Source: pbsuite
Section: science
Priority: optional
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders:
	Afif Elghraoui <afif@debian.org>
Build-Depends:
	debhelper (>= 9),
	dh-python,
	python-all,
Standards-Version: 3.9.8
Homepage: http://sourceforge.net/projects/pb-jelly
Vcs-Git: https://anonscm.debian.org/git/debian-med/pbsuite.git
Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/pbsuite.git

Package: pbsuite
Section: metapackages
Architecture: all
Depends:
	${misc:Depends},
	pbjelly,
	pbhoney,
Description: software for Pacific Biosciences sequencing data
 The PBSuite contains two projects created for analysis of
 Pacific Biosciences long-read sequencing data.
  * PBJelly - genome upgrading tool
  * PBHoney - structural variation discovery

Package: python-pbsuite-utils
Section: python
Architecture: all
Depends:
	${misc:Depends},
	${python:Depends},
	python-pysam (>= 0.8.0),
Description: software for Pacific Biosciences sequencing data -- Python utilities
 The PBSuite currently contains two projects created and maintained
 by Adam English for analysis of Pacific Biosciences long-read
 sequencing data.
  * PBJelly - genome upgrading tool
  * PBHoney - structural variation discovery
 .
 This package contains Python 2 utilities for the suite.

Package: pbjelly
Architecture: all
Depends:
	${misc:Depends},
	${python:Depends},
	python-pbsuite-utils (= ${source:Version}),
	python-networkx,
	blasr (>= 5.3),
Description: genome assembly upgrading tool
 PBJelly is a highly automated pipeline that aligns long sequencing
 reads (such as PacBio RS reads or long 454 reads in fasta format)
 to high-confidence draft assembles. PBJelly fills or reduces as
 many captured gaps as possible to produce upgraded draft genomes.
 .
 PBJelly is part of the PBSuite.

Package: pbhoney
Architecture: all
Depends:
	${misc:Depends},
	${python:Depends},
	python-pbsuite-utils (= ${source:Version}),
	python-pbbanana (= ${source:Version}),
	python-pysam (>= 0.8.0),
	python-networkx,
	python-h5py (>= 2.0.1),
	python-numpy,
	blasr (>= 5.3),
	samtools,
Recommends:
	pbdagcon,
Description: genomic structural variation discovery
 PBHoney is an implementation of two variant-identification
 approaches designed to exploit the high mappability of long reads
 (i.e., greater than 10,000 bp). PBHoney considers both intra-read
 discordance and soft-clipped tails of long reads to identify
 structural variants.
 .
 PBHoney is part of the PBSuite.

Package: python-pbbanana
Section: python
Depends:
	${misc:Depends},
	${python:Depends},
	python-pbsuite-utils (= ${source:Version}),
	python-networkx,
	pbjelly (= ${source:Version}),
	blasr,
Architecture: all
Description: additional utilities for the pbsuite
 PBBanana contains some assembly and consensus utilities
 for the PBSuite.
  * OLCAssembly - A shortcut to calling pacbio's Allora Assembler
  * Polish - A quick consensus caller
  * PBJNovo - DeNovo Assembler of PacBio only reads
 .
 This package is intended for use internally by the PBSuite
