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

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:

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

Accepted python-ruffus 2.6.3+dfsg-3 (source all) into unstable

Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sas...@steinbiss.name> Description: python-ruffus - Python computation pipeline library widely used in bioinformatics python-ruffus-doc - documentation for python-ruffus computation pipeline library py

Accepted sspace 2.1.1+dfsg-1 (source all) into unstable, unstable

org> Changed-By: Sascha Steinbiss <sas...@steinbiss.name> Description: sspace - scaffolding pre-assembled contigs after extension Closes: 826682 Changes: sspace (2.1.1+dfsg-1) unstable; urgency=low . [ Andreas Tille and Sascha Steinbiss ] * Initial release (Closes: #826682) Ch

Accepted spades 3.8.0+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 (3.8.0+dfsg-1) unstable; urgency=medium . * New upstream release. * Drop patches that are no longer necessary. * Upd

Accepted python-csb 1.2.3+dfsg-3 (source all) into unstable

ian-med-packag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sas...@steinbiss.name> Description: python-csb - Python framework for structural bioinformatics python-csb-doc - Python framework for structural bioinformatics (documentation) python3-csb - Python framework fo

Accepted rdp-readseq 2.0.2-2 (source all) into unstable

kag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sas...@steinbiss.name> Description: rdp-readseq - Ribosomal Database Project (RDP) sequence reading and writing Changes: rdp-readseq (2.0.2-2) unstable; urgency=medium . * Team upload. * Make build reproducible. - Force UTF-8 encoding

Accepted python-cobra 0.4.1-2 (source all amd64) into unstable

<debian-med-packag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sas...@steinbiss.name> Description: python-cobra - constraint-based modeling of biological networks (Python 2) python-cobra-data - constraint-based modeling of biological networks (data) python3-cobra - cons

Accepted ariba 1.0.0-1 (source all) into unstable, unstable

hanged-By: Sascha Steinbiss <sas...@steinbiss.name> Description: ariba - Antibiotic Resistance Identification By Assembly Closes: 825529 Changes: ariba (1.0.0-1) unstable; urgency=low . * Initial packaging (Closes: #825529) Checksums-Sha1: 959e982de5a2060bab1309122b42a7d87

Accepted plast 2.3.1+dfsg-4 (source amd64 all) into unstable

kag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sas...@steinbiss.name> Description: plast - Parallel Local Sequence Alignment Search Tool plast-example - Parallel Local Sequence Alignment Search Tool (example data) Changes: plast (2.3.1+dfsg-4) unstable; urgency=medium . *

Accepted soapdenovo2 240+dfsg-3 (source amd64) into unstable

kag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sas...@steinbiss.name> Description: soapdenovo2 - short-read assembly method to build de novo draft assembly Changes: soapdenovo2 (240+dfsg-3) unstable; urgency=medium . [ Sascha Steinbiss ] * Team upload. * Migrate package to Gi

Accepted cain 1.10+dfsg-2 (source all amd64) into unstable

med-packag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sas...@steinbiss.name> Description: cain - simulations of chemical reactions cain-examples - examples for cain cain-solvers - solvers for cain Changes: cain (1.10+dfsg-2) unstable; urgency=medium . * Team uplo

Accepted bowtie 1.1.2-4 (source) into unstable

kag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sas...@steinbiss.name> Description: bowtie - Ultrafast memory-efficient short read aligner bowtie-examples - Examples for bowtie, the ultrafast memory-efficient short read al Changes: bowtie (1.1.2-4) unstable; urgency=medium . *

Accepted toppred 1.10-3 (source) into unstable

org> Changed-By: Sascha Steinbiss <sas...@steinbiss.name> Description: toppred- transmembrane topology prediction Changes: toppred (1.10-3) unstable; urgency=medium . * Team upload. * Make build reproducible. - Fix $SHELL/CONFIG_SHELL to /bin/sh. Ch

Accepted rna-star 2.5.2a+dfsg-3 (source amd64) into unstable

kag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sas...@steinbiss.name> Description: rna-star - ultrafast universal RNA-seq aligner Changes: rna-star (2.5.2a+dfsg-3) unstable; urgency=medium . * Limit architectures to amd64 as supported by upstream. * Add myself to Uploaders.

