Re: libjung (again)

Yes, the package should use libcolt-free-java. You probably saw the nutty lengths I was going to to try to keep nonfree dependencies out. Should be a lot more straightforward now. On Fri, Aug 21, 2015, 04:29 olivier sallou osal...@debian.org wrote: hi Mickael, I have a question regarding your

Re: libjung-free-java uploaded

Wonderful, thank you! On Fri, Aug 21, 2015, 07:48 olivier sallou osal...@debian.org wrote: Hi, I have made a few updates (typo, cleanup, ...) and uploaded the package. git repo is up-to-date Olivier

Re: libjung (again)

...) and upload it, is that fine ? After we should go on for trinity. I made local changes to patch it to compile with gcc5 as well as a patch to compile with jung. Le ven. 21 août 2015 à 13:55, Michael R. Crusoe mcru...@msu.edu a écrit : Yes, the package should use libcolt-free-java. You probably saw

Bug#800412: ITP: transrate-tools -- command line tool used by transrate to process BAM files

Package: wnpp Owner: "Debian Med Team" Severity: wishlist X-Debbugs-CC: debian-med@lists.debian.org * Package name: transrate-tools Version : 1.0.0 Upstream Author : Richard Smith-Unna & Chris Boursnell * URL :

Bug#828196: ITP: r-cran-globals -- R package: Identify Global Objects in R Expressions

Package: wnpp Severity: wishlist Owner: Debian Med team * Package name: r-cran-globals Version : 0.6.1 Upstream Author : Henrik Bengtsson * URL : https://github.com/HenrikBengtsson/globals * License : LGPL-2.1+

Bug#828176: ITP: cnvkit -- Copy number variant detection from targeted DNA sequencing

Package: wnpp Severity: wishlist Owner: Debian Med team * Package name: cnvkit Version : 0.7.11 Upstream Author : Eric Talevich * URL : http://cnvkit.readthedocs.io/ * License : Apache-2.0 Programming

Bug#828189: ITP: r-bioc-dnacopy -- R package: DNA copy number data analysis

Package: wnpp Severity: wishlist Owner: Debian Med team * Package name: r-bioc-dnacopy Version : 1.46.0 Upstream Author : Venkatraman E. Seshan * URL :

Bug#828197: ITP: r-cran-future -- R package: A Future API for R

Package: wnpp Severity: wishlist Owner: Debian Med team * Package name: r-cran-future Version : 1.0.0 Upstream Author : Henrik Bengtsson * URL : https://github.com/HenrikBengtsson/future * License : LGPL-2.1+

Bug#828690: ITP: r-cran-pscbs -- R package: Analysis of Parent-Specific DNA Copy Numbers

Package: wnpp Severity: wishlist Owner: Debian Med team * Package name: r-cran-pscbs Version : 0.61.0 Upstream Author : Henrik Bengtsson * URL : https://github.com/HenrikBengtsson/PSCBS * License : GPL-2+

Bug#828184: ITP: r-cran-r.cache -- R package: Fast and Light-Weight Caching of Objects and Results

Package: wnpp Severity: wishlist Owner: Debian Med team * Package name: r-cran-r.cache Version : 0.12.0 Upstream Author : Henrik Bengtsson * URL : https://github.com/HenrikBengtsson/R.cache * License : LGPL (>=

Bug#828194: ITP: r-cran-listenv -- R package: Environments Behaving (Almost) as Lists

Package: wnpp Severity: wishlist Owner: Debian Med team * Package name: r-cran-listenv Version : 0.6.0 Upstream Author : Henrik Bengtsson * URL : https://github.com/HenrikBengtsson/listenv * License : LGPL 2.1+

Bug#828796: ITP: r-bioc-geneplotter -- R package of functions for plotting genomic data

Package: wnpp Severity: wishlist Owner: Debian Med team * Package name: r-bioc-geneplotter Version : 1.50.0 Upstream Author : Bioconductor Package Maintainer * URL :

Bug#813827: ITP: python-rdflib-jsonld -- rdflib extension adding JSON-LD parser and serializer

Package: wnpp Owner: Debian Med team Severity: wishlist * Package name: python-rdflib-jsonld Version : 0.3 Upstream Author : RDFLib Team * URL : https://github.com/RDFLib/rdflib-jsonld * License : BSD Programming Lang: Python

