Accepted adapterremoval 2.2.2-1 (source amd64 all) into unstable

[Kevin Murray]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Tue, 18 Jul 2017 09:37:44 +1000
Source: adapterremoval
Binary: adapterremoval adapterremoval-examples
Architecture: source amd64 all
Version: 2.2.2-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Kevin Murray <kdmf...@gmail.com>
Description:
 adapterremoval - rapid adapter trimming, identification, and read merging of 
gene
 adapterremoval-examples - rapid adapter trimming, identification, and read 
merging (example
Changes:
 adapterremoval (2.2.2-1) unstable; urgency=medium
 .
   * New upstream version 2.2.2
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Accepted snakemake 3.10.0-1 (source all) into unstable

[Kevin Murray]

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Format: 1.8
Date: Thu, 19 Jan 2017 11:41:55 +1100
Source: snakemake
Binary: snakemake
Architecture: source all
Version: 3.10.0-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging <debian-med-packag...@lists.alioth.debian.org>
Changed-By: Kevin Murray <kdmf...@gmail.com>
Description:
 snakemake  - pythonic workflow management system
Changes:
 snakemake (3.10.0-1) unstable; urgency=medium
 .
   * New upstream version 3.10.0
   * Refresh patches
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Accepted snakemake 3.9.1-2 (source all) into unstable

[Kevin Murray]

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Format: 1.8
Date: Wed, 18 Jan 2017 00:20:04 +
Source: snakemake
Binary: snakemake
Architecture: source all
Version: 3.9.1-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging <debian-med-packag...@lists.alioth.debian.org>
Changed-By: Kevin Murray <kdmf...@gmail.com>
Description:
 snakemake  - pythonic workflow management system
Changes:
 snakemake (3.9.1-2) unstable; urgency=medium
 .
   * Future-proof patch to work-around missing snakemake binary when running
 tests before installation
   * Backport fix for crash with dynamic rules (from bitbucket PR #168).
   * Update my email address
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Accepted snakemake 3.9.0+dfsg-1 (source all) into unstable

[Kevin Murray]

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Format: 1.8
Date: Wed, 07 Dec 2016 09:02:12 +1100
Source: snakemake
Binary: snakemake
Architecture: source all
Version: 3.9.0+dfsg-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging <debian-med-packag...@lists.alioth.debian.org>
Changed-By: Kevin Murray <s...@kdmurray.id.au>
Description:
 snakemake  - pythonic workflow management system
Closes: 845737
Changes:
 snakemake (3.9.0+dfsg-1) unstable; urgency=medium
 .
   [ Kevin Murray ]
   * New upstream version 3.9.0 (Closes: #845737)
 .
   [ Andreas Tille ]
   * debhelper 10
   * d/watch: version=4
   * Ignore failures of test that might happpen in pbuilder
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Accepted r-bioc-limma 3.30.6+dfsg-1 (source amd64) into unstable

[Kevin Murray]

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Hash: SHA256

Format: 1.8
Date: Sun, 11 Dec 2016 12:02:11 +1100
Source: r-bioc-limma
Binary: r-bioc-limma
Architecture: source amd64
Version: 3.30.6+dfsg-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Kevin Murray <kdmf...@gmail.com>
Description:
 r-bioc-limma - linear models for microarray data
Changes:
 r-bioc-limma (3.30.6+dfsg-1) unstable; urgency=medium
 .
   [ Kevin Murray ]
   * New upstream version 3.30.6
   * Add myself to uploaders
 .
   [ Andreas Tille ]
   * debhelper 10
   * d/watch: version=4
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Accepted iqtree 1.5.2+dfsg-1 (source amd64) into unstable

[Kevin Murray]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Sun, 04 Dec 2016 11:25:38 +1100
Source: iqtree
Binary: iqtree
Architecture: source amd64
Version: 1.5.2+dfsg-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Kevin Murray <kdmf...@gmail.com>
Description:
 iqtree - efficient phylogenetic software by maximum likelihood
Closes: 846958
Changes:
 iqtree (1.5.2+dfsg-1) unstable; urgency=medium
 .
   * New upstream version 1.5.2+dfsg (Closes: #846958)
   * Enable build of MPI-parallelised executable
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Accepted adapterremoval 2.2.0-1 (source amd64 all) into unstable

[Kevin Murray]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Sun, 04 Dec 2016 17:22:09 +0100
Source: adapterremoval
Binary: adapterremoval adapterremoval-examples
Architecture: source amd64 all
Version: 2.2.0-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Kevin Murray <s...@kdmurray.id.au>
Description:
 adapterremoval - rapid adapter trimming, identification, and read merging of 
gene
 adapterremoval-examples - rapid adapter trimming, identification, and read 
merging (example
Closes: 846664
Changes:
 adapterremoval (2.2.0-1) unstable; urgency=medium
 .
   [ Kevin Murray ]
   * Team upload
   * New upstream version 2.2.0 (Closes: #846664)
   * Refresh patches
 .
   [ Andreas Tille ]
   * Fix spelling
   * DEP3 for benchmarking patches
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Accepted axe-demultiplexer 0.3.2+dfsg1-1 (source amd64) into unstable

[Kevin Murray]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Thu, 01 Dec 2016 12:32:30 +1100
Source: axe-demultiplexer
Binary: axe-demultiplexer
Architecture: source amd64
Version: 0.3.2+dfsg1-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Kevin Murray <kdmf...@gmail.com>
Description:
 axe-demultiplexer - Trie-based DNA sequencing read demultiplexer
Changes:
 axe-demultiplexer (0.3.2+dfsg1-1) unstable; urgency=medium
 .
   [ Kevin Murray ]
   * New upstream version 0.3.2
   * Bump standards-version to 3.9.8
   * Update uploader email
 .
   [ Andreas Tille ]
   * debhelper 10 (makes --parallel in d/rules superfluous)
   * d/watch: version=4
   * hardening=+all
   * Install test script also as user accessible test
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Accepted snakemake 3.8.2+dfsg-1 (source all) into unstable

