Re: Issue about mutual dependencies for aparapi
On Fri, 5 Jun 2020, Pierre Gruet wrote: > valuable. I think I will first try gbp with a MUT package. Your complimentary reminder that gbp is merely an add-on which some packagers wish to use but not a standard Debian tool, and things work very well without it. (In case gbp indeed still is without support for MUT packages…) bye, //mirabilos -- tarent solutions GmbH Rochusstraße 2-4, D-53123 Bonn • http://www.tarent.de/ Tel: +49 228 54881-393 • Fax: +49 228 54881-235 HRB 5168 (AG Bonn) • USt-ID (VAT): DE122264941 Geschäftsführer: Dr. Stefan Barth, Kai Ebenrett, Boris Esser, Alexander Steeg
Re: Issue about mutual dependencies for aparapi
Hello, Le 04/06/2020 à 22:36, Thorsten Glaser a écrit : > On Thu, 4 Jun 2020, Mechtilde wrote: > >> This is an outdated information. You can collect all source tar.gz >> together in to one orig.tar.xz. In the d/gbp.conf you configure a > > DON’T DO THAT. > > MUTs (multi-origtgz) were invented for a good reason. > > bye, > //mirabilos > Thanks to everyone for the advice and links about this issue! I understand there are various solutions that can be implemented and are valuable. I think I will first try gbp with a MUT package. All the best, Pierre
Re: Perl issues with ensembl-vep
Hi Étienne, On Fri, Jun 05, 2020 at 09:27:41PM +0200, Étienne Mollier wrote: > Hi Andreas, > > > > > > https://salsa.debian.org/med-team/ensembl-vep/-/blob/master/debian/changelog > > > > Sure, let's have a look! :) > > Following up on what I mentionned during today's Jitsi meeting, > just for the record, from the note you left into the changelog: A, I just got ensembl (without -vep). Good you insist here! ;-) > > 1. Can't locate Bio/EnsEMBL/Registry.pm in @INC (you may need > > to install the Bio::EnsEMBL::Registry module) > > Said module turned out to be available in the EnsEMBL Perl core > API, which is available on Github: > > > https://github.com/Ensembl/ensembl/blob/release/100/modules/Bio/EnsEMBL/Registry.pm > https://github.com/Ensembl/ensembl > > and turned out to be quite a challenge to package some time ago: > > https://salsa.debian.org/med-team/ensembl/ May be we should just isolate this module somehow. Packaging whole ensembl seems to much effort. > I fear I'm short on energy for heavy packaging tasks right at > the moment, but for the record, so that it's documented somehow. Thanks a lot also for adding this information to d/changelog. Kind regards Andreas. -- http://fam-tille.de
Re: Perl issues with ensembl-vep
Hi Andreas, Étienne Mollier, on 2020-05-28 20:35:53 +0200: > Andreas Tille, on 2020-05-28 11:42:34 +0200: > > On Thu, May 28, 2020 at 09:56:29AM +0200, Andreas Tille wrote: > > > I'm currently busy with what > > > is called vep in this list but addressed by conda as ensembl-vep which > > > I'll use as package name as well. > > > > I've added ensembl-vep to Salsa[1] but I'd be happy if somebody else > > could pick up this. I've added the needed todos in changelog: > > > > > > https://salsa.debian.org/med-team/ensembl-vep/-/blob/master/debian/changelog > > Sure, let's have a look! :) Following up on what I mentionned during today's Jitsi meeting, just for the record, from the note you left into the changelog: > 1. Can't locate Bio/EnsEMBL/Registry.pm in @INC (you may need > to install the Bio::EnsEMBL::Registry module) Said module turned out to be available in the EnsEMBL Perl core API, which is available on Github: https://github.com/Ensembl/ensembl/blob/release/100/modules/Bio/EnsEMBL/Registry.pm https://github.com/Ensembl/ensembl and turned out to be quite a challenge to package some time ago: https://salsa.debian.org/med-team/ensembl/ I fear I'm short on energy for heavy packaging tasks right at the moment, but for the record, so that it's documented somehow. Take care, -- Étienne Mollier Fingerprint: 5ab1 4edf 63bb ccff 8b54 2fa9 59da 56fe fff3 882d Help find cures against the Covid-19 ! Give CPU cycles: * Rosetta@home: https://boinc.bakerlab.org/rosetta/ * Folding@home: https://foldingathome.org/ signature.asc Description: PGP signature