Bug#814000: ITP: cwltool -- Common workflow language reference implementation

Package: wnpp Severity: wishlist Owner: Debian Med team * Package name: cwltool Version : 1.0.20160203221531 Upstream Author : Common Workflow Language working group * URL :

Bug#814050: ITP: varna -- Visualization Applet for RNA

Package: wnpp Owner: Debian Med team Severity: wishlist * Package name: varna Version : 3-93 Upstream Author : Kevin Darty, Alain Denise and Yann Ponty * URL : http://varna.lri.fr/ * License : GPL-3

Bug#813839: ITP: python-schema-salad -- rdflib extension adding JSON-LD parser and serializer

Package: wnpp Severity: wishlist Owner: Debian Med team * Package name: python-schema-salad Version : 1.6.2016020448 Upstream Author : Common workflow language working group * URL :

Bug#817056: ITP: python-typing -- Type Hints for Python

See https://www.python.org/dev/peps/pep-0484/#suggested-syntax-for-python-2-7-and-straddling-code Pe 8 mar. 2016 06:24, "Brian May" <b...@debian.org> a scris: > "Michael R. Crusoe" <cru...@ucdavis.edu> writes: > > > This is a backport of the standard l

Re: bamtools_2.4.0+dfsg-4_amd64.changes REJECTED

> > Please feel free to respond to this email if you don't understand why > your files were rejected, or if you upload new files which address our > concerns. > > -- Michael R. Crusoe CWL Community Engineer cru...@ucdavis.edu Common Workflow Language project

Bug#817056: ITP: python-typing -- Type Hints for Python

Package: wnpp Severity: wishlist Owner: Debian Med team * Package name: python-typing Version : 3.5.0.1 Upstream Author : Guido van Rossum, Jukka Lehtosalo, Łukasz Langa * URL :

Bug#817056: ITP: python-typing -- Type Hints for Python

:38 PM, Scott Kitterman <deb...@kitterman.com> wrote: > On Monday, March 07, 2016 09:01:30 AM Michael R. Crusoe wrote: > > Package: wnpp > > Severity: wishlist > > Owner: Debian Med team <debian-med@lists.debian.org> > > > > * Package name:

Re: Parallel software performance analysis

; Numerical Algorithms Group (NAG) > > Peter House, Oxford Street, Manchester, M1 5AN > > +44 (0)161 602 3821 > > http://nag.co.uk/ > > > > > > > -- Michael R. Crusoe CWL Community Engineer cru...@ucdavis.edu Common Workflow Language projectUniversity of California, Davis https://impactstory.org/MichaelRCrusoe http://twitter.com/biocrusoe

Bug#823512: ITP: mypy -- Optional static typing for Python

Package: wnpp Severity: wishlist Owner: Debian Med team * Package name: mypy Version : 0.3.1 Upstream Author : Jukka Lehtosalo * URL : http://www.mypy-lang.org/ * License : MIT Programming Lang: Python

Bug#828850: ITP: r-bioc-deseq2 -- R package for RNA-Seq Differential Expression Analysis

Package: wnpp Severity: wishlist Owner: Debian Med team * Package name: r-bioc-deseq2 Version : 1.12.3 Upstream Author : Michael Love * URL : https://bioconductor.org/packages/DESeq2 * License :

Bug#834592: ITP: hisat2 -- graph-based alignment of short nucleotide reads to many genomes

Package: wnpp Severity: wishlist Owner: Debian Med team * Package name: hisat2 Version : 2.0.4 Upstream Author : HISAT2 team * URL : https://ccb.jhu.edu/software/hisat2/index.shtml * License : GPL-3+

Bug#841047: ITP: r-hms-dbmi-spp -- GNU R package for processing ChIP-seq & other functional sequencing data

Package: wnpp Severity: wishlist Owner: Debian Med team * Package name: r-hms-dbmi-spp Version : 1.14 Upstream Author : peterK * URL : http://compbio.med.harvard.edu/Supplements/ChIP-seq/ * License

Bug#851358: ITP: python-pybedtools -- Python wrapper around BEDTools for bioinformatics work

Package: wnpp Severity: wishlist Owner: Debian Med team * Package name: python-pybedtools Version : 0.7.8 Upstream Author : Ryan Dale * URL : https://github.com/daler/pybedtools * License : GPL 2+