[Kevin Murray]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Fri, 02 Dec 2016 13:51:01 +1100
Source: snakemake
Binary: snakemake
Architecture: source all
Version: 3.8.2+dfsg-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging <debian-med-packag...@lists.alioth.debian.org>
Changed-By: Kevin Murray <s...@kdmurray.id.au>
Description:
 snakemake  - pythonic workflow management system
Changes:
 snakemake (3.8.2+dfsg-1) unstable; urgency=medium
 .
   * Update d/watch with bitbucket's new tag page
   * New upstream version 3.8.2
   * Patch to avoid test failure
   * Add new dependencies to d/control
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Accepted python-cutadapt 1.12-1 (source all amd64) into unstable

[Kevin Murray]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Fri, 02 Dec 2016 13:56:33 +1100
Source: python-cutadapt
Binary: python-cutadapt python3-cutadapt cutadapt
Architecture: source all amd64
Version: 1.12-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Kevin Murray <kdmf...@gmail.com>
Description:
 cutadapt   - Clean biological sequences from high-throughput sequencing reads
 python-cutadapt - Clean biological sequences from high-throughput sequencing 
reads
 python3-cutadapt - Clean biological sequences from high-throughput sequencing 
reads
Closes: 846471
Changes:
 python-cutadapt (1.12-1) unstable; urgency=medium
 .
   * New upstream version 1.12 (Closes: #846471)
   * Fix up d/copyright: remove duplicate license stanzas, and Files: pattern
 without matching files.
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Accepted libqes 0.2.7-1 (source amd64) into unstable

[Kevin Murray]

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Format: 1.8
Date: Thu, 01 Dec 2016 12:19:16 +1100
Source: libqes
Binary: libqes-dev libqes0
Architecture: source amd64
Version: 0.2.7-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging <debian-med-packag...@lists.alioth.debian.org>
Changed-By: Kevin Murray <kdmf...@gmail.com>
Description:
 libqes-dev - DNA sequence parsing library -- development
 libqes0- DNA sequence parsing library
Changes:
 libqes (0.2.7-1) unstable; urgency=medium
 .
   * New upstream release (fixes major parsing bug)
   * Update standards version to 3.9.8
   * Update uploader email
   * Hardening+all to pull in bindnow hardening
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Accepted libzstd 1.1.1-1 (source) into unstable

[Kevin Murray]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Sun, 20 Nov 2016 16:12:58 +0100
Source: libzstd
Binary: libzstd-dev libzstd1 zstd
Architecture: source
Version: 1.1.1-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging <debian-med-packag...@lists.alioth.debian.org>
Changed-By: Kevin Murray <kdmf...@gmail.com>
Description:
 libzstd-dev - fast lossless compression algorithm -- development files
 libzstd1   - fast lossless compression algorithm
 zstd   - fast lossless compression algorithm -- CLI tool
Closes: 844248
Changes:
 libzstd (1.1.1-1) unstable; urgency=medium
 .
   * New upstream version 1.1.1 (Closes: #844248)
   * Whitespace fix to d/control
   * Ensure hardening flags pass through to compiler by appending to CPPFLAGS
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Accepted python-skbio 0.5.1-1 (source all amd64) into unstable

[Kevin Murray]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Tue, 15 Nov 2016 18:58:14 +1100
Source: python-skbio
Binary: python-skbio-doc python3-skbio
Architecture: source all amd64
Version: 0.5.1-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Kevin Murray <kdmf...@gmail.com>
Description:
 python-skbio-doc - Data structures, algorithms, educational resources for 
bioinforma
 python3-skbio - Python3 data structures, algorithms, educational resources for 
bi
Changes:
 python-skbio (0.5.1-1) unstable; urgency=medium
 .
   * New upstream release
   * Change uploader mail
   * Use libssw from debian, not internal source
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Accepted libzstd 1.1.0-1 (source) into unstable

[Kevin Murray]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Sun, 13 Nov 2016 11:23:03 +
Source: libzstd
Binary: libzstd-dev libzstd1 zstd
Architecture: source
Version: 1.1.0-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging <debian-med-packag...@lists.alioth.debian.org>
Changed-By: Kevin Murray <kdmf...@gmail.com>
Description:
 libzstd-dev - fast lossless compression algorithm -- development files
 libzstd1   - fast lossless compression algorithm
 zstd   - fast lossless compression algorithm -- CLI tool
Closes: 839960
Changes:
 libzstd (1.1.0-1) unstable; urgency=medium
 .
   * New upstream version 1.1.0 (Closes: #839960)
   * Change uploader email
   * Build new pzstd binary, including manpage
   * Fix miscellaneous issues with d/rules and d/*.install
   * Move docs from libzstd-dev to the zstd binary
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Accepted libzstd 1.0.0-1 (source amd64) into unstable, unstable

[Kevin Murray]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Sun, 04 Sep 2016 14:45:24 +1000
Source: libzstd
Binary: libzstd-dev libzstd1 zstd
Architecture: source amd64
Version: 1.0.0-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging <debian-med-packag...@lists.alioth.debian.org>
Changed-By: Kevin Murray <s...@kdmurray.id.au>
Description:
 libzstd-dev - fast lossless compression algorithm -- development files
 libzstd1   - fast lossless compression algorithm
 zstd   - fast lossless compression algorithm -- CLI tool
Closes: 836574
Changes:
 libzstd (1.0.0-1) unstable; urgency=medium
 .
   * Imported Upstream version 1.0.0 (Closes: #836574)
   * Bump library package name to libzstd1
   * Changed project URLs, copyrights after move to facebook.
   * d/rules: hardening=+all
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Accepted libzstd 0.8.0-1 (source amd64) into unstable

[Kevin Murray]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Thu, 21 Jul 2016 10:56:02 +1000
Source: libzstd
Binary: libzstd-dev libzstd0 zstd
Architecture: source amd64
Version: 0.8.0-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging <debian-med-packag...@lists.alioth.debian.org>
Changed-By: Kevin Murray <s...@kdmurray.id.au>
Description:
 libzstd-dev - fast lossless compression algorithm -- development files
 libzstd0   - fast lossless compression algorithm
 zstd   - fast lossless compression algorithm -- CLI tool
Closes: 834114
Changes:
 libzstd (0.8.0-1) unstable; urgency=medium
 .
   [ Kevin Murray ]
   * New upstream version (Closes: #834114)
 .
   [ Andreas Tille ]
   * hardening=+bindnow
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Accepted snakemake 3.7.1+dfsg-1 (source all) into unstable

