Accepted ugene 1.24.2+dfsg-1 (source all amd64) into unstable

kag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: ugene - integrated bioinformatics toolkit ugene-data - required data for UGENE - integrated bioinformatics toolkit Changes: ugene (1.24.2+dfsg-1) unstable; urgency=medium . * Team upload. *

Accepted swarm-cluster 2.1.9-1 (source amd64) into unstable

kag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: swarm - robust and fast clustering method for amplicon-based studies Changes: swarm-cluster (2.1.9-1) unstable; urgency=medium . * Team upload. * New upstream version. Ch

Accepted python3-typed-ast 0.5.6-1 (source amd64) into unstable

kag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: python3-typed-ast - AST with PEP 484 type comments support Changes: python3-typed-ast (0.5.6-1) unstable; urgency=medium . * Team upload. * New upstream version. * Drop obsolete d/cop

Accepted mssstest 3.0-5 (source amd64) into unstable

org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: mssstest - Normalisation of disease scores for patients with Multiple Sclero Closes: 836930 Changes: mssstest (3.0-5) unstable; urgency=medium . * Team upload. * Fix building with GCC 6. - Add missi

Accepted arb 6.0.3-2 (source all amd64) into unstable

med-packag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: arb- phylogenetic sequence analysis suite - main program arb-common - phylogenetic sequence analysis suite - common files arb-doc- phylogenetic sequence analysis suite - d

Accepted salmon 0.7.2+ds1-2 (source amd64) into unstable

kag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: salmon - wicked-fast transcript quantification from RNA-seq data Changes: salmon (0.7.2+ds1-2) unstable; urgency=medium . * Team upload. * Fix FTBFS by fixing parallel test runs. * Work towards reproducibili

Accepted picard-tools 2.6.0+dfsg-1 (source all) into unstable

<debian-med-packag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: libpicard-java - Java library to manipulate SAM and BAM files libpicard-java-doc - Documentation for the java picard library picard-tools - Command line tools to manipulate

Accepted biosquid 1.9g+cvs20050121-7 (source amd64) into unstable

kag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: biosquid - utilities for biological sequence analysis biosquid-dev - headers and static library for biological sequence analysis Changes: biosquid (1.9g+cvs20050121-7) unstable; urgency=medium

Accepted hmmer 3.1b2+dfsg-3 (source amd64 all) into unstable

med-packag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: hmmer - profile hidden Markov models for protein sequence analysis hmmer-doc - profile hidden Markov models for protein sequence analysis (docs) hmmer-examples - profile hidden M

Accepted hmmer2 2.3.2-12 (source amd64 all) into unstable

kag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: hmmer2 - profile hidden Markov models for protein sequence analysis hmmer2-doc - profile hidden Markov models for protein sequence analysis (docs) hmmer2-pvm - HMMER programs with PVM (Para

Accepted bowtie 1.1.2-5 (source amd64 all) into unstable

kag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: bowtie - Ultrafast memory-efficient short read aligner bowtie-examples - Examples for bowtie, the ultrafast memory-efficient short read al Changes: bowtie (1.1.2-5) unstable; urgency=medium . *

Accepted iva 1.0.7+ds-1 (source amd64) into unstable

org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: iva- iterative virus sequence assembler Changes: iva (1.0.7+ds-1) unstable; urgency=medium . * Add Vcs-Git. * Update uploader email. * New upstream release. * Drop patches applied by upstream. Ch

Accepted vsearch 2.0.3-2 (source amd64) into unstable

org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: vsearch- tool for processing metagenomic sequences Changes: vsearch (2.0.3-2) unstable; urgency=medium . * Team upload. * Make build reproducible. - Stop overriding compiler flags in configure.ac. Ch

Accepted subread 1.5.1+dfsg-2 (source all amd64) into unstable

kag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: subread- toolkit for processing next-gen sequencing data subread-data - data files for subread package Changes: subread (1.5.1+dfsg-2) unstable; urgency=medium . * Team upload.

