Steffen Möller pushed to branch master at Debian Med / bcbio
Commits: 22e2db16 by Steffen Möller at 2019-06-01T15:35:43Z Few updates on bcbio packaging and deps - - - - - 1 changed file: - debian/TODO Changes: ===================================== debian/TODO ===================================== @@ -2,7 +2,9 @@ package bamtofastq from biobambam2 https://salsa.debian.org/med-team/biobambam2 (in new queue) package snpEff -https://salsa.debian.org/med-team/snpeff/blob/master/debian/changelog + http://snpeff.sourceforge.net/ + https://salsa.debian.org/med-team/snpeff/blob/master/debian/changelog + The packaging needs help with its dependencies. package atropos https://salsa.debian.org/med-team/atropos (in new queue) @@ -12,6 +14,10 @@ package mosdepth several nim libraries are needed. These have all been addressed on https://salsa.debian.org/nim-team of which the first already is in the new queue +package hts_nim_tools + https://github.com/brentp/hts-nim-tools + Likely addressed with the other efforts on nim behind mosdepth + package qsignature https://sourceforge.net/p/adamajava/wiki/Home/ https://sourceforge.net/p/adamajava/wiki/qSignature/ @@ -21,6 +27,10 @@ https://sourceforge.net/p/adamajava/code/HEAD/tree/trunk/adamajava/qsignature/ package optitype https://salsa.debian.org/med-team/optitype (rudimentary) +package pyomo + https://github.com/Pyomo/pyomo + needed by optitype + package vcfanno https://salsa.debian.org/med-team/vcfanno Not fun because of many GO packages that are still missing, @@ -34,9 +44,11 @@ add hisat2_extract_splice_sites.py to the hisat2 package Package MutliQC - in salsa https://salsa.debian.org/med-team/multiqc + Who is responsible for this one? package sailfish https://salsa.debian.org/med-team/sailfish + FTBFS package kallisto (in new queue) @@ -45,14 +57,12 @@ package r-wasabi package oncofuse https://salsa.debian.org/med-team/oncofuse - -package hts_nim_tools -https://github.com/brentp/hts-nim-tools + @Andreas, please add a TODO if not ready package Python module geneimpacts https://pypi.org/project/geneimpacts/ https://github.com/brentp/geneimpacts - Steffen addresses this one + https://salsa.debian.org/med-team/python-geneimpacts (in new queue) package seqcluster https://github.com/lpantano/seqcluster/archive/1824d37.tar.gz @@ -65,12 +75,13 @@ package vt https://github.com/atks/vt package fgbio -https://github.com/fulcrumgenomics/fgbio + https://github.com/fulcrumgenomics/fgbio + Anyone much into scala? package manta https://github.com/Illumina/manta/ - - Steffen works on this one https://salsa.debian.org/med-team/manta + @Andreas - where are we on this one? package strelka https://github.com/Illumina/strelka/releases @@ -84,7 +95,7 @@ package lumpy https://github.com/arq5x/lumpy-sv package wham -http://research.cs.wisc.edu/wham/ + http://research.cs.wisc.edu/wham/ (in new queue) # An easy one: package tophat-recondition @@ -97,3 +108,4 @@ package qualimap package gffread https://salsa.debian.org/med-team/gffread + @andreas - What happened to this one? View it on GitLab: https://salsa.debian.org/med-team/bcbio/commit/22e2db16f9988b7a310700970b3faf7d6a0fca8b -- View it on GitLab: https://salsa.debian.org/med-team/bcbio/commit/22e2db16f9988b7a310700970b3faf7d6a0fca8b You're receiving this email because of your account on salsa.debian.org.
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