Bug#851488: ITP: python-gffutils -- Work with GFF and GTF files in a flexible database framework

Package: wnpp Severity: wishlist Owner: Debian Med team * Package name: python-gffutils Version : 0.8.7.1 Upstream Author : Ryan Dale * URL : http://daler.github.io/gffutils/ * License : MIT Programming

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

Package: wnpp Severity: wishlist Owner: Debian Med team * Package name: easel Version : 0.43 Upstream Author : Sean R. Eddy * URL : https://github.com/EddyRivasLab/easel * License : BSD-3-clause Programming

Lack of license for pal2nal

of their software and a better user response. Kind regards and thanks for considering, -- Michael R. Crusoe Co-founder & Lead, Common Workflow Language project <http://www.commonwl.org/> https://impactstory.org/u/-0002-2961-9670 m...@commonwl.org

Bug#890061: ITP: galaxy-lib -- Subset of Galaxy core code base designed to be used

Package: wnpp Severity: wishlist Owner: Debian Med team * Package name: galaxy-lib Version : 17.9.10 Upstream Author : Galaxy Project and Community * URL : https://github.com/galaxyproject/galaxy-lib * License

Bug#890752: ITP: ctdopts -- Gives your Python tools a CTD-compatible interface

Package: wnpp Severity: wishlist Owner: Debian Med team * Package name: ctdopts Version : 1.2 Upstream Author : Andras Szolek et al. * URL : https://github.com/WorkflowConversion/CTDopts * License : GPL-3+ Programming Lang:

Bug#890755: ITP: ctdconverter -- Convert CTD files into Galaxy tool and CWL CommandLineTool files

Package: wnpp Severity: wishlist Owner: Debian Med team * Package name: ctdconverter Version : 2.0 Upstream Author : WorkflowConversion * URL : https://github.com/WorkflowConversion/CTDConverter/ * License : GPL-3 / Apache-2.0

Bug#911076: ITP: libdeflate -- fast, whole-buffer DEFLATE-based compression and decompression

Package: wnpp Severity: wishlist Owner: Debian Med team * Package name: libdeflate Version : 1.0 Upstream Author : Eric Biggers * URL : https://github.com/ebiggers/libdeflate * License : MIT Programming Lang: C Description : fast, whole-buffer

Bug#918343: RM: tnseq-transit [arm64 armel armhf i386 mips mips64el mipsel ppc64el s390x] -- ANAIS; has missing (build-)dependency on amd64 only package

Package: ftp.debian.org Severity: normal Hello, This package was missing a source and binary dependency on BWA which is only built for amd64. Please remove the non-amd64 binary packages of tnseq-transit so that the new Debian package can migrate from sid to testing. Thanks!

Bug#919570: ITP: python-mypy-extensions -- Experimental type system extensions for mypy typechecker (Python 3)

Package: wnpp Severity: wishlist Owner: Debian Med team * Package name: python-mypy-extensions Version : 0.4.1 Upstream Author : Jukka Lehtosalo and contributors * URL : https://github.com/python/mypy_extensions/ * License : Expat Programming Lang: Python

Bug#919681: ITP: sourmash -- tools for comparing DNA sequences with MinHash sketches

Package: wnpp Severity: wishlist Owner: Debian Med team * Package name: sourmash Version : 2.0.0~a11 Upstream Author : C. Titus Brown , Luiz C. Irber, Jr * URL : http://sourmash.readthedocs.io/en/latest/ * License : BSD-3-Clause Programming Lang: Python,

Bug#915852: ITP: bagit -- Create and validate BagIt packages

Package: wnpp Severity: wishlist Owner: Debian Med team * Package name: bagit Version : 1.7.0 Upstream Author : Ed Summers * URL : https://libraryofcongress.github.io/bagit-python/ * License : CC0 Programming Lang: Python Description : Create and

Bug#914991: RM: testing/htslib [i386 hurd-i386 kfreebsd-i386] -- ANAIS; ROM *i386 no longer supported upstream

Package: ftp.debian.org Severity: normal Owner: Debian Med team Upstream report: https://github.com/samtools/htslib/issues/565 The provided workaround does not fix the issue and it has now been a year with no progress Thanks!

Bug#918871: RM: python-bd2k -- ROM; No longer needed by Debian, abandoned upstream

Package: ftp.debian.org Severity: normal Control: block -1 by 918869 To be removed after python-cgloud, #918869 [1] for the same reasons: python-bd2k was originally packaged as a dependency of Toil[2], but by the time Toil arrived in the NEW queue it had dropped its dependency on python-bd2k.

