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| * Packaging lobSTR workflow: Bogdan & Michael got the workflow to run again https://github.com/common-workflow-language/workflows/pull/126#issuecomment-272632458 | * Galaxy status: several dependencies are not yet python3 compatible and will impact Galaxy code. 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. * Packaging lobSTR workflow: Bogdan & Michael got the workflow to run again https://github.com/common-workflow-language/workflows/pull/126#issuecomment-272632458 |
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
- Galaxy status: several dependencies are not yet python3 compatible and will impact Galaxy code. 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.
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