Loading debian/TODO +107 −69 Original line number Diff line number Diff line 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 optitype https://salsa.debian.org/med-team/optitype (rudimentary) 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) 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 Loading @@ -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 Loading @@ -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 Loading @@ -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 Loading
debian/TODO +107 −69 Original line number Diff line number Diff line 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 optitype https://salsa.debian.org/med-team/optitype (rudimentary) 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) 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 Loading @@ -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 Loading @@ -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 Loading @@ -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