Bug#918869: RM: python-cgcloud -- ROM; No longer need by Debian, abandoned upstream

Package: ftp.debian.org Severity: normal This was originally packaged as a dependency of Toil[1], but by the time that made it to the NEW queue Toil had dropped its dependency on cgcloud. [1] https://ftp-master.debian.org/new/toil_3.18.0-1.html

Bug#918117: RM: python-htseq-doc/0.6.1p1-4

Package: release.debian.org Severity: normal User: release.debian@packages.debian.org Usertags: rm Hello, Please remove python-htseq-doc from the testing distribution. It is no longer build by the source package and its presence is blocking a migration from unstable. Thanks! -- System

Bug#918251: d-shlibs: devlibs error: There is no package matching [libsvm3-dev] and noone provides it

Package: d-shlibs Version: 0.83 Severity: normal Dear Maintainer, While fixing the missing linkage to libsvm in libpsortb I received the following message: devlibs error: There is no package matching [libsvm3-dev] and noone provides it, please report bug to d-shlibs maintainer So here I am :-)

Bug#923386: RM: python-schema-salad & python-typing-extensions -- ROM; binary packages for Python 2 no longer needed

Package: ftp.debian.org Severity: normal Hello, Please remove the binary package python-schema-salad version 2.6.20171201034858-3 and the binary package python-typing-extensions version 3.7.2-1 from the archive. We now only need and build for Python 3 and these packages are holding up the

Bug#944735: RM: rapmap [arm64 mips64el ppc64el] -- ANAIS; non-amd64 not supported by upstream

Package: ftp.debian.org Severity: normal Thanks!

Bug#944905: RM: jellyfish [arm64 mips64el ppc64el riscv64] -- ANAIS; Non-AMD64 not supported by upstream

Package: ftp.debian.org Severity: normal Thanks!

Bug#944785: ITP: pufferfish -- An efficient index for the colored, compacted, de Bruijn graph

Package: wnpp Severity: wishlist Subject: ITP: pufferfish -- An efficient index for the colored, compacted, de Bruijn graph Package: wnpp Owner: Michael R. Crusoe Severity: wishlist * Package name: pufferfish Version : 1.0.0 Upstream Author : , 2016 Rob Patro, Avi Srivastava

Bug#946468: ITP: libbio-variation-perl -- BioPerl variation-related functionality

Package: wnpp Severity: wishlist Subject: ITP: libbio-variation-perl -- BioPerl variation-related functionality Package: wnpp Owner: Michael R. Crusoe Severity: wishlist * Package name: libbio-variation-perl Version : 1.7.4 Upstream Author : Copyright: Allen Day , Heikki

Bug#946266: ITP: libbio-db-swissprot-perl -- Database object interface to SwissProt retrieval

Package: wnpp Severity: wishlist Subject: ITP: libbio-db-swissprot-perl -- Database object interface to SwissProt retrieval Package: wnpp Owner: Michael R. Crusoe Severity: wishlist * Package name: libbio-db-swissprot-perl Version : 1.7.3 Upstream Author : Copyright: Jason

Bug#946269: ITP: libbio-db-refseq-perl -- Database object interface for RefSeq retrieval

Package: wnpp Severity: wishlist Subject: ITP: libbio-db-refseq-perl -- Database object interface for RefSeq retrieval Package: wnpp Owner: Michael R. Crusoe Severity: wishlist * Package name: libbio-db-refseq-perl Version : 1.7.3 Upstream Author : Copyright: Heikki Lehvaslaiho

Bug#946272: ITP: libbio-procedural-perl -- Simple low-dependency procedural interfaces to BioPerl

Package: wnpp Severity: wishlist Subject: ITP: libbio-procedural-perl -- Simple low-dependency procedural interfaces to BioPerl Package: wnpp Owner: Michael R. Crusoe Severity: wishlist * Package name: libbio-procedural-perl Version : 1.7.4 Upstream Author : Copyright: Ewan