Accepted smalt 0.7.6-6 (source amd64 all) into unstable

kag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sas...@steinbiss.name> Description: smalt - Sequence Mapping and Alignment Tool smalt-examples - Sequence Mapping and Alignment Tool (examples) Changes: smalt (0.7.6-6) unstable; urgency=medium . * Team upload. * Remove M

Accepted smalt 0.7.6-5 (source amd64 all) into unstable

kag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sas...@steinbiss.name> Description: smalt - Sequence Mapping and Alignment Tool smalt-examples - Sequence Mapping and Alignment Tool (examples) Changes: smalt (0.7.6-5) unstable; urgency=medium . * Team upload. * Make build

Accepted rna-star 2.5.2a+dfsg-2 (source amd64) into unstable

kag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sas...@steinbiss.name> Description: rna-star - ultrafast universal RNA-seq aligner Changes: rna-star (2.5.2a+dfsg-2) unstable; urgency=medium . * Team upload. * Make build reproducible. - Stop recording build environment in binary.

Accepted bowtie2 2.2.9-2 (source amd64 all) into unstable

kag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sas...@steinbiss.name> Description: bowtie2- ultrafast memory-efficient short read aligner bowtie2-examples - Examples for bowtie2 Changes: bowtie2 (2.2.9-2) unstable; urgency=medium . * Team upload. * Make build

Accepted datatables.js 1.10.12+dfsg-1 (source all) into unstable

pkg-javascript-de...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sas...@steinbiss.name> Description: libjs-jquery-datatables - jQuery plug-in that makes nice tables from different data sources Changes: datatables.js (1.10.12+dfsg-1) unstable; urgency=medium . * New upstream releas

Accepted wise 2.4.1-18 (source) into unstable

kag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sas...@steinbiss.name> 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 (2.4.1-18) unstable; ur

Accepted t-coffee 11.00.8cbe486-3 (source) into unstable

kag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sas...@steinbiss.name> Description: t-coffee - Multiple Sequence Alignment t-coffee-examples - annotated examples for the use of T-Coffee Changes: t-coffee (11.00.8cbe486-3) unstable; urgency=medium . * Team upload. *

Accepted ray 2.3.1-4 (source amd64 all) into unstable

kag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sas...@steinbiss.name> Description: ray- de novo genome assemblies of next-gen sequencing data ray-doc- focumentation for ray parallel de novo genome assembler ray-extra - Scripts and XSL sheets for post-processing for ray C

Accepted onioncircuits 0.4-1 (source) into unstable

ain...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sas...@steinbiss.name> Closes: 817086 Description: onioncircuits - GTK+ application to display Tor circuits and streams Changes: onioncircuits (0.4-1) unstable; urgency=medium . * New upstream release. Closes: #817086 *

Accepted snp-sites 2.3.2-1 (source amd64) into unstable

ian-med-packag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sas...@steinbiss.name> Description: libsnp-sites1 - Shared libraries of the package snp-sites libsnp-sites1-dev - Static libraries and header files for the package snp-sites snp-sites - Binary code for the packa

Accepted icdiff 1.8.1-1 (source all) into unstable, unstable

-BEGIN PGP SIGNED MESSAGE- Hash: SHA512 Format: 1.8 Date: Tue, 03 May 2016 05:35:18 + Source: icdiff Binary: icdiff Architecture: source all Version: 1.8.1-1 Distribution: unstable Urgency: low Maintainer: Sascha Steinbiss <sas...@steinbiss.name> Changed-By: Sascha Steinbis

Accepted tophat 2.1.1+dfsg-2 (source) into unstable

org> Changed-By: Sascha Steinbiss <sas...@steinbiss.name> Description: tophat - fast splice junction mapper for RNA-Seq reads Closes: 811881 Changes: tophat (2.1.1+dfsg-2) unstable; urgency=medium . [ Sascha Steinbiss ] * Team upload. * Fix building with GCC 6. Clo

Accepted parsinsert 1.04-2 (source amd64) into unstable

kag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sas...@steinbiss.name> Description: parsinsert - Parsimonious Insertion of unclassified sequences into phylogeneti Closes: 811909 Changes: parsinsert (1.04-2) unstable; urgency=medium . * Team upload. * Fix building with GCC 6. Clo

