Accepted python-screed 0.7.1-2 (source all) into unstable, unstable

2015-02-01 Thread Michael R. Crusoe
...@lists.alioth.debian.org Changed-By: Michael R. Crusoe michael.cru...@gmail.com Description: python-screed - short nucleotide read sequence utils in Python Closes: 776678 Changes: python-screed (0.7.1-2) unstable; urgency=medium . * Initial upload to Debian (Closes: #776678) Checksums-Sha1

Accepted python-bz2file 0.98-1 (source all) into unstable, unstable

2015-06-02 Thread Michael R. Crusoe
...@lists.alioth.debian.org Changed-By: Michael R. Crusoe mcru...@msu.edu Description: python-bz2file - Python library for reading and writing bzip2-compressed files python3-bz2file - Python3 library for reading and writing bzip2-compressed files Closes: 787039 Changes: python-bz2file (0.98-1

Accepted r-cran-blockmodeling 0.1.8-1 (source amd64) into unstable, unstable

2015-05-27 Thread Michael R. Crusoe
...@lists.alioth.debian.org Changed-By: Michael R. Crusoe mcru...@msu.edu Description: r-cran-blockmodeling - Generalized and classical blockmodeling of valued networks Closes: 778587 Changes: r-cran-blockmodeling (0.1.8-1) unstable; urgency=low . * Initial release (Closes: #778587) Checksums-Sha1

Accepted transdecoder 2.0.1+dfsg-1 (source all) into unstable, unstable

2015-05-25 Thread Michael R. Crusoe
...@lists.alioth.debian.org Changed-By: Michael R. Crusoe mcru...@msu.edu Description: transdecoder - find coding regions within transcripts transdecoder-doc - find coding regions within transcripts Closes: 778300 Changes: transdecoder (2.0.1+dfsg-1) unstable; urgency=low . * Initial release

Accepted parafly 0.0.2013.01.21-1 (source amd64) into unstable, unstable

2015-05-26 Thread Michael R. Crusoe
...@lists.alioth.debian.org Changed-By: Michael R. Crusoe mcru...@msu.edu Description: parafly- parallel command processing using OpenMP Closes: 778331 Changes: parafly (0.0.2013.01.21-1) unstable; urgency=low . * Initial release (Closes: #778331) Checksums-Sha1: 7fce78dff89d7cd6af1cd3b1ef923e2c254066ee 1971

Accepted ruby-fix-trinity-output 1.0.0-1 (source all) into unstable, unstable

2015-11-09 Thread Michael R. Crusoe
uby-extras-maintain...@lists.alioth.debian.org> Changed-By: Michael R. Crusoe <cru...@ucdavis.edu> Description: ruby-fix-trinity-output - Fix output fastq files from trinityrnaseq Closes: 800489 Changes: ruby-fix-trinity-output (1.0.0-1) unstable; urgency=medium . * Initial rel

Accepted rsem 1.2.23+dfsg-1 (source amd64) into unstable

2015-11-05 Thread Michael R. Crusoe
org> Changed-By: Michael R. Crusoe <cru...@ucdavis.edu> Description: rsem - RNA-Seq by Expectation-Maximization Closes: 803550 Changes: rsem (1.2.23+dfsg-1) unstable; urgency=medium . [ Michael R. Crusoe ] * New upstream release . [ Andreas Tille ] * Build-Dep

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

2015-10-19 Thread Michael R. Crusoe
org> Changed-By: Michael R. Crusoe <cru...@ucdavis.edu> Description: libgff-dev - GFF/GTF parsing from cufflinks as a library Closes: 800336 Changes: libgff (1.0-1) unstable; urgency=low . * Initial release (Closes: #800336) Checksums-Sha1: a30a3e5164672d9ae8339eb44ed40d629228bf65 1897

Accepted rsem 1.2.22+dfsg-1 (source amd64) into unstable, unstable

2015-10-21 Thread Michael R. Crusoe
org> Changed-By: Michael R. Crusoe <cru...@ucdavis.edu> Description: rsem - RNA-Seq by Expectation-Maximization Closes: 778578 Changes: rsem (1.2.22+dfsg-1) unstable; urgency=low . * Initial release (Closes: #778578) Checksums-Sha1: cf4465ffd932acdc4af9afd8adebe557a59bd7b3 1974

Accepted spdlog 1.4-1 (source amd64) into unstable, unstable

2015-10-18 Thread Michael R. Crusoe
org> Changed-By: Michael R. Crusoe <cru...@ucdavis.edu> Description: libspdlog-dev - Very fast, header only, C++ logging library Closes: 800337 Changes: spdlog (1.4-1) unstable; urgency=low . * Initial release (Closes: #800337) Checksums-Sha1: 536e5690aa8d60362304f67d576c215a9

Accepted ruby-colorize 0.7.7-1 (source all) into unstable

2015-10-12 Thread Michael R. Crusoe
ain...@lists.alioth.debian.org> Changed-By: Michael R. Crusoe <cru...@ucdavis.edu> Description: ruby-colorize - color methods to Ruby String class Changes: ruby-colorize (0.7.7-1) unstable; urgency=medium . * Imported Upstream version 0.7.7 Checksums-Sha1: 3736bd8b6d07fce9826961d81796

Accepted ruby-facade 1.0.7-1 (source all) into unstable, unstable

2015-10-13 Thread Michael R. Crusoe
ain...@lists.alioth.debian.org> Changed-By: Michael R. Crusoe <cru...@ucdavis.edu> Description: ruby-facade - facade pattern aide for Ruby Closes: 800488 Changes: ruby-facade (1.0.7-1) unstable; urgency=medium . * Initial release (Closes: #800488) Checksums-Sha1: 47352eb86dbf51a45d20e6b992dc

