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Source: bcbio
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Steffen Moeller <moeller@debian.org>
Section: contrib/science
Testsuite: autopkgtest-pkg-python
XS-Autobuild: no
Priority: optional
Build-Depends: debhelper-compat (= 13),
dh-sequence-python3,
python3-all,
python3-setuptools,
python3-gffutils,
python3-pandas,
python3-pybedtools,
python3-pysam,
python3-toolz,
python3-tornado,
python3-yaml,
python3-scipy,
python3-psutil,
python3-joblib,
# for testing
atropos <!nocheck>,
bcftools <!nocheck>,
bedtools <!nocheck>,
biobambam2 <!nocheck>,
bowtie2 <!nocheck>,
bwa <!nocheck>,
cnvkit <!nocheck>,
fastqc <!nocheck>,
freebayes <!nocheck>,
gffread <!nocheck>,
grabix <!nocheck>,
gsort <!nocheck>,
hisat2 <!nocheck>,
# hts-nim-tools <!nocheck>,
libfreetype6 <!nocheck>,
lumpy-sv <!nocheck>,
mosdepth <!nocheck>,
multiqc <!nocheck>,
perl <!nocheck>,
libpicard-java <!nocheck>,
libvcflib-tools <!nocheck>,
picard-tools <!nocheck>,
python3-biopython <!nocheck>,
python3-cyvcf2 <!nocheck>,
python3-geneimpacts <!nocheck>,
python3-logbook <!nocheck>,
python3-requests <!nocheck>,
python3-pytest <!nocheck>,
python3-pytest-mock <!nocheck>,
# python3-seqcluster <!nocheck>,
pythonpy <!nocheck>,
rapmap <!nocheck>,
rna-star <!nocheck>,
r-base-core <!nocheck>,
r-bioc-htsfilter <!nocheck>,
r-bioc-degreport <!nocheck>,
r-bioc-purecn <!nocheck>,
r-bioc-summarizedexperiment <!nocheck>,
r-cran-tidyverse <!nocheck>,
r-bioc-titancna <!nocheck>,
r-bioc-tximport <!nocheck>,
r-other-wasabi <!nocheck>,
salmon <!nocheck>,
samblaster <!nocheck>,
samtools <!nocheck>,
seqan-apps <!nocheck>,
seqtk <!nocheck>,
snpeff <!nocheck>,
subread <!nocheck>,
tabix <!nocheck>,
tophat-recondition <!nocheck>,
umis <!nocheck>,
vcfanno <!nocheck>,
vt <!nocheck>,
wham-align <!nocheck>,
xonsh <!nocheck>,
libhts-dev <!nocheck>,
# documentation
python3-sphinx
Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/bcbio
Vcs-Git: https://salsa.debian.org/med-team/bcbio.git
Homepage: https://github.com/bcbio/bcbio-nextgen
Rules-Requires-Root: no
Package: python3-bcbio
Architecture: all
Section: contrib/python
Depends: ${python3:Depends},
${misc:Depends},
python3-biopython,
python3-cyvcf2,
python3-joblib,
python3-logbook,
python3-matplotlib,
python3-psutil,
python3-pysam,
python3-requests,
python3-scipy,
python3-six,
python3-tornado
Recommends: cnvkit,
gsort,
libfreetype6,
libhts-dev,
lumpy-sv,
mosdepth,
multiqc,
python3-arrow,
python3-geneimpacts,
python3-h5py,
# python3-seqcluster,
python3-statsmodels,
python3-tabulate,
r-other-wasabi,
r-bioc-purecn,
r-bioc-titancna,
seqan-apps,
snpeff,
vcfanno,
vt
Suggests: python3-bioblend,
python3-dnapilib,
python3-msgpack,
python3-seqcluster
Description: library for analysing high-throughput sequencing data
This package installs the Python 3 libraries of the bcbio-nextgen
toolkit implementing best-practice pipelines for fully automated high
throughput sequencing analysis.
.
A high-level configuration file specifies inputs and analysis parameters
to drive a parallel pipeline that handles distributed execution,
idempotent processing restarts and safe transactional steps. The project
contributes a shared community resource that handles the data processing
component of sequencing analysis, providing researchers with more time
to focus on the downstream biology.
Package: bcbio
Architecture: all
Depends: ${python3:Depends},
${misc:Depends},
python3-bcbio
Recommends: bcftools,
bwa,
cnvkit,
cufflinks,
delly,
fastqc,
freebayes,
grabix,
libvcflib-tools,
macs,
pythonpy,
rna-star,
hisat2,
sambamba,
samblaster,
samtools,
salmon,
stringtie,
subread,
tabix,
umis,
varscan,
wget,
wham-align
Suggests: toil,
cwltool,
kallisto,
# still missing lumpy-sv,
# still missing manta,
# non-free, install manually: novoalign,
qualimap,
# for cancer heterogeneity analysis with BubbleTree
libglu1-mesa,
# for low mem instead of rna-star
tophat2,
# found in source code but not exactly sure about its importance
tophat-recondition,
r-bioc-summarizedexperiment,
r-cran-tidyverse,
r-other-wasabi
Description: toolkit for analysing high-throughput sequencing data
This package installs the command line tools of the bcbio-nextgen
toolkit implementing best-practice pipelines for fully automated high
throughput sequencing analysis.
.
A high-level configuration file specifies inputs and analysis parameters
to drive a parallel pipeline that handles distributed execution,
idempotent processing restarts and safe transactional steps. The project
contributes a shared community resource that handles the data processing
component of sequencing analysis, providing researchers with more time
to focus on the downstream biology.
.
This package builds and having it in Debian unstable helps the Debian
developers to synchronize their efforts. But unless a series of external
dependencies are not installed manually, the functionality of bcbio in
Debian is only a shadow of itself. Please use the official distribution
of bcbio for the time being, which means "use conda". The TODO file in
the Debian directory should give an overview on progress for Debian
packaging.
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