer counting, filtering & graph > traversal > > > khmer is a library and suite of command line tools for working > with DNA sequence. It is primarily aimed at short-read > sequencing data such as that produced by the Illumina > platform. khmer takes a k-mer-centric approach to sequence > analysis, hence the name. > > > > application/vnd.oxli.countgraph > > So, now you can go on providing more such files for other packages. Lets move on into this direction. Kind regards Andreas. -- http://fam-tille.de
Re: Jon says "thanks" ...
:) Still recovering from massive backlog of urgent things, we will get to it! (and pick up on all other threads) J:) > On Wed, Feb 10, 2016 at 11:14:00PM +0700, Matus Kalas wrote: >> This is absolutely amazing Andreas! Thank you very much to everybody who >> contributed! > > I admit I would sleep even better if somebody would confirm that you can > effectively use this script: > >https://github.com/bio-tools/biotoolsConnect/blob/master/DebianMed/edam.sh > > Can any of you edam people confirm: > > [ ] Yes, I can use the script to query UDD. > [ ] No, I use further help to run the script. > > My plan was to teach you how to get the data and I wonder whether this > plan succeeded. > > Kind regards > > Andreas, > > -- > http://fam-tille.de > >
Re: Associating packages with file types using appstream succeeded
Le Wed, Feb 10, 2016 at 07:15:02PM +0100, Petter Reinholdtsen a écrit : > > The goal was to use appstream to announce file format support in a > non-GUI package (aka one without a .desktop file), and we used the khmer > package as an example. It is now listed as a package supporting the > application/vnd.oxli.countgraph MIME type: > > % appstreamcli what-provides mimetype application/vnd.oxli.countgraph > Identifier: oxli [generic] > Name: khmer > Summary: in-memory DNA sequence kmer counting, filtering & graph traversal > Package: khmer > > % > > To do this, we added debian/khmer.metainfo.xml with the following > content and installed it in /usr/share/appdata/: > > > > oxli > MIT > khmer > in-memory DNA sequence kmer counting, filtering & graph > traversal > > > khmer is a library and suite of command line tools for working > with DNA sequence. It is primarily aimed at short-read > sequencing data such as that produced by the Illumina > platform. khmer takes a k-mer-centric approach to sequence > analysis, hence the name. > > > > application/vnd.oxli.countgraph > > Hi Petter, this is a great result, especially now that it is easy for any project to submit new media types to the IANA. I added the following information to the MimeTypesSupport page in the Debian wiki: Packages can declare support for media types using the AppStream system, by placing metainfo XML files in /usr/share/appdata/, with names such as .metainfo.xml. Commands like appstreamcli will then be able to report which package supports which media types, and package managers will be able to suggest the package for installation. https://wiki.debian.org/MimeTypesSupport#For_package_installation Corrections or improvements are welcome ! Have a nice day, -- Charles
Fwd: Associating packages with file types using appstream succeeded
Hi, since I think this result of the Debian Med sprint might be of more general interest thus I'm simply forwarding to debian-devel what was posted on Debian Med list. Thread start was here: https://lists.debian.org/debian-med/2016/02/msg00049.html Kind regards Andreas. - Forwarded message from Charles Plessy - Date: Thu, 11 Feb 2016 11:52:22 +0900 From: Charles Plessy To: debian-med@lists.debian.org Subject: Re: Associating packages with file types using appstream succeeded Le Wed, Feb 10, 2016 at 07:15:02PM +0100, Petter Reinholdtsen a écrit : > > The goal was to use appstream to announce file format support in a > non-GUI package (aka one without a .desktop file), and we used the khmer > package as an example. It is now listed as a package supporting the > application/vnd.oxli.countgraph MIME type: > > % appstreamcli what-provides mimetype application/vnd.oxli.countgraph > Identifier: oxli [generic] > Name: khmer > Summary: in-memory DNA sequence kmer counting, filtering & graph traversal > Package: khmer > > % > > To do this, we added debian/khmer.metainfo.xml with the following > content and installed it in /usr/share/appdata/: > > > > oxli > MIT > khmer > in-memory DNA sequence kmer counting, filtering & graph > traversal > > > khmer is a library and suite of command line tools for working > with DNA sequence. It is primarily aimed at short-read > sequencing data such as that produced by the Illumina > platform. khmer takes a k-mer-centric approach to sequence > analysis, hence the name. > > > > application/vnd.oxli.countgraph > > Hi Petter, this is a great result, especially now that it is easy for any project to submit new media types to the IANA. I added the following information to the MimeTypesSupport page in the Debian wiki: Packages can declare support for media types using the AppStream system, by placing metainfo XML files in /usr/share/appdata/, with names such as .metainfo.xml. Commands like appstreamcli will then be able to report which package supports which media types, and package managers will be able to suggest the package for installation. https://wiki.debian.org/MimeTypesSupport#For_package_installation Corrections or improvements are welcome ! Have a nice day, -- Charles - End forwarded message - -- http://fam-tille.de