[Kevin Murray]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Tue, 28 Jun 2016 14:54:17 +1000
Source: snakemake
Binary: snakemake
Architecture: source all
Version: 3.7.1+dfsg-1
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging <debian-med-packag...@lists.alioth.debian.org>
Changed-By: Kevin Murray <s...@kdmurray.id.au>
Description:
 snakemake  - pythonic workflow management system
Changes:
 snakemake (3.7.1+dfsg-1) unstable; urgency=low
 .
   * Imported new upstream version 3.7.1
   * Bump standards version to 3.9.8
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Accepted libzstd 0.5.1-1 (source) into unstable

[Kevin Murray]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Thu, 17 Mar 2016 12:59:04 +
Source: libzstd
Binary: libzstd-dev libzstd0 zstd
Architecture: source
Version: 0.5.1-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging <debian-med-packag...@lists.alioth.debian.org>
Changed-By: Kevin Murray <s...@kdmurray.id.au>
Description:
 libzstd-dev - fast lossless compression algorithm -- development files
 libzstd0   - fast lossless compression algorithm
 zstd   - fast lossless compression algorithm -- CLI tool
Closes: 813854
Changes:
 libzstd (0.5.1-1) unstable; urgency=medium
 .
   [ Kevin Murray ]
   * New upstream version (fixes a FTBFS)
   * Package pkgconfig file (Closes: #813854)
   * Fix path to tagged archives in d/watch
   * Add vcs URLs
   * Bump to standards version 3.9.7
 .
   [ Mattia Rizzolo ]
   * debian/rules: Remove a lot of uneeded comments and lines
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Accepted axe-demultiplexer 0.3.1-4 (source) into unstable

[Kevin Murray]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Wed, 02 Mar 2016 14:20:13 +1100
Source: axe-demultiplexer
Binary: axe-demultiplexer
Architecture: source
Version: 0.3.1-4
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Kevin Murray <s...@kdmurray.id.au>
Description:
 axe-demultiplexer - Trie-based DNA sequencing read demultiplexer
Changes:
 axe-demultiplexer (0.3.1-4) unstable; urgency=low
 .
   [ Kevin Murray ]
   * Fix Vcs-git URL
 .
   [ Mattia Rizzolo ]
   * debian/rules: drop useless include
   * debian/control: Bump Standards-Version to 3.9.7, no changes needed
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axe-demultiplexer_0.3.1-4.dsc
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Accepted python-skbio 0.4.2-1 (source) into unstable

[Kevin Murray]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Sat, 13 Feb 2016 11:06:20 -0800
Source: python-skbio
Binary: python-skbio python-skbio-doc python3-skbio
Architecture: source
Version: 0.4.2-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Kevin Murray <s...@kdmurray.id.au>
Description:
 python-skbio - Python data structures, algorithms, educational resources for 
bio
 python-skbio-doc - Data structures, algorithms, educational resources for 
bioinforma
 python3-skbio - Python3 data structures, algorithms, educational resources for 
bi
Changes:
 python-skbio (0.4.2-1) unstable; urgency=medium
 .
   * New upstream version
   * Fix several test failures
   * Add basic autopkgtests
   * Don't build pdf figures (fixes unreproducible build)
   * Secure vcs-git url
   * Bump Standards-Version to 3.9.7, no changes needed
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Accepted scythe 0.994-3 (source) into unstable

[Kevin Murray]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Thu, 17 Mar 2016 12:39:24 +
Source: scythe
Binary: scythe
Architecture: source
Version: 0.994-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Kevin Murray <s...@kdmurray.id.au>
Description:
 scythe - Bayesian adaptor trimmer for sequencing reads
Changes:
 scythe (0.994-3) unstable; urgency=medium
 .
   [ Kevin Murray ]
   * Comment out watchfile, upstream doesn't actually provide tags on github
   * Fix vcs git URL
   * Bump standards version
 .
   [ Mattia Rizzolo ]
   * debian/rules: remove useless include
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Accepted scrm 1.7.0-1 (source amd64) into unstable

[Kevin Murray]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Tue, 09 Feb 2016 17:47:10 -0800
Source: scrm
Binary: scrm
Architecture: source amd64
Version: 1.7.0-1
Distribution: unstable
Urgency: low
Maintainer: Kevin Murray <s...@kdmurray.id.au>
Changed-By: Kevin Murray <s...@kdmurray.id.au>
Description:
 scrm   - simulator of evolution of genetic sequences
Closes: 811099
Changes:
 scrm (1.7.0-1) unstable; urgency=low
 .
   * New upstream release (fixes FTBFS)
 Closes: #811099
   * Add a d/upstream/metadata file with reference to scrm's paper.
   * Use secure Vcs-Git url
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Accepted axe-demultiplexer 0.3.1-3 (source) into unstable

[Kevin Murray]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Sat, 06 Feb 2016 10:26:55 +0100
Source: axe-demultiplexer
Binary: axe-demultiplexer
Architecture: source
Version: 0.3.1-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Kevin Murray <s...@kdmurray.id.au>
Description:
 axe-demultiplexer - Trie-based DNA sequencing read demultiplexer
Changes:
 axe-demultiplexer (0.3.1-3) unstable; urgency=medium
 .
   * Syntax fix for autopkgtest
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Accepted phyml 3:3.2.0+dfsg-1 (source amd64) into unstable

[Kevin Murray]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Sat, 06 Feb 2016 16:06:43 +0100
Source: phyml
Binary: phyml
Architecture: source amd64
Version: 3:3.2.0+dfsg-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Kevin Murray <s...@kdmurray.id.au>
Description:
 phyml  - Phylogenetic estimation using Maximum Likelihood
Changes:
 phyml (3:3.2.0+dfsg-1) unstable; urgency=medium
 .
   [ Kevin Murray ]
   * New upstream release
   * d/watch: Source has changed location on Github
   * Patch CPPFLAGS to allow build of phytime
 .
   [ Andreas Tille ]
   * Upstream confirmed that the development version should be fairly stable
 and most probably suitable for Debian
   * Moved debian/upstream to debian/upstream/metadata
   * cme fix dpkg-control
   * Remove executable binary from archive (as well as LaTeX remainings once
 we are starting to remove files)
   * Move to git
   * Build-Depends: pkg-config, libhmsbeagle-dev
   * debian/rules:
  - hack around removal of PDF manual
  - enable building with libhmsbeagle-dev
   * DEP5
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Accepted axe-demultiplexer 0.3.1-2 (source amd64) into unstable

[Kevin Murray]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Fri, 05 Feb 2016 20:27:46 +0100
Source: axe-demultiplexer
Binary: axe-demultiplexer
Architecture: source amd64
Version: 0.3.1-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Kevin Murray <s...@kdmurray.id.au>
Description:
 axe-demultiplexer - Trie-based DNA sequencing read demultiplexer
Changes:
 axe-demultiplexer (0.3.1-2) unstable; urgency=medium
 .
   * Add autopkgtest
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Bug#813840: ITP: libqcpp -- A C++ library for next-gen sequencing data quality control.