Accepted statsprocessor 0.11-3 (source amd64) into unstable

y-t...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: statsprocessor - word generator based on per-position Markov chains Changes: statsprocessor (0.11-3) unstable; urgency=medium . * Migrate package to pkg-security team. Ch

Accepted maskprocessor 0.73-2 (source amd64) into unstable

y-t...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: maskprocessor - high-performance word generator with a per-position configurable Changes: maskprocessor (0.73-2) unstable; urgency=medium . * Migrate package to pkg-security team. Ch

Accepted genometools 1.5.9+ds-3 (source all amd64) into unstable

Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: genometools - versatile genome analysis toolkit genometools-common - shared data files for

Accepted wise 2.4.1-19 (source all amd64) into unstable

kag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: wise - comparison of biopolymers, like DNA and protein sequences wise-data - data files for the wise package wise-doc - documentation for the wise package Changes: wise (2.4.1-19) unstable; ur

Accepted onioncircuits 0.4-3 (source all) into unstable

ain...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: onioncircuits - GTK+ application to display Tor circuits and streams Closes: 836121 Changes: onioncircuits (0.4-3) unstable; urgency=medium . * Do not use dbus-launch to set up dbus environment.

Accepted ariba 2.2.5+ds-1 (source amd64) into unstable

org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: ariba - Antibiotic Resistance Identification By Assembly Changes: ariba (2.2.5+ds-1) unstable; urgency=medium . * New upstream release. * Drop dependency on samtools and bcftools. Ch

Accepted libhat-trie 0.0~git25f9e946-2 (source amd64) into unstable

ian-med-packag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: libhat-trie-dev - Development headers and static libraries for HAT-trie library libhat-trie0 - HAT-trie, an extremely efficient (space and time) modern variant Changes: libhat-trie (0.0~g

Accepted toppred 1.10-4 (source amd64) into unstable

org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: toppred- transmembrane topology prediction Changes: toppred (1.10-4) unstable; urgency=medium . * Team upload. * Make build reproducible. - Remove entries with build directories (which would be gone anyway)

Accepted mash 1.1.1-1 (source amd64 all) into unstable

kag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: libmash-dev - development headers and static library for Mash mash - fast genome and metagenome distance estimation using MinHash mash-doc - documentation for Mash Changes: mash (1.1.1-1) unsta

Accepted rate4site 3.0.0-4 (source amd64) into unstable

kag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: rate4site - detector of conserved amino-acid sites Changes: rate4site (3.0.0-4) unstable; urgency=medium . * Team upload. * Make build reproducible by ensuring -fdebug-prefix-map is set. Thanks to Rei

Accepted hisat2 2.0.4-2 (source amd64) into unstable

org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: hisat2 - graph-based alignment of short nucleotide reads to many genomes Closes: 834862 834864 Changes: hisat2 (2.0.4-2) unstable; urgency=medium . * Team upload. * Fix Vcs-Git. * Fix build on kFreeBSD. Than

Accepted biosquid 1.9g+cvs20050121-6 (source amd64) into unstable

kag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: biosquid - utilities for biological sequence analysis biosquid-dev - headers and static library for biological sequence analysis Changes: biosquid (1.9g+cvs20050121-6) unstable; urgency=medium

Accepted bowtie2 2.2.9-4 (source amd64 all) into unstable

kag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: bowtie2- ultrafast memory-efficient short read aligner bowtie2-examples - Examples for bowtie2 Changes: bowtie2 (2.2.9-4) unstable; urgency=medium . * Team upload. * Make build reproducib

Accepted ariba 2.2.4+ds-1 (source amd64) into unstable

org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: ariba - Antibiotic Resistance Identification By Assembly Changes: ariba (2.2.4+ds-1) unstable; urgency=medium . * New upstream release. * Adjust pymummer dependency to min version 0.8.1. Ch

Accepted python-pymummer 0.8.1-1 (source all) into unstable

kag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: python3-pymummer - Python 3 interface to MUMmer Changes: python-pymummer (0.8.1-1) unstable; urgency=medium . * Team upload. * New upstream release. * Bump Standards-Version. Ch

Accepted rna-star 2.5.2b+dfsg-1 (source amd64) into unstable

kag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: rna-star - ultrafast universal RNA-seq aligner Changes: rna-star (2.5.2b+dfsg-1) unstable; urgency=medium . * New upstream release. * Remove x32 from archs. Checksums-Sha1: 694febb1bbfc11c35672cae8733e

Accepted ariba 2.2.3+ds-1 (source amd64) into unstable

org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: ariba - Antibiotic Resistance Identification By Assembly Changes: ariba (2.2.3+ds-1) unstable; urgency=medium . * New upstream release. Checksums-Sha1: 8f801f944b434d63ab1377b893a82fa643550047 2205 ariba_2.