Accepted ruby-yell 2.0.5-1 (source all) into unstable, unstable

2015-10-13 Thread Michael R. Crusoe
ain...@lists.alioth.debian.org> Changed-By: Michael R. Crusoe <cru...@ucdavis.edu> Description: ruby-yell - Your Extensible Logging Library for Ruby Closes: 800494 Changes: ruby-yell (2.0.5-1) unstable; urgency=medium . * Initial release (Closes: #800494) Ch

Accepted python-screed 0.9-1 (source all) into unstable, unstable

2015-07-09 Thread Michael R. Crusoe
...@lists.alioth.debian.org Changed-By: Michael R. Crusoe cru...@ucdavis.edu Description: python-screed - short nucleotide read sequence utils in Python 2 python3-screed - short nucleotide read sequence utils in Python 3 Changes: python-screed (0.9-1) unstable; urgency=medium . * Update to latest

Accepted r-bioc-ebseq 1.6.0-1 (source all) into unstable, unstable

2015-09-03 Thread Michael R. Crusoe
kag...@lists.alioth.debian.org> Changed-By: Michael R. Crusoe <mcru...@msu.edu> Description: r-bioc-ebseq - R package for RNA-Seq Differential Expression Analysis Closes: 778586 Changes: r-bioc-ebseq (1.6.0-1) unstable; urgency=low . * Initial release (Closes: #778586) Ch

Accepted jaligner 1.0+dfsg-1 (source all) into unstable, unstable

2015-09-02 Thread Michael R. Crusoe
kag...@lists.alioth.debian.org> Changed-By: Michael R. Crusoe <cru...@ucdavis.edu> Description: jaligner - Smith-Waterman algorithm with Gotoh's improvement Closes: 778489 Changes: jaligner (1.0+dfsg-1) unstable; urgency=medium . * Initial release. (Closes: #778489) Ch

Accepted berkeley-express 1.5.1-1 (source all amd64) into unstable, unstable

2015-09-29 Thread Michael R. Crusoe
<debian-med-packag...@lists.alioth.debian.org> Changed-By: Michael R. Crusoe <cru...@ucdavis.edu> Description: berkeley-express - Streaming quantification for high-throughput sequencing berkeley-express-doc - Documentation for RNA-Seq tool eXpress Closes: 778589 Changes: berkeley-expr

Accepted macs 2.1.0.20150731-1 (source amd64) into unstable

2015-10-05 Thread Michael R. Crusoe
org> Changed-By: Michael R. Crusoe <cru...@ucdavis.edu> Description: macs - Model-based Analysis of ChIP-Seq on short reads sequencers Changes: macs (2.1.0.20150731-1) unstable; urgency=low . * debian/watch: now released via PyPI. * debian/rules: - 2.1.0 uses a s

Accepted jellyfish 2.2.3-3 (source amd64) into unstable

2015-09-20 Thread Michael R. Crusoe
Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Michael R. Crusoe <cru...@ucdavis.edu> Description: jellyfish - count k-mers in DNA sequences jellyfish-examples - count k-mers in DNA sequences (examples for testing) libjellyfish-2.0-2 - count k-mers in D

Accepted bwa 0.7.12-5 (source amd64) into unstable, unstable

2015-10-06 Thread Michael R. Crusoe
kag...@lists.alioth.debian.org> Changed-By: Michael R. Crusoe <cru...@ucdavis.edu> Description: bwa- Burrows-Wheeler Aligner libbwa-dev - Burrows-Wheeler Aligner source files Changes: bwa (0.7.12-5) unstable; urgency=medium . * Make a libbwa-dev package for `salmon`. Ch

Accepted khmer 2.0+dfsg-1 (source amd64) into unstable, unstable

2015-12-19 Thread Michael R. Crusoe
med-packag...@lists.alioth.debian.org> Changed-By: Michael R. Crusoe <cru...@ucdavis.edu> Description: khmer - in-memory DNA sequence kmer counting, filtering & graph traversal khmer-common - common files for the khmer project tools liboxli-dev - in-memory DNA sequence anal

Accepted khmer 2.0+dfsg-3 (source all amd64) into unstable

2016-01-11 Thread Michael R. Crusoe
ian-med-packag...@lists.alioth.debian.org> Changed-By: Michael R. Crusoe <cru...@ucdavis.edu> Description: khmer - in-memory DNA sequence kmer counting, filtering & graph traversal khmer-common - common files for the khmer project tools liboxli-dev - in-memory DNA sequence anal

Accepted mypy 0.4.2-1 (source) into unstable

2016-06-09 Thread Michael R. Crusoe
hanged-By: Michael R. Crusoe <michael.cru...@gmail.com> Description: mypy - Optional static typing for Python Changes: mypy (0.4.2-1) unstable; urgency=medium . * New upstream release Checksums-Sha1: bd5e282735d2fd38d50b282cbb7687e3f762a136 1905 mypy

Accepted rsem 1.2.31+dfsg-1 (source) into unstable

2016-06-04 Thread Michael R. Crusoe
org> Changed-By: Michael R. Crusoe <michael.cru...@gmail.com> Description: rsem - RNA-Seq by Expectation-Maximization Changes: rsem (1.2.31+dfsg-1) unstable; urgency=medium . * New upstream release Checksums-Sha1: 262267867c417f33a1f8497b1015f2c005f725c8 2026 rsem_1.2.3

