Bug#944785: pufferfish now builds

That's great news, please go for it! -- Michael R. Crusoe ; he/him https://orcid.org/-0002-2961-9670 CWL Project Leader, Software Freedom Conservancy, Common Workflow Language project Promovendus, VU Amsterdam, Computer Systems & Bioinformatics Project Leader FAIR Service Architecture in ELIXI

Bug#962717: q2-quality-control seems so uncover segfaults in bowtie2

On Fri, 15 Jan 2021 at 11:22, Andreas Tille wrote: > On Fri, Jan 15, 2021 at 11:16:48AM +0100, Michael Crusoe wrote: > > bowtie2 segfaults for me if eatmydata and/or cowbuilder are being used, > so > > try with clearing out LD_PRELOAD first > > Ahhh, this makes perfectly

Bug#962717: q2-quality-control seems so uncover segfaults in bowtie2

bowtie2 segfaults for me if eatmydata and/or cowbuilder are being used, so try with clearing out LD_PRELOAD first

Bug#939537: ITP: vg -- tools for working with genome variation graphs

snapshot than Debian's #use_packaged_protobuf ? On Mon, Jan 13, 2020 at 11:20 AM Michael Crusoe wrote: > I have 1.20.0 in my local repository, not yet pushed > > According to my build logs that did not succeed either. > > I'll update my local copy to 1.21 as wel

Bug#939537: ITP: vg -- tools for working with genome variation graphs

I have 1.20.0 in my local repository, not yet pushed According to my build logs that did not succeed either. I'll update my local copy to 1.21 as well, and then I'll compare the patch modifications; pushing up the diff if that seems useful On Sun, Jan 12, 2020 at 11:43 AM Andreas Tille wrote:

Bug#932003: ITP: mypyc -- Mypy to Python C Extension Compile

Thanks Andrej! I recently learned that mypyc is being rolled into the main mypy package upstream, so I'm holding off for the next release of mypy -- Michael R. Crusoe Co-founder & Lead, Common Workflow Language project m...@commonwl.org On Wed, Sep 11, 2019, 21:40 Andrej Shadura wrote: > Hi, >

Bug#934629: ITP: seqan3 -- C++ library for the analysis of biological sequences (development)

Correction: This package is maintained by Debian Med Packaging Team at https://salsa.debian.org/med-team/seqan3

Bug#914928: ITP: python-typing-extensions -- Backported and Experimental Type Hints for Python

Thank you for the information. I'm already using this for schema_salad. I'll patch out the need for it and request removal of this package when Py3.6 is retired. -- Michael R. Crusoe În vin., 7 dec. 2018, 01:57 Piotr Ożarowski [Michael Crusoe, 2018-12-06] > > How soon is soon

Bug#914928: ITP: python-typing-extensions -- Backported and Experimental Type Hints for Python

How soon is soon? -- Michael R. Crusoe Co-founder & Lead, Common Workflow Language project https://impactstory.org/u/-0002-2961-9670 m...@commonwl.org În joi, 6 dec. 2018, 19:27 Piotr Ożarowski > The typing module was added to the standard library in Python 3.5 on a > > provisional basis a

Bug#911076: Request for sponsorship: libdeflate -- fast, whole-buffer DEFLATE-based compression and decompression)

g...@salsa.debian.org:med-team/libdeflate.git Thanks! În lun., 15 oct. 2018 la 14:12, Michael R. Crusoe a scris: > Package: wnpp > Severity: wishlist > Owner: Debian Med team > > * Package name: libdeflate > Version : 1.0 > Upstream Author : Eric Biggers > * URL :

Bug#860746: ITP: easel -- a library of C functions for biological sequence analysis

You are welcome! git+ssh://git.debian.org/git/debian-med/easel.git is ready for review 2017-04-19 20:11 GMT+03:00 Andreas Tille : > Very sensible! Thanks for working on this > Andreas. > > On Wed, Apr 19, 2017 at 10:06:57AM -0700, Michael R. Crusoe wrote: > > Package: wnpp > > Severity: wis

Bug#851468: ITP: python-galaxyxml -- XML Generation libraries for Galaxy Tool/ToolDeps XML