Accepted libssw 1.1-1 (source amd64) into unstable

med-packag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: libssw-dev - Development headers and static libraries for libssw libssw-java - Java bindings for libssw libssw0- fast SIMD parallelized implementation of the Smith-Waterman algor ssw-al

Accepted ariba 2.2.2+ds-1 (source amd64) into unstable

org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: ariba - Antibiotic Resistance Identification By Assembly Changes: ariba (2.2.2+ds-1) unstable; urgency=medium . * New upstream release. Checksums-Sha1: dc8b9efe012e6a110ef038d36784fa1e7f2d46af 2205 ariba_2.

Bug#834940: ITP: lambda-align -- Local Aligner for Massive Biological DatA

Package: wnpp Severity: wishlist Owner: Sascha Steinbiss <sa...@debian.org> * Package name: lambda-align Version : 1.0.0 Upstream Author : Hannes Hauswedell <hannes.hauswed...@fu-berlin.de> * URL : https://seqan.github.io/lambda * License : GPL

Accepted dindel 1.01+dfsg-4 (source amd64) into unstable

kag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: dindel - determines indel calls from short-read data Closes: 833958 Changes: dindel (1.01+dfsg-4) unstable; urgency=medium . * Team upload. * Make code compatible with latest Boost version (1.61 and up).

Accepted ariba 2.2.1+ds-1 (source amd64) into unstable

org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: ariba - Antibiotic Resistance Identification By Assembly Changes: ariba (2.2.1+ds-1) unstable; urgency=medium . * New upstream release. Checksums-Sha1: c7003df4b9525d1ab73a15dcbe4c1673516475b8 2205 ariba_2.

Accepted ariba 2.2.0+ds-1 (source amd64) into unstable

org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: ariba - Antibiotic Resistance Identification By Assembly Changes: ariba (2.2.0+ds-1) unstable; urgency=medium . * New upstream release. Checksums-Sha1: 7120067210f6e42f3f5883dfdde16cc9bf77ffe8 2205 ariba_2.

Accepted metastudent-data 2.0.1-1 (source all) into unstable

kag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: metastudent-data - predictor of Gene Ontology terms from protein sequence - data fil Changes: metastudent-data (2.0.1-1) unstable; urgency=medium . * Team upload. . [ Tobias Hamp ] * New upst

Accepted statsprocessor 0.11-2 (source amd64) into unstable

-BEGIN PGP SIGNED MESSAGE- Hash: SHA512 Format: 1.8 Date: Tue, 16 Aug 2016 18:25:36 + Source: statsprocessor Binary: statsprocessor Architecture: source amd64 Version: 0.11-2 Distribution: unstable Urgency: medium Maintainer: Sascha Steinbiss <sa...@debian.org> Changed-By:

Accepted statsprocessor 0.11-1 (source amd64) into unstable, unstable

-BEGIN PGP SIGNED MESSAGE- Hash: SHA512 Format: 1.8 Date: Tue, 16 Aug 2016 05:35:40 + Source: statsprocessor Binary: statsprocessor Architecture: source amd64 Version: 0.11-1 Distribution: unstable Urgency: low Maintainer: Sascha Steinbiss <sa...@debian.org> Changed-By:

Bug#834438: ITP: princeprocessor -- standalone password candidate generator using the PRINCE algorithm

Package: wnpp Severity: wishlist Owner: Sascha Steinbiss <sa...@debian.org> * Package name: princeprocessor Version : 0.21 Upstream Author : Jens Steube <jens.ste...@gmail.com> * URL : https://github.com/hashcat/princeprocessor * License : MIT

Bug#834435: ITP: statsprocessor -- word generator based on per-position Markov chains

Package: wnpp Severity: wishlist Owner: Sascha Steinbiss <sa...@debian.org> * Package name: statsprocessor Version : 0.11 Upstream Author : Jens Steube <jens.ste...@gmail.com> * URL : https://github.com/hashcat/statsprocessor * License : MIT Prog

Accepted sspace 2.1.1+dfsg-2 (source all) into unstable

kag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: sspace - scaffolding pre-assembled contigs after extension Changes: sspace (2.1.1+dfsg-2) unstable; urgency=medium . * Update uploader email address. * Add build time tests. * Add bowtie to B-D. Ch