Accepted prank 0.0.150803-2 (source amd64) into unstable

kag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sas...@steinbiss.name> Description: prank - Probabilistic Alignment Kit for DNA, codon and amino-acid sequenc Closes: 811827 Changes: prank (0.0.150803-2) unstable; urgency=medium . * Team upload. . [ Andreas Tille ] * New homepage

Accepted iva 1.0.6+ds-1 (source amd64) into unstable

org> Changed-By: Sascha Steinbiss <sas...@steinbiss.name> Description: iva- iterative virus sequence assembler Changes: iva (1.0.6+ds-1) unstable; urgency=medium . * New upstream release. * Change orig tarball compression. * Add missing repack suffix to package. Ch

Accepted roary 3.6.2+dfsg-1 (source all) into unstable

org> Changed-By: Sascha Steinbiss <sas...@steinbiss.name> Description: roary - high speed stand alone pan genome pipeline Changes: roary (3.6.2+dfsg-1) unstable; urgency=medium . * New upstream release. * Drop patches applied by upstream. Ch

Accepted iva 1.0.5-1 (source amd64) into unstable, unstable

hanged-By: Sascha Steinbiss <sas...@steinbiss.name> Description: iva- iterative virus sequence assembler Closes: 772547 Changes: iva (1.0.5-1) unstable; urgency=low . * Initial release (Closes: #772547) Checksums-Sha1: 26e0c01d1d5c68fa97542a8ef55c3b507f06bc6c 2098 iva

Accepted datatables.js 1.10.11+dfsg-3 (source all) into unstable

pkg-javascript-de...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sas...@steinbiss.name> Description: libjs-jquery-datatables - jQuery plug-in that makes nice tables from different data sources Changes: datatables.js (1.10.11+dfsg-3) unstable; urgency=medium . * Remove Buil

Accepted roary 3.6.1+dfsg-2 (source all) into unstable

org> Changed-By: Sascha Steinbiss <sas...@steinbiss.name> Description: roary - high speed stand alone pan genome pipeline Changes: roary (3.6.1+dfsg-2) unstable; urgency=medium . * Use correct argument format for easy_init to get rid of warning message. * Bump Standards-Versio

Accepted genometools 1.5.8+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 <sas...@steinbiss.name> Description: genometools - versatile genome analysis toolkit genometools-common - shared data files for

Accepted kmc 2.3+dfsg-5 (source amd64) into unstable

kag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sas...@steinbiss.name> Description: kmc- count kmers in genomic sequences libkmc-dev - library to access KMC k-mer count files Closes: 822390 Changes: kmc (2.3+dfsg-5) unstable; urgency=medium . * Add missing include to header,

Accepted ltrsift 1.0.2-7 (source amd64 all) into unstable

med-packag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sas...@steinbiss.name> Description: ltrsift- postprocessing and classification of LTR retrotransposons ltrsift-dbg - postprocessing and classification of LTR retrotransposons, with d ltrsift-examples - example data

Accepted spades 3.7.1+dfsg-3 (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 (3.7.1+dfsg-3) unstable; urgency=medium . * Force LANG and LANGUAGE to ensure reproducibility. * Enable compiler message

Accepted ltrsift 1.0.2-6 (source amd64 all) into unstable

med-packag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sas...@steinbiss.name> Description: ltrsift- postprocessing and classification of LTR retrotransposons ltrsift-dbg - postprocessing and classification of LTR retrotransposons, with d ltrsift-examples - example data

Accepted roary 3.6.1+dfsg-1 (source all) into unstable

org> Changed-By: Sascha Steinbiss <sas...@steinbiss.name> Description: roary - high speed stand alone pan genome pipeline Changes: roary (3.6.1+dfsg-1) unstable; urgency=medium . * New upstream release. Checksums-Sha1: d70100b12156d22dfa57722a9a51bc374406ab46 2472 roary_3.6.