Package: wnpp Severity: wishlist Owner: anton.kho...@ukr.net * Package name: python-galaxyxml Version : 0.1 Upstream Author : Eric Rasche * URL : https://github.com/erasche/galaxyxml * License : Apache-2.0 Programming Lang: Python Description : XML Gene

Bug#800335: cereal: source package name conflicts

wrote: > [ /me is just doing housekeeping of wnpp bugs and removing > inconsistencies ] > > (please keep me in CC if you want to reply to me) > > On Wed, Sep 30, 2015 at 03:24:25PM -0700, Michael Crusoe wrote: > > Oops, I thought I had renamed the source package to libcereal.

Bug#800828: ITP: macs2 -- Model Based Analysis for ChIP-Seq data

Whoops, totally missed that macs2 was already packaged as `macs` (I only search for macs2 as that was the name in PyPI). FYI: upstream has stopped updating the GitHub tags & releases and switched to PyPI. Differences between macs 2.0.9 and macs2 version 2.1.0 in my package - Upstream's license is

Bug#800828: ITP: macs2 -- Model Based Analysis for ChIP-Seq data

Package: wnpp Owner: "Debian Med Team" Severity: wishlist X-Debbugs-CC: debian-...@lists.debian.org * Package name: macs2 Version : 2.1.0.20150731 Upstream Author : Tao Liu * URL : http://github.com/taoliu/MACS/ * License : BSD-3-clause, Expat Programming L

Bug#800742: ITP: ruby-fixwhich -- ruby module that emulates the 'which' program

Package: wnpp Owner: "Debian Ruby Team" Severity: wishlist X-Debbugs-CC: debian-r...@lists.debian.org * Package name: ruby-fixwhich Version : 1.0.2 Upstream Author : Erik Hollensbe & Richard Smith-Unna * URL : http://github.com/Blahah/which * License : MIT P

Bug#800740: ITP: ruby-pathname2 -- alternate implementation of the Pathname class

Package: wnpp Owner: "Debian Ruby Team" Severity: wishlist X-Debbugs-CC: debian-r...@lists.debian.org * Package name: ruby-pathname2 Version : 1.7.4 Upstream Author : Daniel J. Berger * URL : https://github.com/djberg96/pathname2 * License : MIT Programming

Bug#800737: ITP: ruby-crb-blast -- Run conditional reciprocal best blast

Package: wnpp Owner: "Debian Ruby Team" Severity: wishlist X-Debbugs-CC: debian-r...@lists.debian.org * Package name: ruby-crb-blast Version : 0.6.4 Upstream Author : Chris Boursnell & Richard Smith-Unna * URL : https://github.com/cboursnell/crb-blast * License

Bug#800734: ITP: ruby-threach -- Threaded each

Package: wnpp Owner: "Debian Ruby Team" Severity: wishlist X-Debbugs-CC: debian-r...@lists.debian.org * Package name: ruby-threach Version : 0.2.0 Upstream Author : Bill Dueber * URL : http://github.com/billdueber/threach * License : MIT Programming Lang: Ru

Bug#800733: ITP: transrate -- quality assessment of de-novo transcriptome assemblies

Package: wnpp Owner: "Debian Ruby Team" Severity: wishlist X-Debbugs-CC: debian-r...@lists.debian.org * Package name: transrate Version : 1.0.1 Upstream Author : - Richard Smith-Unna, Chris Boursnell, Rob Patro, Julian Hibberd, Steven Kelly * URL : http://hibberdlab.co

Bug#800335: cereal: source package name conflicts

Oops, I thought I had renamed the source package to libcereal. What's the best way to correct this situation? The package is already in the NEW queue: http://ftp-master.debian.org/new/cereal_1.1.2-1.html

Bug#800494: ITP: ruby-yell -- Your Extensible Logging Library

Package: wnpp Owner: "Debian Ruby Team" Severity: wishlist X-Debbugs-CC: debian-r...@lists.debian.org * Package name: ruby-yell Version : 2.0.5 Upstream Author : Rudolf Schmidt * URL : https://github.com/rudionrails/yell * License : MIT Programming Lang: Ruby