Bug#950607: ITP: bwa-mem2 -- the next version of the bwa-mem algorithm in bwa

Package: wnpp Severity: wishlist Subject: ITP: bwa-mem2 -- the next version of the bwa-mem algorithm in bwa Package: wnpp Owner: Michael R. Crusoe Severity: wishlist * Package name: bwa-mem2 Version : 2.0~pre2 Upstream Author : , Vasimuddin Md, Sanchit Misra, Intel Corporation

Bug#951072: ITP: htscodecs -- Custom compression for CRAM and others

Package: wnpp Severity: wishlist Subject: ITP: htscodecs -- Custom compression for CRAM and others Package: wnpp Owner: Michael R. Crusoe Severity: wishlist * Package name: htscodecs Version : 0.5 Upstream Author : , Genome Research Ltd. * URL : https://github.com

Bug#948518: RM: grabix [s390x] -- ROM; upstream htslib broke s390x and is holding up several transitions

Package: ftp.debian.org Severity: important A follow on to https://bugs.debian.org/948092 as I forgot to include grabix in the list; this appears to be holding up the transition to testing if I'm reading https://release.debian.org/britney/update_output.txt correctly. Thanks!

Bug#948092: RM: htslib, delly, fastqtl, kallisto, libtabixpp, qtltools, rsem, samtools, segemehl, shapeit4, stringtie, stacks [s390x] -- ROM; upstream htslib broke s390x and is holding up several tran

Package: ftp.debian.org Severity: normal Dear ftp.debian.org people, htslib FTBFS on big-endian systems https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=947462 and this is blocking the following transitions: auto-htslib, python2-rm, python3.8, and auto-pbbam I propose we delete the affected

Bug#948329: ITP: libsys-info-driver-linux-perl -- Linux driver for Sys::Info

Package: wnpp Severity: wishlist Subject: ITP: libsys-info-driver-linux-perl -- Linux driver for Sys::Info Package: wnpp Owner: Michael R. Crusoe Severity: wishlist * Package name: libsys-info-driver-linux-perl Version : 0.7905 Upstream Author : , Burak Gursoy * URL

Bug#948325: ITP: libbio-featureio-perl -- Modules for reading, writing, and manipulating sequence features

Package: wnpp Severity: wishlist Subject: ITP: libbio-featureio-perl -- Modules for reading, writing, and manipulating sequence features Package: wnpp Owner: Michael R. Crusoe Severity: wishlist * Package name: libbio-featureio-perl Version : 1.6.905 Upstream Author : BioPerl

Bug#948330: ITP: libsys-info-perl -- Fetch information from the host system

Package: wnpp Severity: wishlist Subject: ITP: libsys-info-perl -- Fetch information from the host system Package: wnpp Owner: Michael R. Crusoe Severity: wishlist * Package name: libsys-info-perl Version : 0.7811 Upstream Author : , Burak Gursoy * URL : https

Debian @ COVID-19 Biohackathon (April 5-11, 2020)

, Michael R. Crusoe on behalf of the Debian-Med team

ELIXIR & Debian(-Med)

I'd like to see Debian/Debian-Med become an official ELIXIR Core Data Resource during the next cycle. https://f1000research.com/articles/5-2422/v2 has the details about the last review round. Would anyone like to help me with the application process? Thanks,

Re: [COVID-19 Hackathon] Bazel build system pending NEW

On Mon, Aug 24, 2020 at 4:51 PM Olek Wojnar wrote: > Hi Mo, > > Sorry about the slow reply, I've been a bit buried with emails and I'm not > answering them as well as I would like. :( > > On Wed, Aug 19, 2020 at 12:40 AM Mo Zhou wrote: > >> Hi Olek, >> >> What a good news! Your hardword is much

Re: Videoconference Saturday 2020-10-17 18:00 UTC (Was: For those who want to keep on contributing (Was: Debian @ COVID-19 Biohackathon (April 5-11, 2020))

On Fri, Oct 16, 2020 at 3:50 PM Andreas Tille wrote: > Hi, > > the video conferences of the Debian Med team have shifted to two > meetings per month now. Do enable different people joing we shift > weekdays by simply meeting on every > >2th and 17th > > of a month. So the next meeting is

Re: Happy! Fwd: pigx-rnaseq_0.0.10+ds-1_amd64.changes ACCEPTED into unstable, unstable

On Sat, Oct 24, 2020 at 4:18 AM Steffen Möller wrote: > Dear all, > > We got our first RNA-seq pipeline as a package in Debian. Many thanks go > to all who contributed. I need to let this sink in for a while, which > coincides with being distracted with what I am paid to do :o) And then > let's