[Kevin Murray]

Package: wnpp
Severity: wishlist
Owner: Kevin Murray <s...@kdmurray.id.au>

* Package name: libqcpp
  Version : 0.1.9
  Upstream Author : Kevin Murray <s...@kdmurray.id.au>
* URL : https://github.com/kdmurray91/libqcpp
* License : LGPL
  Programming Lang: C++
  Description : A C++ library for next-gen sequencing data quality control.

libqc++ implements adaptor trimming, windowed quality trimming, length
filtering and trimming, format conversion, and basic read manipulation.
It also provides classes for implementation of new measures and easy
creation of bespoke filtering tools.

Some tools are packaged of the source package libqcpp, including gbsqc,
a tool specifically for quality control of genotyping by sequencing.

This package will be maintained under the Debian Med team.

---
Kevin Murray
0xA4B4EE6A

Accepted libzstd 0.4.7-1 (source amd64) into unstable

[Kevin Murray]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Wed, 03 Feb 2016 11:26:21 +0200
Source: libzstd
Binary: libzstd-dev libzstd0 zstd
Architecture: source amd64
Version: 0.4.7-1
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging <debian-med-packag...@lists.alioth.debian.org>
Changed-By: Kevin Murray <s...@kdmurray.id.au>
Description:
 libzstd-dev - fast lossless compression algorithm -- development files
 libzstd0   - fast lossless compression algorithm
 zstd   - fast lossless compression algorithm -- CLI tool
Changes:
 libzstd (0.4.7-1) unstable; urgency=low
 .
   * New upstream version
   * Remove build date encoding to enable reproducible build
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Accepted snakemake 3.5.5+dfsg-1 (source all) into unstable

[Kevin Murray]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Fri, 29 Jan 2016 17:18:28 +0200
Source: snakemake
Binary: snakemake
Architecture: source all
Version: 3.5.5+dfsg-1
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging <debian-med-packag...@lists.alioth.debian.org>
Changed-By: Kevin Murray <s...@kdmurray.id.au>
Description:
 snakemake  - pythonic workflow management system
Changes:
 snakemake (3.5.5+dfsg-1) unstable; urgency=low
 .
   * Imported new upstream version 3.5.5
   * Use filenamemangle in d/watch
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Accepted dawg 1.2-1 (source amd64) into unstable, unstable

[Kevin Murray]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Tue, 01 Dec 2015 12:25:35 +1100
Source: dawg
Binary: dawg
Architecture: source amd64
Version: 1.2-1
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging <debian-med-packag...@lists.alioth.debian.org>
Changed-By: Kevin Murray <s...@kdmurray.id.au>
Description:
 dawg   - program to simulate the evolution of recombinant DNA sequences
Closes: 806828
Changes:
 dawg (1.2-1) unstable; urgency=low
 .
   * Initial release (Closes: #806828)
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Accepted libzstd 0.4.5-1 (source amd64) into unstable, unstable

[Kevin Murray]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Tue, 01 Dec 2015 13:54:36 +1100
Source: libzstd
Binary: libzstd-dev libzstd0 zstd
Architecture: source amd64
Version: 0.4.5-1
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging <debian-med-packag...@lists.alioth.debian.org>
Changed-By: Kevin Murray <s...@kdmurray.id.au>
Description:
 libzstd-dev - fast lossless compression algorithm -- development files
 libzstd0   - fast lossless compression algorithm
 zstd   - fast lossless compression algorithm -- CLI tool
Closes: 806767
Changes:
 libzstd (0.4.5-1) unstable; urgency=low
 .
   * Initial release (Closes: #806767)
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libzstd-dev_0.4.5-1_amd64.deb
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libzstd0-dbgsym_0.4.5-1_amd64.deb
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Files:
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 39ff4d7a472c3df0abec0120c352a5d2 246719 libs optional libzstd_0.4.5.orig.tar.gz
 b929a13c8131156aad155e4b40ec9e0c 4336 libs optional 
libzstd_0.4.5-1.debian.tar.xz
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libzstd-dev_0.4.5-1_amd64.deb
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libzstd0-dbgsym_0.4.5-1_amd64.deb
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zstd-dbgsym_0.4.5-1_amd64.deb
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Accepted scrm 1.6.1-1 (source amd64) into unstable, unstable

[Kevin Murray]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Fri, 08 Jan 2016 12:02:44 +1100
Source: scrm
Binary: scrm
Architecture: source amd64
Version: 1.6.1-1
Distribution: unstable
Urgency: low
Maintainer: Kevin Murray <s...@kdmurray.id.au>
Changed-By: Kevin Murray <s...@kdmurray.id.au>
Description:
 scrm   - simulator of evolution of genetic sequences
Closes: 809972
Changes:
 scrm (1.6.1-1) unstable; urgency=low
 .
   * Initial release (Closes: #809972)
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scrm_1.6.1-1.debian.tar.xz
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scrm-dbgsym_1.6.1-1_amd64.deb
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Accepted dwgsim 0.1.11-3 (source amd64) into unstable

[Kevin Murray]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Mon, 04 Jan 2016 14:49:00 +1100
Source: dwgsim
Binary: dwgsim
Architecture: source amd64
Version: 0.1.11-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Kevin Murray <s...@kdmurray.id.au>
Description:
 dwgsim - short sequencing read simulator
Changes:
 dwgsim (0.1.11-3) unstable; urgency=medium
 .
   [Andreas Tille]
   * Correct Maintainer to Debian Med
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Accepted sphinxcontrib-autoprogram 0.1.2-1 (source all) into unstable