Accepted roary 3.6.8+dfsg-2 (source all) into unstable

org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: roary - high speed stand alone pan genome pipeline Changes: roary (3.6.8+dfsg-2) unstable; urgency=medium . * d/tests/control: Add 'allow-stderr' restriction. libfile-slurper-perl update to 0.009-1 introduced a

Accepted ncbi-tools6 6.1.20120620-11 (source amd64 all) into unstable

all Version: 6.1.20120620-11 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: blast2 - Basic Local Alignment Search Tool libncbi6 - NC

Accepted fastaq 3.13.0-1 (source all) into unstable

org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: fastaq - FASTA and FASTQ file manipulation tools Changes: fastaq (3.13.0-1) unstable; urgency=medium . * Update maintainer email. * New upstream version. * Bump Standards-Version. * Fix spelling. Ch

Accepted miniasm 0.2+dfsg-2 (source amd64) into unstable

kag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: miniasm- ultrafast de novo assembler for long noisy DNA sequencing reads Changes: miniasm (0.2+dfsg-2) unstable; urgency=medium . * Change maintainer email. * Add EDAM annotations. * Bump Standards-Versi

Accepted nanopolish 0.4.0-3 (source amd64) into unstable

kag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: nanopolish - consensus caller for nanopore sequencing data Changes: nanopolish (0.4.0-3) unstable; urgency=medium . * Team upload. * Make build reproducible. Checksums-Sha1: 93829bcc8455401e10c281d746e2e40a9

Accepted maskprocessor 0.73-1 (source amd64) into unstable, unstable

-BEGIN PGP SIGNED MESSAGE- Hash: SHA512 Format: 1.8 Date: Thu, 04 Aug 2016 19:36:54 + Source: maskprocessor Binary: maskprocessor Architecture: source amd64 Version: 0.73-1 Distribution: unstable Urgency: low Maintainer: Sascha Steinbiss <sa...@debian.org> Changed-By: Sascha Ste

Accepted dindel 1.01+dfsg-3 (source amd64) into unstable

kag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: dindel - determines indel calls from short-read data Changes: dindel (1.01+dfsg-3) unstable; urgency=medium . * Team upload. * Force use of Boost 1.58 to fix FTBFS with newer Boost versions. * Bump Stand

Accepted infernal 1.1.2-1 (source amd64 all) into unstable

kag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: infernal - inference of RNA secondary structural alignments infernal-doc - inference of RNA secondary structural alignments – documentation Changes: infernal (1.1.2-1) unstable; urgency=medium . *

Accepted nanopolish 0.4.0-2 (source amd64) into unstable

kag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: nanopolish - consensus caller for nanopore sequencing data Closes: 831151 Changes: nanopolish (0.4.0-2) unstable; urgency=medium . * Team upload. * Fix FTBFS with GCC 6 (Closes: #831151) * Enable fu

Accepted trinityrnaseq 2.2.0+dfsg-2 (source amd64 all) into unstable

<debian-med-packag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: trinityrnaseq - RNA-Seq De novo Assembly trinityrnaseq-examples - RNA-Seq De novo Assembly common example and testing files Closes: 831110 Changes: trinityrnaseq (2.2.0+dfsg

Bug#833473: ITP: maskprocessor -- high-performance word generator with a per-position configurable charset

Package: wnpp Severity: wishlist Owner: Sascha Steinbiss <sa...@debian.org> * Package name: maskprocessor Version : 0.73 Upstream Author : Jens Steube <jens.ste...@gmail.com> * URL : https://github.com/hashcat/maskprocessor * License : MIT Program

Accepted ariba 2.1.0+ds-1 (source amd64) into unstable

org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: ariba - Antibiotic Resistance Identification By Assembly Changes: ariba (2.1.0+ds-1) unstable; urgency=medium . * New upstream release. * Adjust dependencies to new upstream requirements. * Drop pat

Accepted fermi-lite 0.1-2 (source amd64) into unstable

kag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: fml-asm- tool for assembling Illumina short reads in small regions libfml-dev - development headers for libfml libfml0- library for assembling Illumina short reads in small regions Changes: fer

Accepted fermi-lite 0.1-1 (source amd64) into unstable, unstable

kag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: fml-asm- tool for assembling Illumina short reads in small regions libfml-dev - development headers for libfml libfml0- library for assembling Illumina short reads in small regions Closes: 83