Accepted khmer 2.0+dfsg-2 (source all amd64) into unstable

2016-01-10 Thread Michael R. Crusoe
ian-med-packag...@lists.alioth.debian.org> Changed-By: Michael R. Crusoe <cru...@ucdavis.edu> Description: khmer - in-memory DNA sequence kmer counting, filtering & graph traversal khmer-common - common files for the khmer project tools liboxli-dev - in-memory DNA sequence anal

Accepted libjung-free-java 2.0.1+dfsg-1 (source all) into unstable, unstable

2016-01-15 Thread Michael R. Crusoe
<debian-med-packag...@lists.alioth.debian.org> Changed-By: Michael R. Crusoe <cru...@ucdavis.edu> Description: libjung-free-java - Java Universal Network/Graph Framework libjung-free-java-doc - Java Universal Network/Graph Framework (documentation) Closes: 368931 Changes: libjung-free

Accepted r-cran-pscbs 0.61.0-1 (source amd64) into unstable, unstable

2016-06-28 Thread Michael R. Crusoe
kag...@lists.alioth.debian.org> Changed-By: Michael R. Crusoe <michael.cru...@gmail.com> Description: r-cran-pscbs - R package: Analysis of Parent-Specific DNA Copy Numbers Closes: 828690 Changes: r-cran-pscbs (0.61.0-1) unstable; urgency=medium . * Initial release. (Closes: #828690) Ch

Accepted r-cran-globals 0.6.1-1 (source amd64) into unstable, unstable

2016-06-26 Thread Michael R. Crusoe
kag...@lists.alioth.debian.org> Changed-By: Michael R. Crusoe <michael.cru...@gmail.com> Description: r-cran-globals - R package: Identify Global Objects in R Expressions Closes: 828196 Changes: r-cran-globals (0.6.1-1) unstable; urgency=medium . * Initial release. (Closes: #828196) Ch

Accepted r-cran-listenv 0.6.0-1 (source amd64) into unstable, unstable

2016-06-26 Thread Michael R. Crusoe
kag...@lists.alioth.debian.org> Changed-By: Michael R. Crusoe <michael.cru...@gmail.com> Description: r-cran-listenv - R package: Environments Behaving (Almost) as Lists Closes: 828194 Changes: r-cran-listenv (0.6.0-1) unstable; urgency=medium . * Initial release. (Closes: #828194) Ch

Accepted r-cran-r.cache 0.12.0-1 (source amd64) into unstable, unstable

2016-06-26 Thread Michael R. Crusoe
kag...@lists.alioth.debian.org> Changed-By: Michael R. Crusoe <michael.cru...@gmail.com> Description: r-cran-r.cache - R package: Fast and Light-Weight Caching of Objects and Results Closes: 828184 Changes: r-cran-r.cache (0.12.0-1) unstable; urgency=medium . * Initial release. (Closes: #82818

Accepted python-rdflib-jsonld 0.3-1 (source all) into unstable, unstable

2016-02-06 Thread Michael R. Crusoe
<debian-med-packag...@lists.alioth.debian.org> Changed-By: Michael R. Crusoe <cru...@ucdavis.edu> Description: python-rdflib-jsonld - rdflib extension adding JSON-LD parser and serializer in Python 2 python3-rdflib-jsonld - rdflib extension adding JSON-LD parser and serializer in Pyt

Accepted salmon 0.4.2+ds1-2 (source) into unstable

2016-02-07 Thread Michael R. Crusoe
org> Changed-By: Michael R. Crusoe <cru...@ucdavis.edu> Description: salmon - wicked-fast transcript quantification from RNA-seq data Closes: 813994 Changes: salmon (0.4.2+ds1-2) unstable; urgency=medium . * Make build reproducible. Closes: #813994 Ch

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

2016-02-07 Thread Michael R. Crusoe
med-packag...@lists.alioth.debian.org> Changed-By: Michael R. Crusoe <cru...@ucdavis.edu> Description: trinityrnaseq - RNA-Seq De novo Assembly trinityrnaseq-examples - RNA-Seq De novo Assembly common example and testing files Closes: 813958 Changes: trinityrnaseq (2.1.1+dfsg-2) unsta

Accepted mira 4.9.5-5 (source) into unstable

2016-02-08 Thread Michael R. Crusoe
kag...@lists.alioth.debian.org> Changed-By: Michael R. Crusoe <cru...@ucdavis.edu> Description: mira-assembler - Whole Genome Shotgun and EST Sequence Assembler mira-doc - documentation for the mira assembler mira-examples - files to experiment with the mira assembler Changes: mira (4.9.5

Accepted varna 3-93+ds-1 (source all) into unstable, unstable

2016-02-08 Thread Michael R. Crusoe
org> Changed-By: Michael R. Crusoe <cru...@ucdavis.edu> Description: varna - Visualization Applet for RNA Closes: 814050 Changes: varna (3-93+ds-1) unstable; urgency=medium . * Initial release. (Closes: #814050) Checksums-Sha1: f358982e09a3098a3a5bf4b16ff823286fd69f3d 1909 varna_3

Accepted khmer 2.0+dfsg-5 (source all amd64) into unstable

2016-02-05 Thread Michael R. Crusoe
ian-med-packag...@lists.alioth.debian.org> Changed-By: Michael R. Crusoe <cru...@ucdavis.edu> Description: khmer - in-memory DNA sequence kmer counting, filtering & graph traversal khmer-common - common files for the khmer project tools liboxli-dev - in-memory DNA sequence anal

Accepted trinityrnaseq 2.1.1+dfsg-1 (source amd64 all) into unstable, unstable

2016-02-05 Thread Michael R. Crusoe
<debian-med-packag...@lists.alioth.debian.org> Changed-By: Michael R. Crusoe <cru...@ucdavis.edu> Description: trinityrnaseq - RNA-Seq De novo Assembly trinityrnaseq-examples - RNA-Seq De novo Assembly common example and testing files Closes: 777697 Changes: trinityrnaseq (2.1.1+dfsg