Bug#800489: ITP: ruby-fix-trinity-output -- Fix output fastq files from trinityrnaseq

Package: wnpp Owner: "Debian Ruby Team" Severity: wishlist X-Debbugs-CC: debian-r...@lists.debian.org * Package name: ruby-fix-trinity-output Version : 1.0.0 Upstream Author : Chris Boursnell * URL : http://rubygems.org/gems/fix-trinity-output * License : MIT

Bug#800488: ITP: ruby-facade -- facade pattern aide for ruby

Package: wnpp Owner: "Debian Ruby Team" Severity: wishlist X-Debbugs-CC: debian-r...@lists.debian.org * Package name: ruby-facade Version : 1.0.7 Upstream Author : Daniel J. Berger * URL : https://github.com/djberg96/facade * License : Artistic-2.0 Programmin

Bug#800340: ITP: snap-aligner -- Scalable Nucleotide Alignment Program

Package: wnpp Owner: "Debian Med Team" Severity: wishlist X-Debbugs-CC: debian-...@lists.debian.org * Package name: snap-aligner Version : 0.18~1.0~beta.18 Upstream Author : The SNAP Team * URL : http://snap.cs.berkeley.edu/ * License : Apache-2.0 Programmin

Bug#800339: ITP: salmon -- wicked-fast transcript quantification from RNA-seq data

Package: wnpp Owner: "Debian Med Team" Severity: wishlist X-Debbugs-CC: debian-...@lists.debian.org * Package name: salmon Version : 0.4.2 Upstream Author : Rob Patro, Carl Kingsford and Steve Mount * URL : https://github.com/COMBINE-lab/salmon * License : GPL

Bug#800337: ITP: libspdlog-dev -- Very fast, header only, C++ logging library

Package: wnpp Owner: "Debian Med Team" Severity: wishlist X-Debbugs-CC: debian-...@lists.debian.org * Package name: libspdlog-dev Version : 1.4 Upstream Author : Gabi Melman * URL : https://github.com/COMBINE-lab/spdlog * License : MIT Programming Lang: C++

Bug#800336: ITP: libgff -- GFF/GTF parsing from cufflinks as a library

Package: wnpp Owner: "Debian Med Team" Severity: wishlist X-Debbugs-CC: debian-...@lists.debian.org * Package name: libgff-dev Version : 1.0 Upstream Author : Rob Patro * URL : http://www.cs.cmu.edu/~robp/files/libgff.tgz * License : BSL-1.0 Programming Lan

Bug#800335: ITP: cereal -- C++11 library for serialization

Package: wnpp Owner: "Debian Med Team" Severity: wishlist X-Debbugs-CC: debian-...@lists.debian.org * Package name: cereal Version : 1.1.2 Upstream Author : Randolph Voorhies, Shane Grant < cereal...@googlegroups.com> * URL : https://github.com/USCiLab/cereal * Licens

Bug#778589: ITP: express -- Streaming quantification for high-throughput sequencing

Control: block 777697 by -1 retitle: ITP: berkeley-express -- Streaming quantification for high-throughput sequencing Package is in the NEW queue under new name: https://ftp-master.debian.org/new/berkeley-express_1.5.1-1.html

Bug#787039: ITP: python-bz2file -- Python library for reading and writing bzip2-compressed files

Package: wnpp Severity: wishlist Owner: Debian Med team X-Debbugs-CC: debian-...@lists.debian.org * Package name: python-bz2file Version : 0.98 Upstream Author : Nadeem Vawda * URL : https://github.com/nvawda/bz2file * License : Apache Programming Lang: Pyt

Bug#778589: ITP: express -- Streaming quantification for high-throughput sequencing

Package: wnpp Severity: wishlist Owner: Debian Med team X-Debbugs-Cc: debian-de...@lists.debian.org, debian-...@lists.debian.org * Package name: express Version : 1.5.1 Upstream Author : Adam Roberts & Lior Pachter * URL : http://bio.math.berkeley.edu/eXpress/index.ht