Help needed: Bug#962292: ITP: flye -- de novo assembler for single molecule sequencing reads using repeat graphs
Control: tags -1 help Hi, I made some progress with this package and I actually expected it to work but there seems to be some issue with a minimap2 call. So if you clone the repository, build and install the package please follow the docs/USAGE.md document for testing by wget https://zenodo.org/record/1172816/files/E.coli_PacBio_40x.fasta flye --pacbio-raw E.coli_PacBio_40x.fasta --out-dir out_pacbio --genome-size 5m --threads 4 For me it runs a couple of minutes but than it exits with an error which is logged here: tail out_pacbio/flye.log [2020-06-05 18:48:06] INFO: Generating sequence [2020-06-05 18:51:45] DEBUG: Writing FASTA [2020-06-05 18:51:45] DEBUG: Peak RAM usage: 2 Gb ---End assembly log [2020-06-05 18:51:45] root: DEBUG: Disjointigs length: 4888051, N50: 4850514 [2020-06-05 18:51:45] root: INFO: >>>STAGE: consensus [2020-06-05 18:51:45] root: INFO: Running Minimap2 [2020-06-05 18:51:45] root: ERROR: Error running minimap2, terminating. See the alignment error log for details: out_pacbio/10-consensus/minimap.stderr [2020-06-05 18:51:45] root: ERROR: Command '['/bin/bash', '-c', 'set -o pipefail; /usr/bin/minimap2 out_pacbio/10-consensus/chunks.fasta E.coli_PacBio_40x.fasta -x map-pb -t 4 -a -p 0.5 -N 10 --sam-hit-only -L -Q --secondary-seq | /usr/bin/samtools view -T out_pacbio/10-consensus/chunks.fasta -u - | /usr/bin/samtools sort -T out_pacbio/10-consensus/sort_200605_185145 -O bam -@ 4 -l 1 -m 1G']' returned non-zero exit status 1. [2020-06-05 18:51:45] root: ERROR: Pipeline aborted (explicit paths shortened) I tried the very command that is actually run: $ /usr/bin/minimap2 out_pacbio/10-consensus/chunks.fasta E.coli_PacBio_40x.fasta -x map-pb -t 4 -a -p 0.5 -N 10 --sam-hit-only -L -Q --secondary-seq [ERROR] unknown option in "E.coli_PacBio_40x.fasta" Exit code: 1 It seems to me as if the code is creating a broken minimap2 command and I wonder whether anybody could fix this. BTW, it would also help if we could find a shorter sequence example than the given one that could be used for an autopkgtest. For my taste its unnecessarily long. Thanks for any help Andreas. [1] https://salsa.debian.org/med-team/flye On Fri, Jun 05, 2020 at 07:39:20PM +0200, Andreas Tille wrote: > Package: wnpp > Severity: wishlist > > Subject: ITP: flye -- de novo assembler for single molecule sequencing reads > using repeat graphs > Package: wnpp > Owner: Andreas Tille > Severity: wishlist > > * Package name: flye > Version : 2.7.1 > Upstream Author : , The Regents of the University of California > * URL : https://github.com/fenderglass/Flye > * License : BSD-3-Clause > Programming Lang: C > Description : de novo assembler for single molecule sequencing reads > using repeat graphs > Flye is a de novo assembler for single molecule sequencing reads, such > as those produced by PacBio and Oxford Nanopore Technologies. It is > designed for a wide range of datasets, from small bacterial projects to > large mammalian-scale assemblies. The package represents a complete > pipeline: it takes raw PacBio / ONT reads as input and outputs polished > contigs. Flye also has a special mode for metagenome assembly. > > Remark: This package is maintained by Debian Med Packaging Team at >https://salsa.debian.org/med-team/flye > > ___ > Debian-med-packaging mailing list > debian-med-packag...@alioth-lists.debian.net > https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-packaging -- http://fam-tille.de
