Wiki

• FrontPage
• RecentChanges
• FindPage
• HelpContents
• DebianMed2019

Wiki/

Debian Med 2019 Sprint

Location, Date

• 09:00, March 9 (Saturday) - 21:00, March 11 (Monday), 2019 **

• Location: Vilnius, Lithuania, NVO Avilys coworking space Tauro g. 12, Vilnius LT-01114, Lithuania https://goo.gl/maps/125dEvYMtBS2

This is an informal co-working and co-learning event, participants are welcome to attend on the days that work for their schedule. There is a possibility to arrive or depart a day earlier or later, ask on the mailing list if this interests you.

• IRC: #debian-med on irc.debian.org (OFTC)

• ?Sprints/2019/DebianMed2019Notes

• https://lists.debian.org/debian-med/2018/10/msg00040.html

Getting there

Use this link to get travel recommendations: https://www.rome2rio.com/map/My-hometown/Tauro-g-12-Vilnius-01114-Lituania

Travel wise you can fly into the VNO airport with many low cost flights. Travel time from the airport to the venue is 7 minutes by taxi, 20 minutes by city bus (1 EUR, pay on the bus)

For a local taxi, one can use invite code 9GVRN and get a free ride up to -4€. Redeem it at https://invite.taxify.eu/9GVRN

Lithuania's second city, Kaunas, also has an airport (KUN) and is 1.5 hours away by train or bus. (The KUN to Vilnius bus schedule is linked to the RyanAir flight schedule: https://www.ollex.lt/en/express/Kaunas-airport/buy-a-ticket# )

Getting around

Vilnius has a dense network of buses and trolleybuses. A comprehensive guide through it is here: https://stops.lt/vilnius/#vilnius/en. A single ride costs 1€ (ticket has to be bought from the driver, best is to pay in coins, no cards accepted). Luggage with dimensions exceeding 120 cm needs additional ticket (same 1€ one). Those willing/having to travel around more can buy a travelcard for ~5€. The travelcard has to be charged by money, which can be spent on travel time (0.6€ for 30 mins of travel, etc.). On Monday 11th public transport will be free of charge.

Vilnius is a small city and its center can thus be easily traversed by foot.

Accommodations proposal

Vilnius University apartments offer single rooms for 24-32 EUR). They're located 15 minutes walk from the venue. Breakfast is not included, but there are plenty of places to eat around. Free Wi-Fi, just ask at the reception.

Address of the apartments: M. K. Čiurlionio g. 1, Vilnius LT-03104, Lithuania Brochure: Vilnius University Apartments.pdf

Payments are to be made at the reception, all sorts of cards should be accepted.

To reserve your room, indicate "requested" in the "booked accom." column below.

The venue has free coffee, espresso, and tea prepared on demand.

Meals

A nice and varied food hall with many local restaurants, vegan options, and beer is open from 11:00 in the morning onwards. It is less than 10 minutes walk from the venue. No cash is accepted, Visa or ?MasterCard charge cards (credit or debit) only: https://www.foodhall.lt/

For specific food needs, please let the local organizers (Andrius and Michael) know.

Participants

(tentative/final list of participants here before/after the sprint)

Please use ISO 3166 two-letter country codes and YYYY-MM-DDTHH:MM format.

Agenda

Michael R. Crusoe

Synchronize our metadata with wikidata; include their identifiers in debian/upstream/metadata. Write this up in a blog post to encourage other (bio.tools, ?OntoTools, etc.) to do the same.

Ship more CWL descriptions in /usr/share/commonwl/ http://www.commonwl.org/v1.0/CommandLineTool.html#Discovering_CWL_documents_on_a_local_filesystem

For app that use <seqan/arg_parse.h> and that lack a curated CWL description:

1. Generate a CTD description for each binary using the hidden --write-ctd option combined

2. Convert that CTD to CWL with https://github.com/WorkflowConversion/CTDConverter

3. Install that CWL description to /usr/share/commonwl as part of the package

Continue the packaging of popular CWL executors with full CWL v1.0.x support like toil-cwl-runner and Arvados. Assist packaging of Galaxy in anticipation of their CWL support.

Bring CWL workflows to Debian in their own right with automated testing.