Accepted salmon 0.4.2+ds1-1 (source amd64) into unstable, unstable

2016-02-05 Thread Michael R. Crusoe
org> Changed-By: Michael R. Crusoe <cru...@ucdavis.edu> Description: salmon - wicked-fast transcript quantification from RNA-seq data Closes: 800339 Changes: salmon (0.4.2+ds1-1) unstable; urgency=low . * Initial release (Closes: #800339) Ch

Accepted libcereal 1.1.2-3 (source amd64 all) into unstable

2016-02-12 Thread Michael R. Crusoe
kag...@lists.alioth.debian.org> Changed-By: Michael R. Crusoe <cru...@ucdavis.edu> Description: libcereal-dev - C++11 library for serialization libcereal-doc - C++11 library for serialization HTML documentation Changes: libcereal (1.1.2-3) unstable; urgency=medium . * Applied patch f

Accepted python-schema-salad 1.6.20160202222448-1 (source all) into unstable, unstable

2016-02-07 Thread Michael R. Crusoe
ian-med-packag...@lists.alioth.debian.org> Changed-By: Michael R. Crusoe <cru...@ucdavis.edu> Description: python-schema-salad - Schema Annotations for Linked Avro Data (SALAD) Closes: 813839 Changes: python-schema-salad (1.6.2016020448-1) unstable; urgency=medium . * Initial rele

Accepted libcereal 1.1.2-4 (source amd64 all) into unstable

2016-02-12 Thread Michael R. Crusoe
kag...@lists.alioth.debian.org> Changed-By: Michael R. Crusoe <cru...@ucdavis.edu> Description: libcereal-dev - C++11 library for serialization libcereal-doc - C++11 library for serialization HTML documentation Closes: 814530 Changes: libcereal (1.1.2-4) unstable; urgency=medium . * D

Accepted khmer 2.0+dfsg-4 (source all amd64) into unstable

2016-02-01 Thread Michael R. Crusoe
ian-med-packag...@lists.alioth.debian.org> Changed-By: Michael R. Crusoe <cru...@ucdavis.edu> Description: khmer - in-memory DNA sequence kmer counting, filtering & graph traversal khmer-common - common files for the khmer project tools liboxli-dev - in-memory DNA sequence anal

Accepted mira 4.9.5-4 (source amd64 all) into unstable

2016-02-02 Thread Michael R. Crusoe
med-packag...@lists.alioth.debian.org> Changed-By: Michael R. Crusoe <cru...@ucdavis.edu> Description: mira-assembler - Whole Genome Shotgun and EST Sequence Assembler mira-doc - documentation for the mira assembler mira-examples - files to experiment with the mira assembler Changes: m

Accepted libcereal 1.1.2-1 (source amd64 all) into unstable, unstable

2016-01-29 Thread Michael R. Crusoe
kag...@lists.alioth.debian.org> Changed-By: Michael R. Crusoe <cru...@ucdavis.edu> Description: libcereal-dev - C++11 library for serialization libcereal-doc - C++11 library for serialization HTML documentation Closes: 800335 Changes: libcereal (1.1.2-1) unstable; urgency=low . * Ini

Accepted ruby-crb-blast 0.6.4-1 (source all) into unstable, unstable

2016-02-03 Thread Michael R. Crusoe
ain...@lists.alioth.debian.org> Changed-By: Michael R. Crusoe <cru...@ucdavis.edu> Description: ruby-crb-blast - Run conditional reciprocal best blast Closes: 800737 Changes: ruby-crb-blast (0.6.4-1) unstable; urgency=medium . * Initial release (Closes: #800737) Ch

Accepted macs 2.1.0.20151222-1 (source amd64) into unstable

2016-02-03 Thread Michael R. Crusoe
kag...@lists.alioth.debian.org> Changed-By: Michael R. Crusoe <cru...@ucdavis.edu> Description: macs - Model-based Analysis of ChIP-Seq on short reads sequencers Changes: macs (2.1.0.20151222-1) unstable; urgency=medium . * New upstream release * A couple more spelling fixes & updated VCS URLs

Accepted libcereal 1.1.2-2 (source amd64 all) into unstable

2016-02-03 Thread Michael R. Crusoe
kag...@lists.alioth.debian.org> Changed-By: Michael R. Crusoe <cru...@ucdavis.edu> Description: libcereal-dev - C++11 library for serialization libcereal-doc - C++11 library for serialization HTML documentation Closes: 813280 813281 813282 Changes: libcereal (1.1.2-2) unstable; ur

Accepted spdlog 1.6-1 (source amd64) into unstable

2016-01-30 Thread Michael R. Crusoe
kag...@lists.alioth.debian.org> Changed-By: Michael R. Crusoe <cru...@ucdavis.edu> Description: libspdlog-dev - Very fast, header only, C++ logging library Changes: spdlog (1.6-1) unstable; urgency=medium . * Update to version 1.6 * Ship examples, tests. Run the tests during build time and added auto

Accepted python-screed 0.9-2 (source all) into unstable

2016-02-02 Thread Michael R. Crusoe
kag...@lists.alioth.debian.org> Changed-By: Michael R. Crusoe <cru...@ucdavis.edu> Description: python-screed - short nucleotide read sequence utils in Python 2 python3-screed - short nucleotide read sequence utils in Python 3 Changes: python-screed (0.9-2) unstable; urgency=medium

