Notes from the 2017 Debian Med Sprint in Bucharest
Progress on meeting goals
Done
Updated cwltool & schema-salad: done. Added cwl-runner via update-alternatives, also for toil
- Packaged Toil resource distributor for CWL workflows (python-bd2k and essential modules of cgcloud with it)
seqan 2.3.1 is packaged & uploaded
Ongoing
- Preparing package for conda
- Complete dependencies for Galaxy
- reiterating on borked python-bx packaging - now in New Queue
- Remaining missing python dependencies (to be validated by all):
- testfixtures (needed only for testing)
- pulsar-galaxy (is it really needed? it is a runner, so could be disabled/removed from package)
- Galaxy fails with python-routes/python-webhelpers from Debian, more recent than galaxy requirements. Would need patching (2 lines modification)
Galaxy status: several dependencies are not yet python3 compatible and will impact Galaxy code (https://github.com/galaxyproject/galaxy/issues/1715). Upstream is working on this, but no roadmap yet. No python3 support is blocking. Auto install of dependencies by Galaxy in a virtualenv, shared with installation of toolshed means code modification in Debian to use system libs. This *may* be managed with --system-site-packages option in virtualenv creation.
- run.sh options --skip-venv --skip-eggs --skip-wheels seem to disable virtualenv and packages installation.
- Tested Galaxy execution and unit tests with Debian package and above command. With a few patching to fix routes for runtime execution and run-test.sh for testing, it looks fine!
- Huge number of Javascript libraries, some internals, other from external sources, to be listed and investigated
- packaging bcbio: MRC working on it and pybedtools dependency
- snpeff: looked at dependencies needed to package it
apfloat => source at http://repo1.maven.org/maven2/org/apfloat/apfloat/1.6.3/
charts4j => from https://code.google.com/archive/p/charts4j/, code at https://github.com/julienchastang/charts4j
akka-actor => source at http://dl.bintray.com/typesafe/maven-releases/com/typesafe/akka/akka-actor/2.0.1/
trove4j => in debian (libtrove-java) freemarker in Debian
distlib => unknown source , only bin jar on maven, but no reference in code...
samtools => v1.107, too old, code not compatible with htsjdk...
- log4j in Debian
- Main issue seems to be samtools-related with imports like import net.sf.samtools.SAMFileReader
Packaging lobSTR workflow: Bogdan & Michael got the workflow to run again https://github.com/common-workflow-language/workflows/pull/126#issuecomment-272632458
Project ideas
List of demands for development discussed/identified during the meeting
- bash autocomplete from CWL tool descriptions
- manual page generation from CWL tool descriptions
using acd2cwl to generate CWL descriptions for the EMBOSS tools
- [simple] add "Files-Excluded" to dh_make template of debian/copyright
- patch uscan to allow for a recursive grep to determine what files to exclude via Files-Excluded
Demonstrate usage of http://snapshot.debian.org/ in a Dockerfile for reproducible computing
- Develop strategy for automated package updates in a 'pantsonfire' distribution