[med-svn] [Git][med-team/bcbio][master] Reordering for importance

Steffen Möller gitlab at salsa.debian.org
Sat Jun 8 19:30:38 BST 2019 


Steffen Möller pushed to branch master at Debian Med / bcbio


Commits:
3975d052 by Steffen Möller at 2019-06-08T18:30:17Z
Reordering for importance

- - - - -


1 changed file:

- debian/TODO


Changes:

=====================================
debian/TODO
=====================================
@@ -1,39 +1,52 @@
-package bamtofastq from biobambam2
-  https://salsa.debian.org/med-team/biobambam2 (in new queue)
+TODO for bcbio with Debian
+==========================
 
-package snpEff
-  http://snpeff.sourceforge.net/
-  https://salsa.debian.org/med-team/snpeff/blob/master/debian/changelog
-  The packaging needs help with its dependencies:
-     apfloat 1.6.3:
-       https://github.com/mtommila/apfloat
-       http://www.apfloat.org/apfloat_java/maven.html
-     charts4j 1.3:
-       https://mvnrepository.com/artifact/com.googlecode.charts4j/charts4j/1.3
-     com.typesafe.akka:akka-actor 2.0.1
-     distlib 0.9.1:
-       https://sourceforge.net/projects/statdistlib/?source=navbar
+The following is a list of packages that are used by at least one of the
+workflows it aggregates. A complete coverage by Debian of all these tools
+seems increasingly unlikely - their packaging would take longer than the
+tools scientific lifespan, i.e. there is a new generation of problem solving
+emerging and/or the workflow as a whole will have mutated in the meantime.
+
+Packages already accepted
+------------------------
+
+Are no longer shown in this list but are added to the dependencies of
+bcbio.
+
+Packages already in the New Queue
+---------------------------------
 
 package atropos
   https://salsa.debian.org/med-team/atropos (in new queue)
 
-package mosdepth
-  https://salsa.debian.org/med-team/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 bamtofastq from biobambam2
+  https://salsa.debian.org/med-team/biobambam2 (in new queue)
 
-package hts_nim_tools
-   https://github.com/brentp/hts-nim-tools
-   Likely addressed with the other efforts on nim behind mosdepth
+package kallisto (in new queue)
 
-package qsignature
-   https://sourceforge.net/p/adamajava/wiki/Home/
-   https://sourceforge.net/p/adamajava/wiki/qSignature/
-   http://sourceforge.net/projects/adamajava/files/qsignature.tar.bz2/download
-   https://sourceforge.net/p/adamajava/code/HEAD/tree/trunk/adamajava/qsignature/
+package Python module geneimpacts
+   https://pypi.org/project/geneimpacts/
+   https://github.com/brentp/geneimpacts
+   https://salsa.debian.org/med-team/python-geneimpacts (in new queue)
+
+package pizzly
+   https://github.com/pmelsted/pizzly (in new queue)
+
+package r-wasabi
+   https://salsa.debian.org/r-pkg-team/r-other-wasabi (in new queue)
+
+package tophat-recondition
+  https://github.com/cbrueffer/tophat-recondition (in new queue)
+
+package wham
+  http://research.cs.wisc.edu/wham/ (in new queue)
 
-package optitype
-  https://salsa.debian.org/med-team/optitype (rudimentary)
+
+Packages just waiting for someone addressing the last mile for the upload
+-------------------------------------------------------------------------
+
+package gffread
+  https://salsa.debian.org/med-team/gffread
 
 package pyomo
   https://github.com/Pyomo/pyomo
@@ -45,57 +58,88 @@ package pyutilib
   https://salsa.debian.org/python-team/modules/pyutilib - builds, tests fail
     needed by pyomo for testing
 
+package seqcluster
+   https://github.com/lpantano/seqcluster/archive/1824d37.tar.gz
+   https://salsa.debian.org/med-team/python-seqcluster
+      Some nitty-gritty was going on there wrt Python3 transition
+      and an upcoming new release. Needs another review and
+      likely some communication with upstream.
+
+
+Packages presumed easy to package
+---------------------------------
+
 package gjh_asl_json
   https://github.com/ghackebeil/gjh_asl_json
     needed by pyomo for testing
 
+package hts_nim_tools
+   https://github.com/brentp/hts-nim-tools
+   Likely addressed with the other efforts on nim behind mosdepth
+
 package "asl solver"
   http://www.ampl.com/netlib/ampl/solvers.tgz
     needed by gjh_asl_json
 
+Package MutliQC - in salsa
+   https://salsa.debian.org/med-team/multiqc
+    Steffen will address this one
+
+
+
+Packages of importance for basic NGS workflow well beyond bcbio
+---------------------------------------------------------------
+
+package mosdepth
+  https://salsa.debian.org/med-team/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 oncofuse
+   https://salsa.debian.org/med-team/oncofuse
+
+package optitype
+  https://salsa.debian.org/med-team/optitype (rudimentary)
+
 package vcfanno
   https://salsa.debian.org/med-team/vcfanno
   Not fun because of many GO packages that are still missing,
   "biogo" being one of them.
 