Accepted rsem 1.2.26+dfsg-1 (source amd64) into unstable

2016-02-01 Thread Michael R. Crusoe
org> Changed-By: Michael R. Crusoe <cru...@ucdavis.edu> Description: rsem - RNA-Seq by Expectation-Maximization Changes: rsem (1.2.26+dfsg-1) unstable; urgency=medium . * New upstream release Checksums-Sha1: f36d5089a523c01bb9f078adf7f5649298056dc9 2028 rsem_1.2.2

Accepted python-schema-salad 1.6.20160202222448-2 (source) into unstable

2016-02-24 Thread Michael R. Crusoe
med-packag...@lists.alioth.debian.org> Changed-By: Michael R. Crusoe <cru...@ucdavis.edu> Description: python-schema-salad - Schema Annotations for Linked Avro Data (SALAD) Changes: python-schema-salad (1.6.2016020448-2) unstable; urgency=medium . * debian/watch, debian/control:

Accepted snap-aligner 0.18~1.0~beta.18+dfsg1-3 (source) into unstable

2016-02-24 Thread Michael R. Crusoe
kag...@lists.alioth.debian.org> Changed-By: Michael R. Crusoe <cru...@ucdavis.edu> Description: snap-aligner - Scalable Nucleotide Alignment Program Closes: 812550 812551 Changes: snap-aligner (0.18~1.0~beta.18+dfsg1-3) unstable; urgency=medium . * Add support for kfreebsd and non-x86, tha

Accepted spdlog 1.6-2 (source) into unstable

2016-02-28 Thread Michael R. Crusoe
org> Changed-By: Michael R. Crusoe <cru...@ucdavis.edu> Description: libspdlog-dev - Very fast, header only, C++ logging library Changes: spdlog (1.6-2) unstable; urgency=medium . * Fix VCS-Git URL. Checksums-Sha1: bf7734c1675ebf86cfa21cc685391337d673a6a0 1904 spdl

Accepted trinityrnaseq 2.1.1+dfsg2-1 (source) into unstable

2016-02-25 Thread Michael R. Crusoe
med-packag...@lists.alioth.debian.org> Changed-By: Michael R. Crusoe <cru...@ucdavis.edu> Description: trinityrnaseq - RNA-Seq De novo Assembly trinityrnaseq-examples - RNA-Seq De novo Assembly common example and testing files Changes: trinityrnaseq (2.1.1+dfsg2-1) unstable;

Accepted snap-aligner 0.18~1.0~beta.18+dfsg1-1 (source amd64) into unstable, unstable

2016-01-22 Thread Michael R. Crusoe
kag...@lists.alioth.debian.org> Changed-By: Michael R. Crusoe <cru...@ucdavis.edu> Description: snap-aligner - Scalable Nucleotide Alignment Program Closes: 800340 Changes: snap-aligner (0.18~1.0~beta.18+dfsg1-1) unstable; urgency=low . * Initial release (Closes: #800340) Ch

Accepted ruby-fixwhich 1.0.2-1 (source all) into unstable, unstable

2016-01-25 Thread Michael R. Crusoe
ain...@lists.alioth.debian.org> Changed-By: Michael R. Crusoe <cru...@ucdavis.edu> Description: ruby-fixwhich - ruby module that emulates the 'which' program Closes: 800742 Changes: ruby-fixwhich (1.0.2-1) unstable; urgency=medium . * Initial release (Closes: #800742) Ch

Accepted ruby-threach 0.2.0-1 (source all) into unstable, unstable

2016-01-25 Thread Michael R. Crusoe
ain...@lists.alioth.debian.org> Changed-By: Michael R. Crusoe <cru...@ucdavis.edu> Description: ruby-threach - Threaded each Closes: 800734 Changes: ruby-threach (0.2.0-1) unstable; urgency=medium . * Initial release (Closes: #800734) Checksums-Sha1: 3a34c15d335229a5656281b575e2006ebd791f

Accepted snap-aligner 0.18~1.0~beta.18+dfsg1-2 (source amd64) into unstable

2016-01-24 Thread Michael R. Crusoe
kag...@lists.alioth.debian.org> Changed-By: Michael R. Crusoe <cru...@ucdavis.edu> Description: snap-aligner - Scalable Nucleotide Alignment Program Closes: 812376 Changes: snap-aligner (0.18~1.0~beta.18+dfsg1-2) unstable; urgency=medium . * Drop -msse flag for wider platform c

Accepted ruby-pathname2 1.7.4-1 (source all) into unstable, unstable

2016-01-24 Thread Michael R. Crusoe
ain...@lists.alioth.debian.org> Changed-By: Michael R. Crusoe <cru...@ucdavis.edu> Description: ruby-pathname2 - alternate implementation of the Pathname class Closes: 800740 Changes: ruby-pathname2 (1.7.4-1) unstable; urgency=medium . * Initial release (Closes: #800740) Ch

Accepted bamtools 2.4.0+dfsg-6 (source) into unstable

2016-03-10 Thread Michael R. Crusoe
Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Michael R. Crusoe <cru...@ucdavis.edu> Description: bamtools - toolkit for manipulating BAM (genome alignment) files libbamtools-dev - C++ API for manipulating BAM (genome alignment) files libbamtools-doc - docs for dyn

Accepted bamtools 2.4.0+dfsg-5 (source) into unstable

2016-03-09 Thread Michael R. Crusoe
Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Michael R. Crusoe <cru...@ucdavis.edu> Description: bamtools - toolkit for manipulating BAM (genome alignment) files libbamtools-dev - C++ API for manipulating BAM (genome alignment) files libbamtools-doc - docs for dyn

Accepted jellyfish 2.2.5-1 (source amd64) into unstable, unstable

2016-03-19 Thread Michael R. Crusoe
Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Michael R. Crusoe <cru...@ucdavis.edu> Description: jellyfish - count k-mers in DNA sequences jellyfish-examples - count k-mers in DNA sequences (examples for testing)

