Loading debian/TODO +20 −8 Original line number Diff line number Diff line Loading @@ -2,7 +2,9 @@ package bamtofastq from biobambam2 https://salsa.debian.org/med-team/biobambam2 (in new queue) package snpEff 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) Loading @@ -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/ Loading @@ -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, Loading @@ -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) Loading @@ -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 Loading @@ -66,11 +76,12 @@ https://github.com/atks/vt package 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 Loading @@ -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 Loading @@ -97,3 +108,4 @@ package qualimap package gffread https://salsa.debian.org/med-team/gffread @andreas - What happened to this one? Loading
debian/TODO +20 −8 Original line number Diff line number Diff line Loading @@ -2,7 +2,9 @@ package bamtofastq from biobambam2 https://salsa.debian.org/med-team/biobambam2 (in new queue) package snpEff 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) Loading @@ -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/ Loading @@ -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, Loading @@ -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) Loading @@ -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 Loading @@ -66,11 +76,12 @@ https://github.com/atks/vt package 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 Loading @@ -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 Loading @@ -97,3 +108,4 @@ package qualimap package gffread https://salsa.debian.org/med-team/gffread @andreas - What happened to this one?