Accepted vsearch 2.0.3-1 (source amd64) into unstable

org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: vsearch- tool for processing metagenomic sequences Closes: 831131 Changes: vsearch (2.0.3-1) unstable; urgency=medium . * Team upload. . [ Andreas Tille ] * New upstream version (builds with GCC6, clo

Accepted dindel 1.01+dfsg-2 (source amd64) into unstable

kag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: dindel - determines indel calls from short-read data Closes: 831208 Changes: dindel (1.01+dfsg-2) unstable; urgency=medium . * Team upload. * Fix FTBFS with GCC 6. Closes: #831208 Ch

Accepted prime-phylo 1.0.11-4 (source amd64) into unstable

kag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: prime-phylo - bayesian estimation of gene trees taking the species tree into ac Closes: 84 Changes: prime-phylo (1.0.11-4) unstable; urgency=medium . * Team upload. * fix FTBFS with Boost 1.60 (Clo

Accepted roary 3.6.8+dfsg-1 (source all) into unstable

org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: roary - high speed stand alone pan genome pipeline Changes: roary (3.6.8+dfsg-1) unstable; urgency=medium . * New upstream release. Checksums-Sha1: 792f9e0691d3c2bc8a7f9fbfbba9398310792916 2467 roary_3.6.

Accepted python-dendropy 4.1.0+dfsg-1 (source all) into unstable

<debian-med-packag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: python-dendropy - DendroPy Phylogenetic Computing Library (Python 2) python3-dendropy - DendroPy Phylogenetic Computing Library (Python 3) sumtrees - Phylogenetic Tree S

Accepted minimap 0.2-3 (source amd64) into unstable

kag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: libminimap-dev - development headers for libminimap libminimap0 - library for approximate mapping of long biosequences minimap- tool for approximate mapping of long biosequences such as DNA

Bug#832757: ITP: fermi-lite -- standalone C library for assembling Illumina short reads in small regions

Package: wnpp Severity: wishlist Owner: Sascha Steinbiss <sa...@debian.org> * Package name: fermi-lite Version : 0.1 Upstream Author : Heng Li <l...@me.com> * URL : https://github.com/lh3/fermi-lite * License : MIT Programming Lang: C

Accepted ugene 1.23.1+dfsg-1 (source all amd64) into unstable

kag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: ugene - integrated bioinformatics toolkit ugene-data - required data for UGENE - integrated bioinformatics toolkit Closes: 831326 831374 Changes: ugene (1.23.1+dfsg-1) unstable; urgency=medium . *

Accepted roary 3.6.6+dfsg-1 (source all) into unstable

org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: roary - high speed stand alone pan genome pipeline Changes: roary (3.6.6+dfsg-1) unstable; urgency=medium . * New upstream release. Checksums-Sha1: 5d619836eccb0b5f871c4cbe5fcd02e257908c22 2467 roary_3.6.

Accepted prime-phylo 1.0.11-3 (source amd64) into unstable

kag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: prime-phylo - bayesian estimation of gene trees taking the species tree into ac Closes: 812031 Changes: prime-phylo (1.0.11-3) unstable; urgency=medium . * Team upload. * Fix building with GCC 6 (Clo

Accepted spades 3.9.0+dfsg-1 (source amd64) into unstable

kag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: spades - genome assembler for single-cell and isolates data sets Changes: spades (3.9.0+dfsg-1) unstable; urgency=medium . * New upstream release. * Add copyright entry for cxxopts. * Add rnaSPAdes manpa

Accepted genometools 1.5.9+ds-2 (source all amd64) into unstable

Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: genometools - versatile genome analysis toolkit genometools-common - shared data files for

Accepted swarm-cluster 2.1.8-2 (source amd64) into unstable

kag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: swarm - robust and fast clustering method for amplicon-based studies Closes: 811893 Changes: swarm-cluster (2.1.8-2) unstable; urgency=medium . * Team upload. * Fix building with GCC 6. Closes: #811893

Accepted genometools 1.5.9+ds-1 (source all amd64) into unstable

Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: genometools - versatile genome analysis toolkit genometools-common - shared data files for

Accepted roary 3.6.5+dfsg-1 (source all) into unstable

org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: roary - high speed stand alone pan genome pipeline Changes: roary (3.6.5+dfsg-1) unstable; urgency=medium . * New upstream release. Checksums-Sha1: 68494ea719fa1d9efa2899456c58c015dc62fdbd 2467 roary_3.6.