Accepted cwltool 1.0.20160209222805-1 (source all) into unstable, unstable

2016-03-20 Thread Michael R. Crusoe
kag...@lists.alioth.debian.org> Changed-By: Michael R. Crusoe <cru...@ucdavis.edu> Description: cwltool- Common workflow language reference implementation Closes: 814000 Changes: cwltool (1.0.20160209222805-1) unstable; urgency=medium . * Initial release. (Closes: #814000) Ch

Accepted bamtools 2.4.0+dfsg-4 (source amd64 all) into unstable, unstable

2016-03-07 Thread Michael R. Crusoe
Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Michael R. Crusoe <cru...@ucdavis.edu> Description: bamtools - toolkit for manipulating BAM (genome alignment) files libbamtools-dev - C++ API for manipulating BAM (genome alignment) files libbamtool

Accepted macs 2.1.1.20160226-1 (source) into unstable

2016-03-05 Thread Michael R. Crusoe
org> Changed-By: Michael R. Crusoe <cru...@ucdavis.edu> Description: macs - Model-based Analysis of ChIP-Seq on short reads sequencers Changes: macs (2.1.1.20160226-1) unstable; urgency=medium . * New upstream release Checksums-Sha1: 58581c26240f3af439d19537d30e71f65

Accepted rsem 1.2.26+dfsg-2 (source) into unstable

2016-03-05 Thread Michael R. Crusoe
org> Changed-By: Michael R. Crusoe <cru...@ucdavis.edu> Description: rsem - RNA-Seq by Expectation-Maximization Closes: 811615 Changes: rsem (1.2.26+dfsg-2) unstable; urgency=medium . * Now compatible with g++-6 (Closes: #811615) * Section set to 'extra' due to dependency on bo

Accepted transdecoder 2.0.1+dfsg-3 (source) into unstable

2016-04-25 Thread Michael R. Crusoe
kag...@lists.alioth.debian.org> Changed-By: Michael R. Crusoe <michael.cru...@gmail.com> Description: transdecoder - find coding regions within RNA transcript sequences transdecoder-doc - find coding regions within transcripts Closes: 822268 Changes: transdecoder (2.0.1+dfsg-3) unsta

Accepted transdecoder 3.0.0+dfsg-1 (source) into unstable

2016-05-20 Thread Michael R. Crusoe
kag...@lists.alioth.debian.org> Changed-By: Michael R. Crusoe <michael.cru...@gmail.com> Description: transdecoder - find coding regions within RNA transcript sequences transdecoder-doc - find coding regions within transcripts Changes: transdecoder (3.0.0+dfsg-1) unstable; urgency=medium

Accepted transdecoder 3.0.0+dfsg-2 (source) into unstable

2016-05-23 Thread Michael R. Crusoe
kag...@lists.alioth.debian.org> Changed-By: Michael R. Crusoe <michael.cru...@gmail.com> Description: transdecoder - find coding regions within RNA transcript sequences transdecoder-doc - find coding regions within transcripts Changes: transdecoder (3.0.0+dfsg-2) unstable; ur

Accepted trinityrnaseq 2.2.0+dfsg-1 (source) into unstable

2016-05-23 Thread Michael R. Crusoe
med-packag...@lists.alioth.debian.org> Changed-By: Michael R. Crusoe <michael.cru...@gmail.com> Description: trinityrnaseq - RNA-Seq De novo Assembly trinityrnaseq-examples - RNA-Seq De novo Assembly common example and testing files Changes: trinityrnaseq (2.2.0+dfsg-1) unstable; ur

Accepted khmer 2.0+dfsg-7 (source) into unstable

2016-05-23 Thread Michael R. Crusoe
kag...@lists.alioth.debian.org> Changed-By: Michael R. Crusoe <michael.cru...@gmail.com> Description: khmer - in-memory DNA sequence kmer counting, filtering & graph traversal khmer-common - common files for the khmer project tools liboxli-dev - in-memory DNA sequence anal

Accepted jaligner 1.0+dfsg-3 (source) into unstable

2016-05-23 Thread Michael R. Crusoe
org> Changed-By: Michael R. Crusoe <michael.cru...@gmail.com> Description: jaligner - Smith-Waterman algorithm with Gotoh's improvement Changes: jaligner (1.0+dfsg-3) unstable; urgency=medium . * flip the reproducible switch for asciidoctor Ch

Accepted ruby-colorize 0.7.7-2 (source) into unstable

2016-05-23 Thread Michael R. Crusoe
ain...@lists.alioth.debian.org> Changed-By: Michael R. Crusoe <michael.cru...@gmail.com> Description: ruby-colorize - color methods to Ruby String class Changes: ruby-colorize (0.7.7-2) unstable; urgency=medium . * bump Standards-Version to 3.9.8 * fix tests Ch

Accepted python-rdflib-jsonld 0.4.0-1 (source) into unstable

2016-05-24 Thread Michael R. Crusoe
<debian-med-packag...@lists.alioth.debian.org> Changed-By: Michael R. Crusoe <michael.cru...@gmail.com> Description: python-rdflib-jsonld - rdflib extension adding JSON-LD parser and serializer in Python 2 python3-rdflib-jsonld - rdflib extension adding JSON-LD parser and serializer

Accepted spdlog 1.8-1 (source) into unstable

2016-05-17 Thread Michael R. Crusoe
org> Changed-By: Michael R. Crusoe <michael.cru...@gmail.com> Description: libspdlog-dev - Very fast, header only, C++ logging library Changes: spdlog (1.8-1) unstable; urgency=medium . * new upstream release Checksums-Sha1: d5af3675576c6d16465ddeda0fab6dd7258616e3 1917 spdl