Re: RFS: snap-aligner

Done. I also ran `routine-update -f` which did a number of cleanups. It would be nice if you ran that yourself in the future :-) I also fixed a spelling error in the upstream source that lintian now notices. Uploaded. Thanks! On Thu, Jul 9, 2020 at 8:52 AM Pranav Ballaney wrote: > Hi, > I've

Re: "Computational Strategies to Combat COVID-19: Useful Tools to Accelerate SARS-CoV-2 and Coronavirus Research"

Alas the DOI is too new! It will work later. https://www.preprints.org/manuscript/202005.0376/v1 works today. -- Michael R. Crusoe On Thu, Jun 4, 2020, 20:11 Michael R. Crusoe wrote: > Pardon me, https://doi.org/10.0.81.208/preprints202005.0376.v1 is the > correct link > > --

Re: "Computational Strategies to Combat COVID-19: Useful Tools to Accelerate SARS-CoV-2 and Coronavirus Research"

Pardon me, https://doi.org/10.0.81.208/preprints202005.0376.v1 is the correct link -- Michael R. Crusoe On Thu, Jun 4, 2020, 20:06 Michael R. Crusoe wrote: > https://10.20944/preprints202005.0376.v1 > > -- > Michael R. Crusoe >

"Computational Strategies to Combat COVID-19: Useful Tools to Accelerate SARS-CoV-2 and Coronavirus Research"

https://10.20944/preprints202005.0376.v1 -- Michael R. Crusoe

Re: "Computational Strategies to Combat COVID-19: Useful Tools to Accelerate SARS-CoV-2 and Coronavirus Research"

On Thu, Jun 4, 2020 at 9:07 PM Andreas Tille wrote: > Hi Michael, > > On Thu, Jun 04, 2020 at 08:12:01PM +0200, Michael R. Crusoe wrote: > > Alas the DOI is too new! > Here is the working DOI link: https://doi.org/10.20944/preprints202005.0376.v1 > > >

Re: Videoconference today Friday 2020-06-12 18:00 UTC (Was: For those who want to keep on contributing (Was: Debian @ COVID-19 Biohackathon (April 5-11, 2020)))

Thank you Andreas for announcing the meeting, and thanks to the attendees for their participation. Our meeting notes are at https://storm.debian.net/shared/6NfKT87njAmCg3tr_uhkE2Qp9SQhVxy8mwD1fQUzfMy On Fri, Jun 12, 2020 at 1:07 PM Andreas Tille wrote: > Hi, > > for those who would like to join

Notes from the 2020-07-17 Bazel-Debian-Google meeting

! -- Michael R. Crusoe

Re: armhf regressions in a few packages

Bus error tends to be about unaligned memory access. I personally don't fix such issues, but I do report them upstream and then disable that architecture for building. For bioinformatics, there is no reason to support armhf. -- Michael R. Crusoe On Sat, Nov 21, 2020, 22:11 Nilesh Patra wrote

Re: Project idea: port GKL to non-x86

Should I upload gkl (after some routine-update)? > Already done :-) > I also wonder why that package is in java-team if only Debian Med > members are working on it and its relevant for Debian Med. > I don't know! -- Michael R. Crusoe

Re: shapeit4 and AVX2

ance gain for that > software when extensions are available? > > Michael R. Crusoe, on 2020-11-05 21:26:30 +0100: > > As documented at > > https://wiki.debian.org/SIMDEverywhere > > shapeit4 provides a dedicated code path for "-mfma -mavx2" build > opt

Re: [Debian-med-packaging] kmc_3.1.1+dfsg-2_source.changes ACCEPTED into unstable

s: > > kmc (3.1.1+dfsg-2) unstable; urgency=medium > > . > >* Team upload. > > . > >[ Étienne Mollier ] > >* Remove non-portable -m64 flag put back by error. > > . > >[ Michael R. Crusoe ] > >* Support non-x86 systems via l

Re: Reminders about using SIMDe

On Wed, 27 Jan 2021 at 10:59, Nilesh Patra wrote: > Hi Michael > > On Wed, 27 Jan 2021 at 14:51, Michael R. Crusoe wrote: > >> Hello, >> >> After scheduling a binary rebuild[0] of packages using libsimde-dev >> > > First off, thanks a lot for doing t