Accepted mash 1.1-3 (source amd64 all) into unstable

kag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: libmash-dev - development headers and static library for Mash mash - fast genome and metagenome distance estimation using MinHash mash-doc - documentation for Mash Closes: 832068 Changes:

Accepted subread 1.5.0-p3+dfsg-3 (source all amd64) into unstable

kag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: subread- toolkit for processing next-gen sequencing data subread-data - data files for subread package Changes: subread (1.5.0-p3+dfsg-3) unstable; urgency=medium . * Team upload. * Fur

Accepted mash 1.1-2 (source amd64 all) into unstable

kag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: libmash-dev - development headers and static library for Mash mash - fast genome and metagenome distance estimation using MinHash mash-doc - documentation for Mash Changes: mash (1.1-2) unsta

Accepted mash 1.1-1 (source amd64 all) into unstable, unstable

kag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: libmash-dev - development headers and static library for Mash mash - fast genome and metagenome distance estimation using MinHash mash-doc - documentation for Mash Closes: 831781 Changes:

Accepted gubbins 2.0.0-1 (source amd64) into unstable

org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: gubbins- phylogenetic analysis of genome sequences Changes: gubbins (2.0.0-1) unstable; urgency=medium . * Team upload. * New upstream release. * Fix Vcs-Git. * Remove dependencies on FastML. * Update m

Accepted spades 3.8.2+dfsg2-1 (source amd64) into unstable

kag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: spades - genome assembler for single-cell and isolates data sets Changes: spades (3.8.2+dfsg2-1) unstable; urgency=medium . * Make sure bundled headers are not used by cleaning orig tarball. Ch

Bug#831781: ITP: mash -- fast genome and metagenome distance estimation using MinHash

Package: wnpp Severity: wishlist Owner: Sascha Steinbiss <sa...@debian.org> * Package name: mash Version : 1.1 Upstream Author : Brian Ondov, Todd Treangen, Sergey Koren, and Adam Phillippy <adam.philli...@nih.gov> * URL : https://mash.readthedocs.

Accepted subread 1.5.0-p3+dfsg-2 (source all amd64) into unstable

kag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: subread- toolkit for processing next-gen sequencing data subread-data - data files for subread package Changes: subread (1.5.0-p3+dfsg-2) unstable; urgency=medium . * Team upload.

Accepted snap 2013-11-29-3 (source amd64) into unstable

org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: snap - location of genes from DNA sequence with hidden markov model Closes: 831165 Changes: snap (2013-11-29-3) unstable; urgency=medium . * Team upload. * add CPPFLAGS for full hardening. * Fix buildin

Accepted dnaclust 3-4 (source amd64) into unstable

org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: dnaclust - tool for clustering millions of short DNA sequences Closes: 831193 Changes: dnaclust (3-4) unstable; urgency=medium . * Team upload. * Enable full hardening. * Use secure Vcs-Git. * Bump Stand

Accepted bowtie2 2.2.9-3 (source amd64 all) into unstable

kag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: bowtie2- ultrafast memory-efficient short read aligner bowtie2-examples - Examples for bowtie2 Closes: 831157 Changes: bowtie2 (2.2.9-3) unstable; urgency=medium . * Team upload. * Fix build

Accepted reapr 1.0.18+dfsg-3 (source amd64) into unstable

kag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: reapr - universal tool for genome assembly evaluation Changes: reapr (1.0.18+dfsg-3) unstable; urgency=medium . * Rearrange linking order to fix FTBFS with ld --as-needed (Thanks to Logan Rosen for the patch

Accepted spades 3.8.2+dfsg-1 (source amd64) into unstable

kag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: spades - genome assembler for single-cell and isolates data sets Changes: spades (3.8.2+dfsg-1) unstable; urgency=medium . * New upstream release. * Adapt patches for new upstream code. * Remove unu

Accepted roary 3.6.4+dfsg-1 (source all) into unstable

org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: roary - high speed stand alone pan genome pipeline Changes: roary (3.6.4+dfsg-1) unstable; urgency=medium . * New upstream release. Checksums-Sha1: 6b54a27521fbc3f185a630f02cac94ff6c57d4c9 2467 roary_3.6.