Bug#778587: ITP: r-cran-blockmodeling -- Generalized and classical blockmodeling of valued networks

Package: wnpp Severity: wishlist Owner: Debian Med team X-Debbugs-Cc: debian-de...@lists.debian.org, debian-...@lists.debian.org * Package name: r-cran-blockmodeling Version : 0.1.8 Upstream Author : Ales Ziberna * URL : http://cran.fhcrc.org/web/packages/blockmodelin

Bug#778586: ITP: r-bioc-ebseq -- R package for RNA-Seq Differential Expression Analysis

Package: wnpp Severity: wishlist Owner: Debian Med team X-Debbugs-Cc: debian-de...@lists.debian.org, debian-...@lists.debian.org * Package name: r-bioc-ebseq Version : 1.6.0 Upstream Author : Ning Leng * URL : https://www.biostat.wisc.edu/~kendzior/EBSEQ/ * License

Bug#778578: ITP: rsem -- RNA-Seq by Expectation-Maximization

Package: wnpp Severity: wishlist Owner: Debian Med team X-Debbugs-Cc: debian-de...@lists.debian.org, debian-...@lists.debian.org * Package name: rsem Version : 1.2.19 Upstream Author : Bo Li * URL : http://deweylab.biostat.wisc.edu/rsem/ * License : GPL-3 Pr

Bug#778489: ITP: jaligner -- implementation of the Smith-Waterman algorithm with Gotoh's improvement

Package: wnpp Severity: wishlist Owner: Debian Med team X-Debbugs-Cc: debian-de...@lists.debian.org, debian-...@lists.debian.org * Package name: jaligner Version : 1.0 Upstream Author : Ahmed Moustafa * URL : http://jaligner.sf.net * License : GPL Programmin

Bug#368931: I've started work on this package

Just three jars for now (+ an embedded collections15): jung-api.jar, jung-graph-impl.jar, and jung-algorithms.jar Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-med/libjung-java.git Vcs-Git: git://anonscm.debian.org/debian-med/libjung-java.git Patches welcome

Bug#778331: ITP: parafly -- parallel command processing using OpenMP

Package: wnpp Severity: wishlist Owner: Debian Med team X-Debbugs-Cc: debian-de...@lists.debian.org, debian-...@lists.debian.org * Package name: parafly Version : 0.0.2013.01.21 Upstream Author : Brian Haas * URL : http://parafly.sourceforge.net * License : BS

Bug#778300: ITP: transdecoder -- find coding regions within transcripts

Package: wnpp Severity: wishlist Owner: Debian Med team X-Debbugs-Cc: debian-de...@lists.debian.org, debian-...@lists.debian.org * Package name: transdecoder Version : 2.0.1 Upstream Author : Brian Haas * URL : http://transdecoder.github.io/ * License : BSD-3-

Bug#692498: ITP: bamtools -- C++ API and toolkit for manipulating BAM (genome alignment) files

And here's the package, https://github.com/mr-c/bamtools/tree/debian My packaging skills are a bit rusty, so your feedback would be appreciated. On Tue, Nov 6, 2012 at 1:28 PM, Michael Crusoe wrote: > X-Debbugs-Cc: debian-...@lists.debian.org > X-Debbugs-Cc: debian-de...@lists

Bug#692498: ITP: bamtools -- C++ API and toolkit for manipulating BAM (genome alignment) files

X-Debbugs-Cc: debian-...@lists.debian.org X-Debbugs-Cc: debian-de...@lists.debian.org Package: wnpp Severity: wishlist Owner: debian-...@lists.debian.org * Package name: bamtools Version : 2.2 Upstream Author : Derek Barnett * URL : https://github.com/pezmaster31/bamto

Bug#692332: ITP: sga -- A de novo genome assembler based on the concept of string graphs. The major goal of SGA is to be very memory efficient, which is achieved by using a compressed representation o

Package: wnpp Severity: wishlist Owner: "Michael R. Crusoe" * Package name: sga Version : 0.9.35 Upstream Author : Jared Simpson * URL : https://github.com/jts/sga * License : GPLv3 Programming Lang: C++ Description : A de novo genome assembler based o