Re: hyphy - amd64 Test failures

Thanks both :-) Yeah, I remember thinking about this, but in my rush I forgot. I've pulled the installation of the simd-dispatcher script into override_dh_install-indep. Cheers, On Sun, 31 Jan 2021 at 00:41, Juhani Numminen wrote: > Hi Nilesh and Michael, > > On Sat, 30 Jan 2021, 23.24 Nilesh

Re: vcflib does not install scripts - missing bgziptabix

Thanks for catching this, Steffen! A bug report would be appreciated, so we don't lose track of this. -- Michael R. Crusoe On Sun, May 23, 2021, 14:51 Steffen Möller wrote: > Hello, > > cudaSV needs bgziptabix to be happy, which is how I became aware fo all > the scripts in >

Re: Python louvain packages naming confusion.

cally run autodep8 which > fails because the import name is community and not louvain. > In the short term I recommend fixing this by adding a file to the Debian python-louvain package named "debian/tests/autopkgtest-pkg-python.conf" with the contents "import_name = community" -- Michael R. Crusoe

Reminders about using SIMDe

://bugs.debian.org/cgi-bin/bugreport.cgi?bug=980997 [1] https://github.com/simd-everywhere/simde-no-tests [2] https://github.com/simd-everywhere/simde/blob/master/amalgamate.py -- Michael R. Crusoe

Some patches for gmap from Debian

? We would like to link to it, and we could also provide these and future patches in the form of pull(merge)-requests. Many thanks for providing your software under an open source license. Cheers, -- Michael R. Crusoe OpenPGP_signature Description: OpenPGP digital signature

2021 Europe* BioHackathon, applications due 2021-04-01

CC'd) -- Michael R. Crusoe

Source-only upload of debmutate 0.35 or 0.36

Hello Jelmer, Can you make a source-only upload of debmutate 0.35-1 or later? This is blocking lintian-brush & routine-updates's migration back into testing. I'm happy to make a NMU, if you wish. Cheers,

Re: Restricting kma architectures to 64 bit?

On Mon, Aug 23, 2021 at 5:32 PM Nilesh Patra wrote: > > > On 8/23/21 9:00 PM, Nilesh Patra wrote: > > Recently I added autopkgtest to the latest version of resfinder, which > uses kma_index binary from src:kma package. That started failing on > > 32 bit architectures[1] > > > > I reported the

Re: ncbi-vdb plans (fixing i386, enabling arm64)

On Tue, Nov 2, 2021 at 3:25 AM Aaron M. Ucko wrote: > sra-sdk in unstable fixes this bug, but is blocked by ncbi-vdb, which > FTBFS on i386 as of the latest release. I have a fix worked out > (disabling vdb3 for now, which AFAICT has no effect on the resulting > binaries), and plans for some

Re: [hamap] Changing HAMAP license to match UniProt (CC-BY-4.0)?

This is wonderful news, thank you very much! On Monday, September 25, 2023, Nicole Redaschi via RT wrote: > Hi Michael, > > I got the go ahead to change the HAMAP license to CC-BY-4.0. We intend to do > this for the next release, which is due on Nov 8. > > Hope that helps! > > Cheers, > Nicole >

Re: CWL media type and file extension now in /etc/mime.types

Great, thank you! I forget, what's the best way to advertise that cwltool and the toil packages can handle those media types? On Sun, May 15, 2022 at 10:22 AM Charles Plessy wrote: > Hello everybody, > > I just updated the media-types package in Sid, which brings (among other > changes) the

Re: [Help] Could someone please have a look at gmap build failure

Here is my fix https://salsa.debian.org/med-team/gmap/-/commit/596beba027da3944b0f45a9ffc9e03d1d9dca5ba On Thu, Jul 13, 2023 at 11:15 AM Michael R. Crusoe < michael.r.cru...@gmail.com> wrote: > Thanks César; I've done much of this already. I'll push my changes shortly > (testing the

Re: [Help] Could someone please have a look at gmap build failure

The real error is at gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2

Re: [Help] Could someone please have a look at gmap build failure

AVX512, it > would be good to create multiple binaries (as we did in VeryFastTree) with > different levels so that modern hardware can take advantage of them while > preserving compatibility. > > El jue, 13 jul 2023 a las 9:36, Michael R. Crusoe (< > michael.r.cru...@gmail.com