[Kevin Murray]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Sun, 10 Jan 2016 10:52:56 +1100
Source: sphinxcontrib-autoprogram
Binary: sphinxcontrib-autoprogram python3-sphinxcontrib.autoprogram
Architecture: source all
Version: 0.1.2-1
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Kevin Murray <s...@kdmurray.id.au>
Description:
 python3-sphinxcontrib.autoprogram - automated documentation of CLI programs 
for Sphinx (Python 3)
 sphinxcontrib-autoprogram - automated documentation of CLI programs for Sphinx 
(Python 2)
Changes:
 sphinxcontrib-autoprogram (0.1.2-1) unstable; urgency=low
 .
   * New upstream version
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sphinxcontrib-autoprogram_0.1.2-1.debian.tar.xz
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python3-sphinxcontrib.autoprogram_0.1.2-1_all.deb
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sphinxcontrib-autoprogram_0.1.2-1_all.deb

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Accepted snakemake 3.5.4+dfsg-1 (source all) into unstable

[Kevin Murray]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Thu, 17 Dec 2015 21:11:20 +1100
Source: snakemake
Binary: snakemake
Architecture: source all
Version: 3.5.4+dfsg-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging <debian-med-packag...@lists.alioth.debian.org>
Changed-By: Kevin Murray <s...@kdmurray.id.au>
Description:
 snakemake  - pythonic workflow management system
Changes:
 snakemake (3.5.4+dfsg-1) unstable; urgency=medium
 .
   * Imported Upstream version 3.5.4+dfsg
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snakemake_3.5.4+dfsg-1.debian.tar.xz
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Bug#810576: ITP: hail -- Efficiently extract arbitrary lines from a file or stream

[Kevin Murray]

Package: wnpp
Severity: wishlist
Owner: Kevin Murray <s...@kdmurray.id.au>

* Package name: hail
  Version : 0.1.1
  Upstream Author : Kevin Murray
* URL : https://github.com/kdmurray91/hail
* License : GPL
  Programming Lang: C
  Description : Efficiently extract arbitrary lines from a file or stream

Hail gets its name from a contraction of head and tail, the common alternative
to this program. It extracts lines from a file, taken on stdin, and prints them
on stdout. It's so simple that the Unix wizards of old never bothered.

Hail will be co-maintained in the Debian Med team.

Bug#809972: ITP: scrm -- A coalescent simulator for genome-scale sequences

[Kevin Murray]

Package: wnpp
Severity: wishlist
Owner: Kevin Murray <s...@kdmurray.id.au>

* Package name: scrm
  Version : 1.6.1
  Upstream Author : Paul R. Staab <deve...@paulstaab.de>
* URL : https://github.com/scrm/scrm
* License : GPL
  Programming Lang: C++
  Description : A coalescent simulator for genome-scale sequences

scrm simulates the evolution of genetic sequences. It takes a neutral
evolutionary model as input, and generates random sequences that evolved under
the model. As coalescent simulator, it traces the ancestry of the sampled
sequences backwards in time and is therefore extremely efficient. Compared to
other coalescent simulators, it can simulate chromosome-scale sequences without
a measurable reduction of genetic linkage between different sites.

This package will be maintained by the Debian Med team.

Accepted filo 1.1.0-3 (source amd64) into unstable

[Kevin Murray]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Tue, 22 Dec 2015 00:54:45 +1100
Source: filo
Binary: filo
Architecture: source amd64
Version: 1.1.0-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Kevin Murray <s...@kdmurray.id.au>
Description:
 filo   - FILe and stream Operations
Closes: 716357
Changes:
 filo (1.1.0-3) unstable; urgency=medium
 .
   * Fix Mayhem-induced segfault
 Closes: #716357
   * Re-import tarball with pristine-tar
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Accepted libqes 0.1.21-1 (source amd64) into unstable

[Kevin Murray]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Tue, 22 Dec 2015 10:59:59 +1100
Source: libqes
Binary: libqes-dev libqes0
Architecture: source amd64
Version: 0.1.21-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging <debian-med-packag...@lists.alioth.debian.org>
Changed-By: Kevin Murray <s...@kdmurray.id.au>
Description:
 libqes-dev - DNA sequence parsing library -- development
 libqes0- DNA sequence parsing library
Closes: 808710
Changes:
 libqes (0.1.21-1) unstable; urgency=medium
 .
   * New upstream release (Closes: #808710)
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Accepted python-skbio 0.4.1-1 (source amd64 all) into unstable, unstable

[Kevin Murray]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Mon, 21 Dec 2015 16:45:00 +1100
Source: python-skbio
Binary: python-skbio python-skbio-doc python3-skbio
Architecture: source amd64 all
Version: 0.4.1-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Kevin Murray <s...@kdmurray.id.au>
Description:
 python-skbio - Python data structures, algorithms, educational resources for 
bio
 python-skbio-doc - Data structures, algorithms, educational resources for 
bioinforma
 python3-skbio - Python3 data structures, algorithms, educational resources for 
bi
Closes: 806594
Changes:
 python-skbio (0.4.1-1) unstable; urgency=medium
 .
   [ Kevin Murray ]
   * New upstream version
   * Build documentation and create new python-skbio-doc package (Closes:
 #806594)
 .
   [ Andreas Tille ]
   * Do not require lots of dependencies on local machine just to run clean
 target
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Accepted axe-demultiplexer 0.3.1-1 (source amd64) into unstable

[Kevin Murray]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Mon, 21 Dec 2015 14:31:47 +1100
Source: axe-demultiplexer
Binary: axe-demultiplexer
Architecture: source amd64
Version: 0.3.1-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Kevin Murray <s...@kdmurray.id.au>
Description:
 axe-demultiplexer - Trie-based DNA sequencing read demultiplexer
Closes: 808570
Changes:
 axe-demultiplexer (0.3.1-1) unstable; urgency=medium
 .
   * Imported Upstream version 0.3.1 (Closes: #808570)
   * Change arch to any, non 64 bit archs should work now
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Accepted axe-demultiplexer 0.3.0+dfsg-2 (source amd64) into unstable

[Kevin Murray]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Mon, 07 Dec 2015 08:37:49 +1100
Source: axe-demultiplexer
Binary: axe-demultiplexer
Architecture: source amd64
Version: 0.3.0+dfsg-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Kevin Murray <s...@kdmurray.id.au>
Description:
 axe-demultiplexer - Trie-based DNA sequencing read demultiplexer
Closes: 807184
Changes:
 axe-demultiplexer (0.3.0+dfsg-2) unstable; urgency=medium
 .
   * Depend on GSL2 for the ongoing GSL transition (Closes: #807184)
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Bug#806828: ITP: dawg -- program to simulate the evolution of recombinant DNA sequences

