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| * 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 |
* Packaged Toil resource distributor for CWL workflows (python-bd2k and essential modules of cgcloud with it) * Working on completion of clinically relevant workflow with CWL and Debian |
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| * [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 |
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
- Packaged Toil resource distributor for CWL workflows (python-bd2k and essential modules of cgcloud with it)
- Working on completion of clinically relevant workflow with CWL and Debian
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 (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.
Packaging lobSTR workflow: Bogdan & Michael got the workflow to run again https://github.com/common-workflow-language/workflows/pull/126#issuecomment-272632458
seqan 2.3.1 is packaged & uploaded
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