Accepted fastaq 3.12.1-1 (source all) into unstable

org> Changed-By: Sascha Steinbiss <sas...@steinbiss.name> Description: fastaq - FASTA and FASTQ file manipulation tools Changes: fastaq (3.12.1-1) unstable; urgency=medium . * New upstream version. * Add new dependency on python3-pkg-resources. Ch

Accepted fastaq 3.12.0-1 (source all) into unstable

org> Changed-By: Sascha Steinbiss <sas...@steinbiss.name> Description: fastaq - FASTA and FASTQ file manipulation tools Changes: fastaq (3.12.0-1) unstable; urgency=medium . * New upstream version. * Bump Standards-Version. Checksums-Sha1: 3f12a9a74b5bcc862ae909628e1b058d0

Accepted augustus 3.2.2+dfsg-1 (source all amd64) into unstable, unstable

ian-med-packag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sas...@steinbiss.name> Description: augustus - gene prediction in eukaryotic genomes augustus-data - data files for AUGUSTUS augustus-doc - documentation files for AUGUSTUS Closes: 819355 Changes: augustus (

Accepted proda 1.0-10 (source amd64) into unstable

org> Changed-By: Sascha Steinbiss <sas...@steinbiss.name> Description: proda - multiple alignment of protein sequences Closes: 812039 Changes: proda (1.0-10) unstable; urgency=medium . * Team upload. * Fix FTBFS with GCC-6. Closes: #812039. * Bump Standards-Version. * Us

Accepted ray 2.3.1-3 (source amd64 all) into unstable

kag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sas...@steinbiss.name> Description: ray- de novo genome assemblies of next-gen sequencing data ray-doc- focumentation for ray parallel de novo genome assembler ray-extra - Scripts and XSL sheets for post-processing for ray Cl

Accepted roary 3.6.0+dfsg-4 (source all) into unstable

org> Changed-By: Sascha Steinbiss <sas...@steinbiss.name> Description: roary - high speed stand alone pan genome pipeline Changes: roary (3.6.0+dfsg-4) unstable; urgency=medium . * Remove patch for PRANK. * Disable tests due to nondeterminism until upstream has fixed the issu

Accepted datatables.js 1.10.11+dfsg-2 (source all) into unstable

kag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sas...@steinbiss.name> Description: libjs-jquery-datatables - jQuery plug-in that makes nice tables from different data sources Changes: datatables.js (1.10.11+dfsg-2) unstable; urgency=medium . * Update to PHP7.0 build-

Accepted salmon 0.4.2+ds1-3 (source amd64) into unstable

kag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sas...@steinbiss.name> Description: salmon - wicked-fast transcript quantification from RNA-seq data Closes: 818397 Changes: salmon (0.4.2+ds1-3) unstable; urgency=medium . [ Sascha Steinbiss ] * Team upload. * Re-intro

Accepted roary 3.6.0+dfsg-3 (source all) into unstable

org> Changed-By: Sascha Steinbiss <sas...@steinbiss.name> Description: roary - high speed stand alone pan genome pipeline Changes: roary (3.6.0+dfsg-3) unstable; urgency=medium . * Attempt to fix FTBFS in reproducibility tests by choosing a fixed random seed for PRANK. Ch

Accepted kmc 2.3+dfsg-4 (source amd64) into unstable

kag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sas...@steinbiss.name> Description: kmc- count kmers in genomic sequences libkmc-dev - library to access KMC k-mer count files Changes: kmc (2.3+dfsg-4) unstable; urgency=low . * Move LDFLAGS to end of linker call. Thanks to St

Accepted aegean 0.15.2+dfsg-1 (source amd64) into unstable

kag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sas...@steinbiss.name> Description: aegean - integrated genome analysis toolkit aegean-dbg - integrated genome analysis toolkit, with debug symbols Changes: aegean (0.15.2+dfsg-1) unstable; urgency=medium . * New upstream versio

Accepted spades 3.7.1+dfsg-2 (source) into unstable

org> Changed-By: Sascha Steinbiss <sas...@steinbiss.name> Description: spades - genome assembler for single-cell and isolates data sets Closes: 818584 Changes: spades (3.7.1+dfsg-2) unstable; urgency=medium . [ Sascha Steinbiss ] * Use asciidoctor instead of ronn for reproducib

Accepted mussort 0.4-1 (source all) into unstable

-BEGIN PGP SIGNED MESSAGE- Hash: SHA512 Format: 1.8 Date: Sat, 19 Mar 2016 22:20:03 + Source: mussort Binary: mussort Architecture: source all Version: 0.4-1 Distribution: unstable Urgency: medium Maintainer: Sascha Steinbiss <sas...@steinbiss.name> Changed-By: Sascha Steinbis