Accepted spdlog 1.7-1 (source) into unstable

2016-05-14 Thread Michael R. Crusoe
org> Changed-By: Michael R. Crusoe <michael.cru...@gmail.com> Description: libspdlog-dev - Very fast, header only, C++ logging library Changes: spdlog (1.7-1) unstable; urgency=medium . * new upstream release * Standards-Version: increment to 3.9.8 * Match upstream's switch to cma

Accepted ruby-yell 2.0.6-1 (source) into unstable

2016-05-14 Thread Michael R. Crusoe
ain...@lists.alioth.debian.org> Changed-By: Michael R. Crusoe <michael.cru...@gmail.com> Description: ruby-yell - Your Extensible Logging Library for Ruby Changes: ruby-yell (2.0.6-1) unstable; urgency=medium . * New upstream release. * drop rspec3 patch, applied upstream * Standards-Version:

Accepted mira 4.9.6-1 (source amd64 all) into unstable, unstable

2016-05-13 Thread Michael R. Crusoe
ian-med-packag...@lists.alioth.debian.org> Changed-By: Michael R. Crusoe <michael.cru...@gmail.com> Description: mira-assembler - Whole Genome Shotgun and EST Sequence Assembler mira-doc - documentation for the mira assembler mira-rfam-12s-rrna - extract of RFAM 12 rRNA database Ch

Accepted transdecoder 2.1.0+dfsg-1 (source) into unstable

2016-05-18 Thread Michael R. Crusoe
kag...@lists.alioth.debian.org> Changed-By: Michael R. Crusoe <michael.cru...@gmail.com> Description: transdecoder - find coding regions within RNA transcript sequences transdecoder-doc - find coding regions within transcripts Changes: transdecoder (2.1.0+dfsg-1) unstable; urgency=medium

Accepted macs 2.1.1.20160309-1 (source) into unstable

2016-05-13 Thread Michael R. Crusoe
org> Changed-By: Michael R. Crusoe <michael.cru...@gmail.com> Description: macs - Model-based Analysis of ChIP-Seq on short reads sequencers Changes: macs (2.1.1.20160309-1) unstable; urgency=medium . * New upstream release. * Bump Standards-Version to 3.9.8 * Refresh

Accepted rsem 1.2.30+dfsg-1 (source) into unstable

2016-05-15 Thread Michael R. Crusoe
org> Changed-By: Michael R. Crusoe <michael.cru...@gmail.com> Description: rsem - RNA-Seq by Expectation-Maximization Changes: rsem (1.2.30+dfsg-1) unstable; urgency=medium . * New upstream release * Use upstream's modified samtools-1.3 as that is required for correct opera

Accepted jaligner 1.0+dfsg-2 (source) into unstable

2016-05-04 Thread Michael R. Crusoe
org> Changed-By: Michael R. Crusoe <michael.cru...@gmail.com> Description: jaligner - Smith-Waterman algorithm with Gotoh's improvement Changes: jaligner (1.0+dfsg-2) unstable; urgency=medium . * Make build reproducible by switching to asciidoctor from ruby-ronn for manual pag

Accepted mypy 0.3.1-1 (source all) into unstable, unstable

2016-05-06 Thread Michael R. Crusoe
org> Changed-By: Michael R. Crusoe <michael.cru...@gmail.com> Description: mypy - Optional static typing for Python Closes: 823512 Changes: mypy (0.3.1-1) unstable; urgency=medium . * Initial release. (Closes: #823512) Checksums-Sha1: e08a4331a568bfcc87c3026c2c9810d4d853e82d 1923 mypy

Accepted mypy 0.4.1-1 (source) into unstable

2016-05-10 Thread Michael R. Crusoe
hanged-By: Michael R. Crusoe <michael.cru...@gmail.com> Description: mypy - Optional static typing for Python Changes: mypy (0.4.1-1) unstable; urgency=medium . * New upstream release Checksums-Sha1: c265cbc2aed83c60bf0ea9b057c1bc2cc4c58b78 1905 mypy

Accepted khmer 2.0+dfsg-6 (source) into unstable

2016-05-04 Thread Michael R. Crusoe
kag...@lists.alioth.debian.org> Changed-By: Michael R. Crusoe <michael.cru...@gmail.com> Description: khmer - in-memory DNA sequence kmer counting, filtering & graph traversal khmer-common - common files for the khmer project tools liboxli-dev - in-memory DNA sequence anal

Accepted mypy 0.4-1 (source) into unstable

2016-05-07 Thread Michael R. Crusoe
hanged-By: Michael R. Crusoe <michael.cru...@gmail.com> Description: mypy - Optional static typing for Python Changes: mypy (0.4-1) unstable; urgency=medium . * New upstream release Checksums-Sha1: 2476838fe585d53421050c6e96edd6cfed46a72b 1891 my

Accepted mypy 0.4.3-1 (source) into unstable

2016-08-02 Thread Michael R. Crusoe
hanged-By: Michael R. Crusoe <michael.cru...@gmail.com> Description: mypy - Optional static typing for Python Changes: mypy (0.4.3-1) unstable; urgency=medium . * New upstream release * patch typeshed/tests/pytype_test.py to use python3 Checksums-Sha1: 1a46cc9ef86fabd2ac82669afdb1

Accepted libcereal 1.2.1-1 (source) into unstable

2016-08-14 Thread Michael R. Crusoe
kag...@lists.alioth.debian.org> Changed-By: Michael R. Crusoe <michael.cru...@gmail.com> Description: libcereal-dev - C++11 library for serialization libcereal-doc - C++11 library for serialization HTML documentation Closes: 834187 Changes: libcereal (1.2.1-1) unstable; urgency=medium . *

