Notes from the 2017 Debian Med Sprint in Bucharest

Progress on meeting goals

Complete dependencies for Galaxy
- reiterating on borked python-bx packaging - now in New Queue
Package Toil resource distributor for CWL workflows
- uploaded dependency https://github.com/BD2KGenomics/bd2k-python-lib as python-bd2k - now in New Queue
- Working on non-trivial dependency 'cgcloud', ITP is out
- Working on dependency futures for cgcloud-core
- ITP for Toil ist out
Updating cwltool & schema-salad: done. Sascha is adding cwl-runner via update-alternatives
- uploaded
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 samtoosl 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

List of demands for development discussed/identified during the meeting