Accepted snp-sites 2.3.1-1 (source amd64) into unstable

ian-med-packag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sas...@steinbiss.name> Description: libsnp-sites1 - Shared libraries of the package snp-sites libsnp-sites1-dev - Static libraries and header files for the package snp-sites snp-sites - Binary code for the packa

Accepted reapr 1.0.18+dfsg-2 (source amd64) into unstable

kag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sas...@steinbiss.name> Description: reapr - universal tool for genome assembly evaluation Changes: reapr (1.0.18+dfsg-2) unstable; urgency=medium . * make manpage building reproducible by not using ronn anymore * enable full hardening Ch

Accepted snp-sites 2.2.2-1 (source amd64) into unstable

ian-med-packag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sas...@steinbiss.name> Description: libsnp-sites1 - Shared libraries of the package snp-sites libsnp-sites1-dev - Static libraries and header files for the package snp-sites snp-sites - Binary code for the packa

Accepted pbsim 1.0.3-2 (source amd64) into unstable

org> Changed-By: Sascha Steinbiss <sas...@steinbiss.name> Description: pbsim - simulator for PacBio sequencing reads Changes: pbsim (1.0.3-2) unstable; urgency=medium . * switch man page building to asciidoctor from ronn - get reproducible output - ronn is unmaintain

Accepted tantan 13-4 (source amd64) into unstable

org> Changed-By: Sascha Steinbiss <sas...@steinbiss.name> Description: tantan - low complexity and tandem repeat masker for biosequences Changes: tantan (13-4) unstable; urgency=medium . * Use stable compilation order for reproducibility. * Add full hardening support. Ch

Accepted tantan 13-3 (source amd64) into unstable

org> Changed-By: Sascha Steinbiss <sas...@steinbiss.name> Description: tantan - low complexity and tandem repeat masker for biosequences Changes: tantan (13-3) unstable; urgency=medium . * Bump Standards-Version. * Add autopkgtest. Checksums-Sha1: 8a2af4dc66a75cdb1e3d35c14c1ef4258

Accepted spades 3.7.1+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 (3.7.1+dfsg-1) unstable; urgency=medium . * New upstream release. * Add gbp.conf to always use pristine-tar. Ch

Accepted barrnap 0.7+dfsg-2 (source all) into unstable

kag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sas...@steinbiss.name> Description: barrnap- rapid ribosomal RNA prediction Changes: barrnap (0.7+dfsg-2) unstable; urgency=medium . [Afif Elghraoui] * Bump Standards-Version. * Use secure Vcs-Git. * Migrate to git. . [Sasc

Accepted mussort 0.3-7 (source all) into unstable

-BEGIN PGP SIGNED MESSAGE- Hash: SHA512 Format: 1.8 Date: Fri, 11 Mar 2016 17:04:53 + Source: mussort Binary: mussort Architecture: source all Version: 0.3-7 Distribution: unstable Urgency: medium Maintainer: Sascha Steinbiss <sa...@tetrinetsucht.de> Changed-By: Sascha Steinbi

Accepted genometools 1.5.8+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 <sas...@steinbiss.name> Description: genometools - versatile genome analysis toolkit genometools-common - shared data files for

Accepted roary 3.6.0+dfsg-2 (source all) into unstable

org> Changed-By: Sascha Steinbiss <sas...@steinbiss.name> Description: roary - high speed stand alone pan genome pipeline Changes: roary (3.6.0+dfsg-2) unstable; urgency=medium . * Add autopkgtest. Checksums-Sha1: 788b9b0f1793bb189de489e00a332d3ed0edb807 2472 roary_3.6.

Accepted kmc 2.3+dfsg-3 (source amd64) into unstable

kag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sas...@steinbiss.name> Description: kmc- count kmers in genomic sequences libkmc-dev - library to access KMC k-mer count files Changes: kmc (2.3+dfsg-3) unstable; urgency=medium . * Switch to asciidoctor for reproducible man p

Accepted snpomatic 1.0-3 (source amd64) into unstable

kag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sas...@steinbiss.name> Description: snpomatic - fast, stringent short-read mapping software Changes: snpomatic (1.0-3) unstable; urgency=medium . * Fix locale in attempt to ensure reproducible manpages. * Switch to asciidoctor instead of

Accepted kmc 2.3+dfsg-2 (source amd64) into unstable

kag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sas...@steinbiss.name> Description: kmc- count kmers in genomic sequences libkmc-dev - library to access KMC k-mer count files Changes: kmc (2.3+dfsg-2) unstable; urgency=medium . * Make man page building reproducible. * Clea