[Kevin Murray]

Package: wnpp
Severity: wishlist
Owner: Kevin Murray <s...@kdmurray.id.au>

* Package name: dawg
  Version : 1.2.0
  Upstream Author : Reed A. Cartwright
* URL : http://scit.us/projects/dawg
* License : GPL-2
  Programming Lang: C++
  Description : program to simulate the evolution of recombinant DNA 
sequences


DNA Assembly with Gaps (Dawg) is an application designed to simulate the
evolution of recombinant DNA sequences in continuous time based on the robust
general time reversible model with gamma and invariant rate heterogeneity and
a novel length-dependent model of gap formation. The application accepts
phylogenies in Newick format and can return the sequence of any node,
allowing for the exact evolutionary history to be recorded at the discretion
of users. Dawg records the gap history of every lineage to produce the true
alignment in the output. Many options are available to allow users to
customize their simulations and results.

Bug#806767: ITP: libzstd -- fast lossless compression algorithm, targeting real-time compression scenarios

[Kevin Murray]

Package: wnpp
Severity: wishlist
Owner: Kevin Murray <s...@kdmurray.id.au>

* Package name: libzstd
  Version : 0.4.0
  Upstream Author : Yann Collet 
* URL : https://github.com/Cyan4973
* License : BSD
  Programming Lang: C
  Description : fast lossless compression algorithm

Zstd, short for Zstandard, is a fast lossless compression algorithm, targeting
real-time compression scenarios at zlib-level compression ratio. Zstd can also
offer stronger compression ratio at the cost of compression speed. Speed /
Ratio trade-off is configurable by small increment, to fit different
situations. Note however that decompression speed is preserved and remain
roughly the same at all settings, a property shared by most LZ compression
algorithms, such as zlib. 

This will be co-maintained under Debian Med.

Accepted axe-demultiplexer 0.3.0+dfsg-1 (source amd64) into unstable

[Kevin Murray]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Tue, 01 Dec 2015 09:39:20 +1100
Source: axe-demultiplexer
Binary: axe-demultiplexer
Architecture: source amd64
Version: 0.3.0+dfsg-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Kevin Murray <s...@kdmurray.id.au>
Description:
 axe-demultiplexer - Trie-based DNA sequencing read demultiplexer
Closes: 801696 801900
Changes:
 axe-demultiplexer (0.3.0+dfsg-1) unstable; urgency=medium
 .
   * New upstream release, refresh patches (Closes: #801900)
   * Split libqes to separate package
   * Restrict arch to amd64 & i386 (Closes: #801696)
   * Correct license details in d/copyright
   * Don't use bundled copy of GSL, build-dep on libgsl0-dev
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axe-demultiplexer_0.3.0+dfsg-1_amd64.deb
Files:
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axe-demultiplexer_0.3.0+dfsg-1.dsc
 a8bbf959ba43b7f515cbd079328d3ebe 258939 science optional 
axe-demultiplexer_0.3.0+dfsg.orig.tar.gz
 f9dfc440adf7de4937be702906e0f883 4652 science optional 
axe-demultiplexer_0.3.0+dfsg-1.debian.tar.xz
 0b3a2e8ceda3ddc03045e0096ce4dbb6 32994 science optional 
axe-demultiplexer_0.3.0+dfsg-1_amd64.deb

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Accepted libqes 0.1.20-1 (source amd64) into unstable, unstable

[Kevin Murray]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Wed, 21 Oct 2015 16:20:26 +1100
Source: libqes
Binary: libqes-dev libqes0
Architecture: source amd64
Version: 0.1.20-1
Distribution: unstable
Urgency: medium
Maintainer: Kevin Murray <s...@kdmurray.id.au>
Changed-By: Kevin Murray <s...@kdmurray.id.au>
Description:
 libqes-dev - DNA sequence parsing library -- development
 libqes0- DNA sequence parsing library
Closes: 805153
Changes:
 libqes (0.1.20-1) unstable; urgency=medium
 .
   * Initial release (Closes: #805153)
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libqes_0.1.20-1.debian.tar.xz
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libqes-dev_0.1.20-1_amd64.deb
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Accepted snakemake 3.4.2+dfsg-2 (source all) into unstable

[Kevin Murray]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Thu, 19 Nov 2015 11:20:03 +1100
Source: snakemake
Binary: snakemake
Architecture: source all
Version: 3.4.2+dfsg-2
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging <debian-med-packag...@lists.alioth.debian.org>
Changed-By: Kevin Murray <s...@kdmurray.id.au>
Description:
 snakemake  - pythonic workflow management system
Changes:
 snakemake (3.4.2+dfsg-2) unstable; urgency=low
 .
   * Fix watch file and d/control with new upstream URL
Checksums-Sha1:
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snakemake_3.4.2+dfsg-2.debian.tar.xz
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Files:
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snakemake_3.4.2+dfsg-2.dsc
 52bf21aa212657c6303b541eaa7e3cce 7640 science optional 
snakemake_3.4.2+dfsg-2.debian.tar.xz
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snakemake_3.4.2+dfsg-2_all.deb

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Bug#805153: ITP: libqes -- a next-gen sequencing format parsing and utility library for C

[Kevin Murray]

Package: wnpp
Severity: wishlist
Owner: Kevin Murray <s...@kdmurray.id.au>

* Package name: libqes
  Version : 0.1.20
  Upstream Author : Kevin Murray <s...@kdmurray.id.au>
* URL : https://github.com/kdmurray91/libqes
* License : GPL-3+
  Programming Lang: C
  Description : Next-gen sequencing format parsing and utility library for C

This is packaged as a build-dep of the Axe demultiplexer (src pkg
axe-demultiplexer). It will be co-maintained with Debian Med.

Bug#804646: ITP: partitionfinder -- programs for simultaneously choosing partitioning schemes and models of molecular evolution for sequence data.

[Kevin Murray]

X-Debbugs-CC: Debian Med Packaging 
<debian-med-packag...@lists.alioth.debian.org>
Package: wnpp
Severity: wishlist
Owner: Kevin Murray <s...@kdmurray.id.au>

* Package name: partitionfinder
  Version : 2.0.0
  Upstream Author : Brett Calcott and Rob Lanfear
* URL : https://github.com/brettc/partitionfinder
* License : GPL-3+
  Programming Lang: Python
  Description : programs for simultaneously choosing partitioning schemes
and models of molecular evolution for sequence data.

