[med-svn] [Git][med-team/bcbio][master] Few updates on bcbio packaging and deps

[Steffen Möller]

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.

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20190601/20e06dbd/attachment-0001.html>