Re: [Help] Could someone please have a look at gmap build failure

Hey César, Can you look at the build failures for non-x86? https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1041451 https://buildd.debian.org/status/fetch.php?pkg=gmap=arm64=2023-06-01%2Bds-1=1689254473=0 Note: /<>/build/src/gmap.nosimd does not exist. For faster speed, may want to compile

Re: [Help] One remaining build time error in toil

I thought I patched out all the WDL tests; I suggest adding `WdlToilTest` to the skip list. On Thu, Jul 13, 2023 at 9:42 PM Andreas Tille wrote: > Hi folks, > > before I switch of my laptop for today I'd like to hand over some > remaining build time error in toil: > > ___

In Japan, June 24-July 6

inar -- Michael R. Crusoe OpenPGP_signature Description: OpenPGP digital signature

Re: pychopper has switched to a non-free license in new upstream version

That's a shame. The 2.7.3 release (which is quite small) is still under the original license https://github.com/epi2me-labs/pychopper/compare/v2.7.2...v2.7.3 https://github.com/epi2me-labs/pychopper/releases/tag/v2.7.3 On Thu, Jun 15, 2023 at 5:54 PM Nilesh Patra wrote: > Hi, > > I'm dropping

Re: regarding filtering architectures

This is a great tip, thanks! I've pushed commits that use the provisions from the architecture-properties package to clean up d/control for the following packages: abyss bazel-bootstrap bowtie bowtie2 canu diamond-aligner gmap jellyfish kallisto mmseqs2 pbcopper python-skbio subread On Sun, Mar

Re: Debian-Med policy proposal: 64-bit & little-endian only* for new packages

On 01/04/2024 21.12, Sascha Steinbiss wrote: Hi all, first of all thanks Michael for this idea and also for the elaborate proposal email that outlines the intended way to go quite well. Thanks! [...] Support Debian-Med packages for 32-bit and/or big-endian architectures is not a good

Re: Debian-Med policy proposal: 64-bit & little-endian only* for new packages

On 28/03/2024 14.51, Michael R. Crusoe wrote: Dear colleagues and users, [snip] Fweh, that's a long email. Please do share your feedback here and on the Debian-Med Matrix channel for instant discussions: https://app.element.io/#/room/#debian-med:matrix.org Thank you all for the thoughtful

Re: Debian-Med policy proposal: 64-bit & little-endian only* for new packages

On 29/03/2024 07.21, Andreas Tille wrote: Hi, I'm personally fine with Michaels suggestion in general. :+1: Am Fri, Mar 29, 2024 at 10:13:40AM +0530 schrieb Nilesh Patra: On 28 March 2024 7:21:01 pm IST, "Michael R. Crusoe" wrote: There are also packages inside debian me

Re: Debian-Med policy proposal: 64-bit & little-endian only* for new packages

On 29/03/2024 19.44, Steven Robbins wrote: On Thursday, March 28, 2024 8:51:01 A.M. CDT Michael R. Crusoe wrote: Therefore I personally conclude that: Support Debian-Med packages for 32-bit and/or big-endian architectures is not a good use of our limited resources. I am left with a question

Re: Debian-Med policy proposal: 64-bit & little-endian only* for new packages

On 02/04/2024 07.54, Andreas Tille wrote: Hi, Am Mon, Apr 01, 2024 at 09:12:49PM +0200 schrieb Sascha Steinbiss: New packages that aren't "Architecture: all": 1. Add "architecture-is-64-bit" and "architecture-is-little-endian" to the "Build-Depends" list in "debian/control". Nice, didn't

Re: Debian-Med policy proposal: 64-bit & little-endian only* for new packages

On 29/03/2024 05.43, Nilesh Patra wrote: On 28 March 2024 7:21:01 pm IST, "Michael R. Crusoe" wrote: Alas this is an involved process. If we have to do it a lot, it would be nice if someone writes a tool to automate any aspect of the above! --- Fweh, that's a long email. Pleas

Re: Debian-Med policy proposal: 64-bit & little-endian only* for new packages

On 30/03/2024 01.00, Diane Trout wrote: On Thu, 2024-03-28 at 14:51 +0100, Michael R. Crusoe wrote: Like all policy proposals, this is not meant to be a hard rule for all time. We can and should revisit the issue later! What do you think of the policy being instead of "-med team pac

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