Accepted aragorn 1.2.37-1 (source amd64) into unstable

kag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: aragorn- tRNA and tmRNA detection in nucleotide sequences Changes: aragorn (1.2.37-1) unstable; urgency=medium . * New upstream release. * Drop patch applied by upstream. * Update uploader email. * Bu

Accepted spades 3.8.1+dfsg-2 (source amd64) into unstable

kag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: spades - genome assembler for single-cell and isolates data sets Changes: spades (3.8.1+dfsg-2) unstable; urgency=medium . * Stop using embedded libnlopt, libssw and libhat-trie. * Update email addresses. Ch

Accepted genometools 1.5.8+ds-4 (source all amd64) into unstable

Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: genometools - versatile genome analysis toolkit genometools-common - shared data files for

Accepted roary 3.6.3+dfsg-1 (source all) into unstable

org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: roary - high speed stand alone pan genome pipeline Changes: roary (3.6.3+dfsg-1) unstable; urgency=medium . * New upstream release. * Update uploader email address. Checksums-Sha1: 7d3352feba11cbe821f11ac84a51

Accepted ariba 1.0.1-1 (source all) into unstable

org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: ariba - Antibiotic Resistance Identification By Assembly Changes: ariba (1.0.1-1) unstable; urgency=medium . * New upstream release. * Update uploader email. Checksums-Sha1: da19c2f32fd62851ceb01f14ddaa771ac

Accepted libssw 1.0-2 (source amd64) into unstable

med-packag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: libssw-dev - Development headers and static libraries for libssw libssw-java - Java bindings for libssw libssw0- fast SIMD parallelized implementation of the Smith-Waterman algor ssw-al

Accepted libssw 1.0-1 (source amd64) into unstable, unstable

med-packag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: libssw-dev - Development headers and static libraries for libssw libssw-java - Java bindings for libssw libssw0- fast SIMD parallelized implementation of the Smith-Waterman algor ssw-al

Accepted hmmer2 2.3.2-11 (source amd64 all) into unstable

kag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: hmmer2 - profile hidden Markov models for protein sequence analysis hmmer2-doc - profile hidden Markov models for protein sequence analysis (docs) hmmer2-pvm - HMMER programs with PVM (Para

Accepted libhat-trie 0.0~git25f9e946-1 (source amd64) into unstable, unstable

ian-med-packag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: libhat-trie-dev - Development headers and static libraries for HAT-trie library libhat-trie0 - HAT-trie, an extremely efficient (space and time) modern variant Closes: 827937 Changes:

Bug#828042: ITP: libssw -- fast SIMD parallelized implementation of the Smith-Waterman algorithm

Package: wnpp Severity: wishlist Owner: Sascha Steinbiss <sa...@debian.org> * Package name: libssw Version : git20160511.7d84de2 Upstream Author : Mengyao Zhao <zhaomeng...@gmail.com> * URL : https://github.com/mengyao/Complete-Striped-Smith-Waterman-Libra

Bug#827937: ITP: libhat-trie -- HAT-trie, an extremely efficient (space and time) modern variant of tries

Package: wnpp Severity: wishlist Owner: Sascha Steinbiss <sa...@debian.org> * Package name: libhat-trie Version : 0.0~git25f9e946 Upstream Author : Daniel C. Jones <dcjo...@cs.washington.edu> * URL : https://github.com/dcjones/hat-trie * License

Accepted mussort 0.4-2 (source all) into unstable

-BEGIN PGP SIGNED MESSAGE- Hash: SHA512 Format: 1.8 Date: Wed, 22 Jun 2016 09:25:05 + Source: mussort Binary: mussort Architecture: source all Version: 0.4-2 Distribution: unstable Urgency: medium Maintainer: Sascha Steinbiss <sa...@debian.org> Changed-By: Sascha Steinbi

Accepted onioncircuits 0.4-2 (source all) into unstable

ain...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: onioncircuits - GTK+ application to display Tor circuits and streams Closes: 827805 Changes: onioncircuits (0.4-2) unstable; urgency=medium . * use https for d/copyright's Format entry * simplify d

Accepted spades 3.8.1+dfsg-1 (source amd64) into unstable

kag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sas...@steinbiss.name> Description: spades - genome assembler for single-cell and isolates data sets Changes: spades (3.8.1+dfsg-1) unstable; urgency=medium . * New upstream release. Checksums-Sha1: 606eae76c4db029e23c9fcaa25d481928

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