+
+
+Difficult to package to the degree that one is tempted to use conda for the meantime
+------------------------------------------------------------------------------------
+
+package snpEff
+  http://snpeff.sourceforge.net/
+  https://salsa.debian.org/med-team/snpeff/blob/master/debian/changelog
+  The packaging needs help with its dependencies:
+     apfloat 1.6.3:
+       https://github.com/mtommila/apfloat
+       http://www.apfloat.org/apfloat_java/maven.html
+     charts4j 1.3:
+       https://mvnrepository.com/artifact/com.googlecode.charts4j/charts4j/1.3
+     com.typesafe.akka:akka-actor 2.0.1
+     distlib 0.9.1:
+       https://sourceforge.net/projects/statdistlib/?source=navbar
+
+package qsignature
+   https://sourceforge.net/p/adamajava/wiki/Home/
+   https://sourceforge.net/p/adamajava/wiki/qSignature/
+   http://sourceforge.net/projects/adamajava/files/qsignature.tar.bz2/download
+   https://sourceforge.net/p/adamajava/code/HEAD/tree/trunk/adamajava/qsignature/
+
 Now at https://github.com/AdamaJava/adamajava
 
 add hisat2_extract_splice_sites.py to the hisat2 package
   -> Done in Git in preparation for 2.1.0-3
   -> Added arch-indep python3-hisat2 package
 
-Package MutliQC - in salsa
-   https://salsa.debian.org/med-team/multiqc
-     Nobody active on this one - needs some peer review and upload
-
 package sailfish
    https://salsa.debian.org/med-team/sailfish
     FTBFS
 
-package kallisto (in new queue)
-
-package r-wasabi
-   https://salsa.debian.org/r-pkg-team/r-other-wasabi (in new queue)
-
-package oncofuse
-   https://salsa.debian.org/med-team/oncofuse
-     Nobody active on this one - needs some peer review and upload
-
-package Python module geneimpacts
-   https://pypi.org/project/geneimpacts/
-   https://github.com/brentp/geneimpacts
-   https://salsa.debian.org/med-team/python-geneimpacts (in new queue)
-
-package seqcluster
-   https://github.com/lpantano/seqcluster/archive/1824d37.tar.gz
-   https://salsa.debian.org/med-team/python-seqcluster
-      Some nitty-gritty was going on there wrt Python3 transition
-      and an upcoming new release. Needs another review and
-      likely some communication with upstream.
-
-
-package pizzly
-   https://github.com/pmelsted/pizzly (in new queue)
 
 package vt
    https://github.com/atks/vt
@@ -111,7 +155,6 @@ package fgbio
 package manta
 https://github.com/Illumina/manta/
   https://salsa.debian.org/med-team/manta
-  @Andreas - where are we on this one?
 
 package strelka
 https://github.com/Illumina/strelka/releases
@@ -121,21 +164,16 @@ https://github.com/Illumina/strelka/releases
   #set(HTSLIB_CFLAGS '-O0 -g -fsanitize=address -fno-omit-frame-pointer -fno-optimize-sibling-calls')
 
 
-package lumpy
-https://github.com/arq5x/lumpy-sv
-
-package wham
-  http://research.cs.wisc.edu/wham/ (in new queue)
-
 # An easy one:
-package tophat-recondition
-https://github.com/cbrueffer/tophat-recondition (in new queue)
-
 package qualimap
   https://salsa.debian.org/med-team/qualimap
   Unfortunately some of the Java code that is needed as predepenceny is simply lost see
      https://alioth-lists.debian.net/pipermail/debian-med-packaging/2016-January/038322.html
 
-package gffread
-  https://salsa.debian.org/med-team/gffread
-    @andreas - What happened to this one?
+
+Packages no longer used by bcbio
+--------------------------------
+
+package lumpy
+https://github.com/arq5x/lumpy-sv
+



View it on GitLab: https://salsa.debian.org/med-team/bcbio/commit/3975d052b2f40110b87c667bbc0fef2bf147d43b

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