Write up Google Summer of Code proposal about benchmarking of auto-vectorization and per CPU optimization to produce "fat" binaries for bioinformatics software: https://twitter.com/kloetzl/status/1076082255481720832

Steffen Möller

• Revisit ?AutoDockTools

• bcbio workflow and its dependencies + Python 3 ports
• shared computer
  • establish bioinformatics routine workflows
  • auto-update databases in support of these workflows
  • continuously test functionality of workflows
• revisit RRID assignments and what to do with them
• preparation for booth at upcoming conference(s)

Andrius Merkys

• Squash Debian Med bugs

• discuss compiled data packages
• sign keys

• ITP#909742 - pilercr - simple albeit well-cited tool for CRISPR detection, seems to fit the scope of Debian Med: could someone with DD permission upload it (merkys-guest/pilercr on salsa.d.o)? (Uploaded. Sascha)

Any takers???

Benchmark test between Debian Med and ?BioConda.

We have several packages featuring an autopkgtest. We take those package to automate the following benchmark:

1. Setup pbuilder chroot / lxc container

2. install Debian package / install program via ?BioConda

3. Record:
   1. Time to install package/program
   2. Time to run test

Finally graph the compared results.

Matus Kalas

• Add & update EDAM annotations and catalogue IDs for Debian Med src packages

• Discuss news in Bio.Tools strategy (more open) & more streamlined collaboration with Debian Med ++ then contribute our common ideas|recommendations|requirements to the shaping new Bio.Tools dev & curation model

Tony Travis

• Work on bio-linux meta-packages
• Update on experience of installing and using med-bio under Ubuntu-MATE 18.04 LTS
• Bio-Linux 9-alpha USB-stick with casper-rw persistence and support for installation to md RAID

Sascha Steinbiss

• Work on open-source polishing and packaging of Vmatch and ?GenomeThreader.

• Miscellaneous bug squashing and on-demand work.
• Look at my packages depending on Bioperl and figure out what to do re #921495 -- do I need to do anything?
• Sign ALL the keys

Olivier Sallou

• Update biomaj related packages
• Package python-irodsclient
• Bug fixing in debianmed packages
• Discussions on bio-tools/Debian coordination , conda ,...
• Update/integrate debian-med related tools in Biocontainers (European Docker registry for bioinformatics)

Reports

Personal Reports

Andreas Tille

1. Introduction into Debian Med Sprints

2. Working with Tony Travis on

   1. Bio-Linux packaging todo list

   2. Bio-Linux Blends metapackages

   3. Find and fix bug in blends-dev (wrong method to detect short name)

3. Life packaging session for five attendies at the example of dendroscope

4. Discussing and helping attendees several things
5. Bugfixes

   1. hydroffice.bag (922390)

6. Sponsored uploads
   1. mirtop (done by Karolis Kalantojus)
   2. galaxy-lib (finalised by Michael Crusoe)
7. Help with packaging

   1. Liubov Chuprikova bismark

8. Unfinished packaging work

   1. antismash

   2. treegraph (dependency of antismash)

   3. conda

   4. https://salsa.debian.org/med-team/python-pycosat (dependency of conda)

Andrius Merkys

1. Fixed 903759.

2. Making lintian happier with hhsuite and fsm-lite.

3. Finished pilercr and had it uploaded (thanks Sascha).

4. Started packaging OpenMM.

Sascha Steinbiss

1. Getting an understanding of the build system and preparing a first version of packaging for Vmatch.

2. Sponsoring pilercr and migrating the repo to Debian Med space (https://salsa.debian.org/med-team/pilercr)

3. Start of code adaptations necessary for Vmatch to get into Debian.

Karolis Kalantojus

1. Packaged https://salsa.debian.org/med-team/mirtop

2. Seqcluster devel version needs a bit of work, opened a PR at https://github.com/lpantano/seqcluster/pull/40 with an attempt to wing it and just fix the tests. They were passing with the fixes applied. Fixes are not production ready, needs involvement of the original maintainer.

3. Some initial work on https://github.com/kkarolis/cledocker

Olivier Sallou

• Updated biomaj related packages and gkl package
• Prepare new release of beast2-mcmc, not uploaded, pushed to git
• Packaged new python-irodsclient
• Fixed a few bugs in debianmed packages (in git repo)
• Updated debian-med related tools in Biocontainers (European Docker registry for bioinformatics)

Coinciding events

March 11 is celebrated as Day of Restoration of Lithuanian Independence. There usually are various festivities on this day in the Old Town.

Acknowledgements

the sprint has been possible thanks to:

• donations to the Debian project [confirmation pending]

• http://www.nvoavilys.lt/ NVO Avilys for donation of the work space, WiFi, and coffee!

• VšĮ "Darbo eigos" (VIDE) for M. Crusoe's time

---

CategorySprint