PartitionFinder is a series of programs for simultaneously choosing
partitioning schemes and models of molecular evolution for sequence data.

You can use them before running a phylogenetic analysis, in order to decide how
to divide up your sequence data into separate blocks before analysis, and to
simultaneously perform model selection on each of those blocks.

This package will be co-maintained under Debian Med.

---
Kevin Murray

GPG pubkey: http://www.kdmurray.id.au/static/A4B4EE6A.asc
FPR: 656C 0632 1EAB 2C3F 3837  9767 17C2 8EB1 A4B4 EE6A

Accepted dwgsim 0.1.11-2 (source amd64) into unstable

[Kevin Murray]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Mon, 26 Oct 2015 11:54:58 +1100
Source: dwgsim
Binary: dwgsim
Architecture: source amd64
Version: 0.1.11-2
Distribution: unstable
Urgency: medium
Maintainer: Kevin Murray <s...@kdmurray.id.au>
Changed-By: Kevin Murray <s...@kdmurray.id.au>
Description:
 dwgsim - short sequencing read simulator
Closes: 803009
Changes:
 dwgsim (0.1.11-2) unstable; urgency=medium
 .
   * Add d/*.install to git (Closes: #803009)
   * Fix some lintian warnings
Checksums-Sha1:
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Files:
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Accepted dwgsim 0.1.11-1 (source amd64) into unstable, unstable

[Kevin Murray]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Wed, 23 Sep 2015 09:14:48 +1000
Source: dwgsim
Binary: dwgsim
Architecture: source amd64
Version: 0.1.11-1
Distribution: unstable
Urgency: low
Maintainer: Kevin Murray <s...@kdmurray.id.au>
Changed-By: Kevin Murray <s...@kdmurray.id.au>
Description:
 dwgsim - short sequencing read simulator
Closes: 799830
Changes:
 dwgsim (0.1.11-1) unstable; urgency=low
 .
   * Initial release (Closes: #799830)
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Accepted snakemake 3.4.2+dfsg-1 (source all) into unstable, unstable

[Kevin Murray]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Sun, 13 Sep 2015 22:58:41 +1000
Source: snakemake
Binary: snakemake
Architecture: source all
Version: 3.4.2+dfsg-1
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging <debian-med-packag...@lists.alioth.debian.org>
Changed-By: Kevin Murray <s...@kdmurray.id.au>
Description:
 snakemake  - pythonic workflow management system
Closes: 798824
Changes:
 snakemake (3.4.2+dfsg-1) unstable; urgency=low
 .
   * Initial release (Closes: #798824)
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Accepted python-skbio 0.4.0-3 (source amd64) into unstable

[Kevin Murray]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Tue, 13 Oct 2015 22:18:07 +1100
Source: python-skbio
Binary: python-skbio python3-skbio
Architecture: source amd64
Version: 0.4.0-3
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Kevin Murray <s...@kdmurray.id.au>
Description:
 python-skbio - Python data structures, algorithms, educational resources for 
bio
 python3-skbio - Python3 data structures, algorithms, educational resources for 
bi
Changes:
 python-skbio (0.4.0-3) unstable; urgency=low
 .
   [ Kevin Murray ]
   * Revert deletion of CI files in d/rules clean target
   * Add lintian overrides for duplicated compressed files
   * Fix my email address in d/control
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Accepted scythe 0.994-2 (source amd64) into unstable

[Kevin Murray]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Mon, 19 Oct 2015 11:27:51 +1100
Source: scythe
Binary: scythe
Architecture: source amd64
Version: 0.994-2
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Kevin Murray <s...@kdmurray.id.au>
Description:
 scythe - Bayesian adaptor trimmer for sequencing reads
Changes:
 scythe (0.994-2) unstable; urgency=low
 .
   * Fix copyright of kseq.h in d/control
   * Patch Makefile to pull in hardening flags correctly
   * Add compiled readme to gitignore
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Accepted axe-demultiplexer 0.2.8-1 (source amd64) into unstable, unstable

[Kevin Murray]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Mon, 12 Oct 2015 16:54:45 +1100
Source: axe-demultiplexer
Binary: axe-demultiplexer
Architecture: source amd64
Version: 0.2.8-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Kevin Murray <s...@kdmurray.id.au>
Description:
 axe-demultiplexer - Trie-based DNA sequencing read demultiplexer
Closes: 794088
Changes:
 axe-demultiplexer (0.2.8-1) unstable; urgency=medium
 .
   * Initial debian release. (Closes: #794088)
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Bug#801306: ITP: python-oset -- An ordered set data structure for Python

[Kevin Murray]

Package: wnpp
Severity: wishlist
Owner: Kevin Murray <s...@kdmurray.id.au>

* Package name: python-oset
  Version : 0.1.3
  Upstream Author : Carlos Martin, Raymond Hettinger
* URL : https://gitorious.com/sleipnir/python-oset
* License : BSD
  Programming Lang: Python
  Description : An ordered set data structure for Python

A set data structure that remembers original insertion order.  The
implementation based on a doubly linked link and an internal dictionary.
This design gives OrderedSet the same big-Oh running times as regular
sets including O(1) adds, removes, and lookups as well as O(n)
iteration.

This is a dependency of sphinxcontrib-bibtex, which is required to build
seqan's documentation.

This package will be co-maintained in the Debian Med team.

Bug#801307: ITP: pybtex-docutils -- A docutils backend for pybtex

[Kevin Murray]

Package: wnpp
Severity: wishlist
Owner: Kevin Murray <s...@kdmurray.id.au>

* Package name: pybtex-docutils
  Version : 0.2.1
  Upstream Author : Matthias C. M. Troffaes
* URL : https://github.com/mcmtroffaes/pybtex-docutils
* License : Expat
  Programming Lang: Python
  Description : A docutils backend for pybtex

Pybtex is a drop-in replacement for BibTeX written in Python. pybtex-docutils
is a docutils backend for pybtex.

pybtex-docutils is a dependency for sphinxcontrib-bibtex, required for the
build of seqan's documentation.

This package will be co-maintained with the Debian Med team.