[RFS] solvate
Hi, I've added autopkgtests for solvate. It builds in a clean chroot with passing tests. My changes have been pushed to the team-repo here[1]. Needs review and sponsorship. [1]: https://salsa.debian.org/med-team/solvate Regards, Nilesh
Creating official Debian package of flappie
Hi Tim, the Debian Med team is a team inside Debian that is packaging free software in life sciences and medicine. Currently we are running a COVID-19 effort to package software that is relevant to fight the pandemie. Someone has put flappie[1] on our todo list and so I injected some initial packaging code in the Debian packaging git[2]. When I was checking the code I stumbled upon the string CMakeLists.txt:set (CPACK_DEBIAN_PACKAGE_MAINTAINER "Tim Massingham ") which motivated me to contact you before continuing. Are you interested in cooperation to create an official flappie package? We are working with several upstreams of software together quite successfully and I'd be happy to grant you commit permissions to this repository if you like to become involved. Kind regards Andreas. [1] https://github.com/nanoporetech/flappie [2] https://salsa.debian.org/med-team/flappie -- http://fam-tille.de
Re: Workflows and their dependencies - Jun's dep spreadsheet - status
> I started to really like that spreadsheet - have also added bcbio to the list of pending workflow engines. I don't really know where this spreadsheet could go. I also like the spreadsheet too! Currently the spreadsheet is managed on my personal account's Google Drive. It's happy to move it to a more appropriate place such as Debian's Google Drive in the future or any time. > It is useful for us now, but I wonder what kind of questions it can help answering - is it a similarity score for workflows implementations? A flexibility score for workflows? An indication for packages to be substituteable? Something to rank significance for all those packages left uncited in scientific publications? Once all the packages are in Debian, we can auto-create that matrix. But now? Any idea on the bio.tools front about this? I do not understand what "similarity score" and "flexibility score" mean. And I have no idea about your other questions. Can you explain more about it? Jun -- Jun | He - His - Him
Re: Videoconference today Friday 2020-06-05 18:00 UTC (Was: For those who want to keep on contributing (Was: Debian @ COVID-19 Biohackathon (April 5-11, 2020)))
Hi, for those who would like to join our next videomeeting it will happen at https://www.timeanddate.com/worldclock/fixedtime.html?msg=Debian+CoViD-19+Biohackathon+Video+Conference&iso=20200605T20&p1=37&ah=1 Please note: The MiniDebConf online has proven that the Jitsi instance running by Debian Social team works nicely so from today on we'll meet here: https://jitsi.debian.social/DebianMedCovid19 BTW, if you want to watch my talk I gave at MiniDebConf online right about the topic ouf our sprint you can find my concept text online[0]. The video is linked from there as well. (Sorry about the 5-10min interruption. Since five years we had the first power cut-off right in the time when I was speaking - Murphy is calling ...) These weekly video meetings were started in the Debian Med Biohackathon[1]. The topic is what contributors have done in the past week and to coordinate the work for next week. Despite the one week of hackathon is over Covid-19 is not and there is a lot of remaining work to do. Newcomers are always welcome. BTW, we are discussing another dedicated COVID-19 sprint week. See you Andreas. [0] https://people.debian.org/~tille/talks/20200531_minidebconf_online/ [1] https://lists.debian.org/debian-devel-announce/2020/03/msg00010.html -- http://fam-tille.de