Accepted snpomatic 1.0-2 (source amd64) into unstable

kag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sas...@steinbiss.name> Description: snpomatic - fast, stringent short-read mapping software Changes: snpomatic (1.0-2) unstable; urgency=medium . * Make manpage generation reproducible. * Use install instead of cp. Ch

Accepted genometools 1.5.8+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 <sas...@steinbiss.name> Description: genometools - versatile genome analysis toolkit genometools-common - shared data files for

Accepted snpomatic 1.0-1 (source amd64) into unstable

kag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sas...@steinbiss.name> Description: snpomatic - fast, stringent short-read mapping software Changes: snpomatic (1.0-1) unstable; urgency=medium . * Use new upstream versioning scheme. * Add autopkgtest. * Bump Standards-Version. * Use se

Accepted onioncircuits 0.3-1 (source all) into unstable, unstable

ain...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sas...@steinbiss.name> Description: onioncircuits - GTK+ application to display Tor circuits and streams Closes: 796265 Changes: onioncircuits (0.3-1) unstable; urgency=low . * Initial release (Closes: #796265) Ch

Accepted roary 3.6.0+dfsg-1 (source all) into unstable

org> Changed-By: Sascha Steinbiss <sas...@steinbiss.name> Description: roary - high speed stand alone pan genome pipeline Changes: roary (3.6.0+dfsg-1) unstable; urgency=medium . * New upstream release. Checksums-Sha1: 8453c50d3a2ddc2534476a1f4232314c485130c3 2449 roary_3.6.

Accepted codonw 1.4.4-3 (source amd64) into unstable

org> Changed-By: Sascha Steinbiss <sas...@steinbiss.name> Description: codonw - Correspondence Analysis of Codon Usage Changes: codonw (1.4.4-3) unstable; urgency=low . * Fix typo in d/copyright * Add EDAM annotation * Bump Standards-Version. * Use secure Vcs-Git. *

Accepted reapr 1.0.18+dfsg-1 (source amd64) into unstable, unstable

org> Changed-By: Sascha Steinbiss <sas...@steinbiss.name> Description: reapr - universal tool for genome assembly evaluation Closes: 813385 Changes: reapr (1.0.18+dfsg-1) unstable; urgency=low . * Initial release (Closes: #813385) Checksums-Sha1: 76c80750fe985b55583592bff59d3c9dc

Accepted biosquid 1.9g+cvs20050121-5 (source amd64) into unstable

kag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sas...@steinbiss.name> Description: biosquid - utilities for biological sequence analysis biosquid-dev - headers and static library for biological sequence analysis Closes: 815883 Changes: biosquid (1.9g+cvs20050121-5) unsta

Accepted roary 3.5.9+dfsg-2 (source all) into unstable

org> Changed-By: Sascha Steinbiss <sas...@steinbiss.name> Description: roary - high speed stand alone pan genome pipeline Changes: roary (3.5.9+dfsg-2) unstable; urgency=medium . * Change priority to extra due to parallel and fasttree being extra. * Bump Standards-Version. *

Accepted spades 3.7.0+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 (3.7.0+dfsg-1) unstable; urgency=medium . * Make changelog building reproducible. * New upstream release. * Update

Accepted spades 3.6.2+dfsg-2 (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 (3.6.2+dfsg-2) unstable; urgency=medium . * Use Debian's jemalloc. * Fix spelling issues. * Bump Standards-Version. Ch

Accepted spades 3.6.2+dfsg-1 (source amd64) into unstable, unstable

org> Changed-By: Sascha Steinbiss <sas...@steinbiss.name> Description: spades - genome assembler for single-cell and isolates data sets Closes: 813988 Changes: spades (3.6.2+dfsg-1) unstable; urgency=low . * Initial release (Closes: #813988) Ch

Accepted roary 3.5.9+dfsg-1 (source all) into unstable

org> Changed-By: Sascha Steinbiss <sas...@steinbiss.name> Description: roary - high speed stand alone pan genome pipeline Changes: roary (3.5.9+dfsg-1) unstable; urgency=medium . * New upstream release. Checksums-Sha1: c749f56134e681309dd4c160984d91d475985f47 2452 roary_3.5.

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