Accepted r-cran-future 1.0.0-1 (source all) into unstable, unstable

2016-06-27 Thread Michael R. Crusoe
kag...@lists.alioth.debian.org> Changed-By: Michael R. Crusoe <michael.cru...@gmail.com> Description: r-cran-future - R package: A Future API for R Closes: 828197 Changes: r-cran-future (1.0.0-1) unstable; urgency=medium . * Initial release. (Closes: #828197) Ch

Accepted r-bioc-dnacopy 1.46.0-1 (source amd64) into unstable, unstable

2016-06-27 Thread Michael R. Crusoe
kag...@lists.alioth.debian.org> Changed-By: Michael R. Crusoe <michael.cru...@gmail.com> Description: r-bioc-dnacopy - R package: DNA copy number data analysis Closes: 828189 Changes: r-bioc-dnacopy (1.46.0-1) unstable; urgency=medium . * Initial release. (Closes: #828189) Ch

Accepted snap-aligner 0.18~1.0~beta.18+dfsg1-4 (source) into unstable

2016-08-05 Thread Michael R. Crusoe
kag...@lists.alioth.debian.org> Changed-By: Michael R. Crusoe <michael.cru...@gmail.com> Description: snap-aligner - Scalable Nucleotide Alignment Program Closes: 831138 Changes: snap-aligner (0.18~1.0~beta.18+dfsg1-4) unstable; urgency=medium . * Build with -std=gnu++98, closes: 831138 Ch

Accepted r-bioc-geneplotter 1.50.0-1 (source all) into unstable, unstable

2016-06-29 Thread Michael R. Crusoe
kag...@lists.alioth.debian.org> Changed-By: Michael R. Crusoe <michael.cru...@gmail.com> Description: r-bioc-geneplotter - R package of functions for plotting genomic data Closes: 828796 Changes: r-bioc-geneplotter (1.50.0-1) unstable; urgency=medium . * Initial release (Closes: #828796) Ch

Accepted mypy 0.470-complete-1 (source) into unstable

2017-02-01 Thread Michael R. Crusoe
org> Changed-By: Michael R. Crusoe <michael.cru...@gmail.com> Description: mypy - Optional static typing for Python Closes: 852819 Changes: mypy (0.470-complete-1) unstable; urgency=medium . * Use complete upstream source from PyPI, not incomplete tarball from GitHub. (Clo

Accepted python-gffutils 0.8.7.1-1 (source all) into unstable, unstable

2017-02-07 Thread Michael R. Crusoe
kag...@lists.alioth.debian.org> Changed-By: Michael R. Crusoe <michael.cru...@gmail.com> Description: python3-gffutils - Work with GFF and GTF files in a flexible database framework Closes: 851488 Changes: python-gffutils (0.8.7.1-1) unstable; urgency=medium . * Initial release. (Closes: #85148

Accepted python-pybedtools 0.7.8-1 (source amd64) into unstable, unstable

2017-02-07 Thread Michael R. Crusoe
kag...@lists.alioth.debian.org> Changed-By: Michael R. Crusoe <michael.cru...@gmail.com> Description: python3-pybedtools - Python 3 wrapper around BEDTools for bioinformatics work Closes: 851358 Changes: python-pybedtools (0.7.8-1) unstable; urgency=medium . * Initial release. (Clo

Accepted khmer 2.0+dfsg-9 (source) into unstable

2017-01-26 Thread Michael R. Crusoe
kag...@lists.alioth.debian.org> Changed-By: Michael R. Crusoe <michael.cru...@gmail.com> Description: khmer - in-memory DNA sequence kmer counting, filtering & graph traversal khmer-common - common files for the khmer project tools liboxli-dev - in-memory DNA sequence anal

Accepted python3-typed-ast 0.5.5-1 (source amd64) into unstable, unstable

2016-08-19 Thread Michael R. Crusoe
kag...@lists.alioth.debian.org> Changed-By: Michael R. Crusoe <michael.cru...@gmail.com> Description: python3-typed-ast - AST with PEP 484 type comments support Closes: 834590 Changes: python3-typed-ast (0.5.5-1) unstable; urgency=medium . * Initial release. (Closes: #834590) Ch

Accepted hisat2 2.0.4-1 (source amd64) into unstable, unstable

2016-08-19 Thread Michael R. Crusoe
org> Changed-By: Michael R. Crusoe <michael.cru...@gmail.com> Description: hisat2 - graph-based alignment of short nucleotide reads to many genomes Closes: 834592 Changes: hisat2 (2.0.4-1) unstable; urgency=medium . * Initial release. (Closes: #834592) Ch

Accepted mypy 0.4.5-1 (source) into unstable

2016-10-08 Thread Michael R. Crusoe
hanged-By: Michael R. Crusoe <michael.cru...@gmail.com> Description: mypy - Optional static typing for Python Changes: mypy (0.4.5-1) unstable; urgency=medium . * recommend python3-typed-ast for the fast parser * new upstream-release Checksums-Sha1: e7aafc66b059f0c22fd57c000d16

Accepted transdecoder 3.0.0+dfsg-3 (source) into unstable

2016-10-10 Thread Michael R. Crusoe
kag...@lists.alioth.debian.org> Changed-By: Michael R. Crusoe <michael.cru...@gmail.com> Description: transdecoder - find coding regions within RNA transcript sequences transdecoder-doc - find coding regions within transcripts Closes: 839297 Changes: transdecoder (3.0.0+dfsg-3) unsta

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