Bug#801309: ITP: python-latexcodec -- A lexer and codec to work with LaTeX code in Python.

[Kevin Murray]

Package: wnpp
Severity: wishlist
Owner: Kevin Murray <s...@kdmurray.id.au>

* Package name: python-latexcodec
  Version : 1.0.1
  Upstream Author : Matthias C. M. Troffaes
* URL : https://github.com/mcmtroffaes/pybtex-docutils
* License : Expat
  Programming Lang: Python
  Description : A lexer and codec to work with LaTeX code in Python.

A dependency of the sphinxcontrib-bibtex package.

This will be co-maintained with the Debian Med team.

Bug#800358: ITP: python-sphinxcontrib.bibtex -- allows the use of Bibtex citations in sphinx documentation

[Kevin Murray]

Package: wnpp
Severity: wishlist
Owner: Kevin Murray <s...@kdmurray.id.au>

* Package name: python-sphinxcontrib.bibtex
  Version : 0.3.2
  Upstream Author : Matthias C. M. Troffaes
* URL : 
https://github.com/mcmtroffaes/sphinxcontrib-bibtex/blob/develop/LICENSE.rst
* License : BSD
  Programming Lang: Python
  Description : allows the use of Bibtex citations in sphinx documentation

This sphinx extension allows the use of Bibtex citations in sphinx
documentation. It will be packaged into both py2 and py3 packages. I
will co-maintain this as part of the Debian Med packaging team.

It is required to build the documentation of, e.g., seqan.

Accepted bamtools 2.4.0+dfsg-2 (source amd64) into unstable

[Kevin Murray]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Thu, 24 Sep 2015 17:27:16 +1000
Source: bamtools
Binary: bamtools libbamtools-dev libbamtools2.4.0
Architecture: source amd64
Version: 2.4.0+dfsg-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Kevin Murray <s...@kdmurray.id.au>
Description:
 bamtools   - toolkit for manipulating BAM (genome alignment) files
 libbamtools-dev - C++ API for manipulating BAM (genome alignment) files
 libbamtools2.4.0 - dynamic library for manipulating BAM (genome alignment) 
files
Changes:
 bamtools (2.4.0+dfsg-2) unstable; urgency=medium
 .
   [ Kevin Murray ]
   * Fix re-upload confusion
   * Fix build of doxygen docs, add docs-base
   * Use uscan file renaming to name upstream tarball bamtools-Vxxx.tar.gz
   * Refresh patch queue
 .
   [ Andreas Tille]
   * Fix linitan overides for bamtools
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Bug#799830: ITP: dwgsim -- DWGSIM is an improved short read simulator

[Kevin Murray]

Package: wnpp
Severity: wishlist
Owner: Kevin Murray <s...@kdmurray.id.au>

* Package name: dwgsim
  Version : 0.1.11
  Upstream Author : Nils Homer
* URL : https://github.com/nh13/DWGSIM
* License : GPLv2, MIT/X
  Programming Lang: C
  Description : DWGSIM: an improved short read simulator

DWGSIM is a whole-genome shotgun sequencing read simulator. It simulates
reads from Illuima, SOLiD and Ion Torrent platforms.

This package will be maintained by the Debian Med Packaging Team.

Bug#794088: ITP: axe-demultiplexer -- demultiplexes DNA sequencing reads based upon 5' read barcodes

[Kevin Murray]

Package: wnpp
Severity: wishlist
Owner: Kevin Murray s...@kdmurray.id.au

* Package name: axe-demultiplexer
  Version : 0.2.8
  Upstream Author : Kevin Murray s...@kdmurray.id.au
* URL : https://github.com/kdmurray91/axe
* License : GPL3+
  Programming Lang: C
  Description : Axe demultiplexes DNA sequencing reads based upon 5' read 
barcodes

Axe very rapidly selects the optimal barcode present in a sequence read,
even in the presence of sequencing errors. The algorithm is able to
handle combinatorial barcoding, barcodes of differing length, and
several mismatches per barcode.

As I am the upstream author, I'm not sure what Debian Med policy is
regarding uploader-ship. But I have prepared a Debian package.


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Accepted sphinxcontrib-autoprogram 0.1.1-2 (source all) into unstable, unstable

[Kevin Murray]

-BEGIN PGP SIGNED MESSAGE-
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Format: 1.8
Date: Mon, 13 Jul 2015 00:02:46 +1000
Source: sphinxcontrib-autoprogram
Binary: sphinxcontrib-autoprogram python3-sphinxcontrib.autoprogram
Architecture: source all
Version: 0.1.1-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
debian-med-packag...@lists.alioth.debian.org
Changed-By: Kevin Murray s...@kdmurray.id.au
Description:
 python3-sphinxcontrib.autoprogram - automated documentation of CLI programs 
for Sphinx (Python 3)
 sphinxcontrib-autoprogram - automated documentation of CLI programs for Sphinx 
(Python 2)
Closes: 792188
Changes:
 sphinxcontrib-autoprogram (0.1.1-2) unstable; urgency=medium
 .
   * Add a python3 package, python3-sphinxcontrib.autoprogram. Closes: #792188
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Accepted wgsim 0.3.1-r13-1 (source amd64) into unstable, unstable

[Kevin Murray]

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Format: 1.8
Date: Sat, 04 Jul 2015 10:43:34 +1000
Source: wgsim
Binary: wgsim
Architecture: source amd64
Version: 0.3.1-r13-1
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team 
debian-med-packag...@lists.alioth.debian.org
Changed-By: Kevin Murray s...@kdmurray.id.au
Description:
 wgsim  - simulate sequencing reads from a reference genome
Closes: 791395
Changes:
 wgsim (0.3.1-r13-1) unstable; urgency=low
 .
   * Initial release (Closes: #791395)
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Accepted scythe 0.994-1 (source amd64) into unstable, unstable

[Kevin Murray]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Sun, 25 Jan 2015 11:09:57 +1100
Source: scythe
Binary: scythe
Architecture: source amd64
Version: 0.994-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
debian-med-packag...@lists.alioth.debian.org
Changed-By: Kevin Murray s...@kdmurray.id.au
Description:
 scythe - Bayesian adaptor trimmer for sequencing reads
Closes: 776179
Changes:
 scythe (0.994-1) unstable; urgency=medium
 .
   * Initial release. (Closes: #776179)
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