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TODO for bcbio with Debian
==========================
TL;DR
-----
We yet fail to run bcbio workflows successfully. The package builds but
tests fail. You get pretty close if installing
* GATK (many Java dependencies not packaged)
* qualimap (sources of Java dependencies no longer available)
manually. However, for the immediate future we suggest to install
bcbio via conda - and cordially invite to help us in bringing bcbio
to Debian.
IF YOU ARE READING THIS AND FEEL LIKE HELPING OUT - PLEASE CONTACT US
---------------------------------------------------------------------
The following is a list of packages that are used by at least one of the
workflows bcbio 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.
We yet have to find an answer to this challenge. A series of repositories
of packages that are still waiting in the new queue for their acceptance
in the distribution is available as
deb http://med.functional.domains/r unstable main contrib non-free
deb http://med.functional.domains/med unstable main contrib non-free
deb http://med.functional.domains/nim unstable main contrib non-free
deb http://med.functional.domains/python unstable main contrib non-free
deb http://med.functional.domains/science unstable main contrib non-free
Anyway, for quite some of our users this is to just go and use Conda.
We should also consider mixing Conda with Debian, though. But let us
first see where we are with bcbio:
Packages referenced by bioconda
-------------------------------
The following package names are listed on
https://bioconda.github.io/recipes/bcbio-nextgen/README.html?highlight=bcbio%20nextgen#recipe-Recipe%20'bcbio-nextgen'
To see packages impored in the source tree, run a line like
grep -ri import | cut -f2 -d:| sed -e 's/^[ \t]*//'|grep -v ^from|grep -v except|grep -v ^abstract|sort|uniq -c|sort -n
For now this is just copy'n'pasted without much further thinking about
it. Some packages like python-dateutil may once have been added for
dependencies that only surfaced as a need because of some better testing
- for python-dateutil (once demanded by seqcluster) I am pretty much
convinced that this is no longer required.
Unclear
beautifulsoup4 https://www.crummy.com/software/BeautifulSoup/
ipyparallel >=6.0.2
ipython-cluster-helper >=0.6.1
#py # conda-specific
python-dateutil >=2.5.0 # likely obsolete?
pyyaml https://pyyaml.org/wiki/PyYAML
To be packaged
fadapa https://github.com/fadapa/fadapa
pycrypto
Available in Debian but not added as a dependency (yet)
boto
dnapi https://github.com/jnktsj/DNApi
htslib # not called directly?
#pip # ridiculous
openssl >=1.1.1c,<1.1.2a
pytest-cov
seaborn # not called directly?
viennarna dragged in via python3-seqcluster
yamllint
Already a dependency
pytest # an implicit python build dependency
arrow
bioblend
biopython
cyvcf2
geneimpacts
gffutils
h5py
joblib >=0.12
logbook
matplotlib
msgpack-python https://msgpack.org/
mosdepth
python
pandas
psutil
pybedtools
pysam >=0.13.0
pyvcf
requests
scipy >=1.3.0
seqcluster (python3-seqcluster)
statsmodels
tabulate
toolz
Packages already accepted
-------------------------
Are no longer shown in this list but are added to the dependencies of
bcbio. See above for conda references to get an impression.
Packages already in the New Queue
---------------------------------
package libjs-scribl (rejected)
https://salsa.debian.org/med-team/libjs-scribl
http://chmille4.github.io/Scribl/
A surprisingly neat JavaScript library to show genomic features
Needed for DFSG-compliance of seqcluster
Packages just waiting for someone addressing the last mile for the upload
-------------------------------------------------------------------------
package pyomo (in crash space)
https://github.com/Pyomo/pyomo
https://salsa.debian.org/science-team/pyomo
needed by optitype
Status: Builds if errors in build time tests will be ignored
gjh_asl_json recently added to archive
Packages presumed easy to package
---------------------------------
package "asl solver"
http://www.ampl.com/netlib/ampl/solvers.tgz
needed by gjh_asl_json
https://bioconductor.org/packages/release/bioc/html/HTSFilter.html
Needed by seqcluster
needs r-bioc-edger and r-bioc-deseq (also deseq2) as build dependends which are not in Debian
Packages of importance for basic NGS workflows with motivation beyond bcbio
---------------------------------------------------------------------------
package oncofuse
https://salsa.debian.org/med-team/oncofuse
Stuck over typical Java issues
package optitype
https://salsa.debian.org/med-team/optitype (rudimentary)
Stuck over too many dependencies
Difficult to package to the degree that one is tempted to use conda for the meantime
------------------------------------------------------------------------------------
package arvados
https://github.com/arvados/arvados
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 sailfish
https://salsa.debian.org/med-team/sailfish
FTBFS
package fgbio
https://github.com/fulcrumgenomics/fgbio
Anyone much into scala?
package manta
https://github.com/Illumina/manta/
https://salsa.debian.org/med-team/manta
package strelka
https://github.com/Illumina/strelka/releases
- Steffen works on this one
# Strelka self-compiles htslib with these options - we should cross-check with what we are doing
## Addresss sanitizer build options for htslib/samtools
#set(HTSLIB_CFLAGS '-O0 -g -fsanitize=address -fno-omit-frame-pointer -fno-optimize-sibling-calls')
# An easy one if there was not a loss of a Java dependency
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
Packages no longer used by bcbio but available in Debian
--------------------------------------------------------
package lumpy
https://github.com/arq5x/lumpy-sv
|
