Re: RFS paml - fixed #957659
Hi Julien, Andreas Tille, on 2020-05-10 07:06:09 +0200: > On Sat, May 09, 2020 at 10:32:32PM +0200, Julien Yann Dutheil wrote: > > For once, maybe I can be of some help there. I shall be able to reach the > > author of PAML directly... shall I give it a try? > > Yes, please forward the patch - basically in the interest of the PAML > authors themselves. Sure! In case you're afraid of colliding with Michael or someone else, it's better to have a duplicate entry in a bug tracker, and mark is as such, than no entry at all. :) Kind Regards, -- 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
Re: Tandem Repeats Finder License Terms
Dear Gary, This is amazing! Thank you so much for your decision! Yes please, let us know once the source code is available, so the packaging of Tandem Repeats Finder can start. Kind Regards, Étienne Mollier for the Debian Med Team Gary Benson, on 2020-05-09 16:32:03 -0400: > Dear Étienne, > > I'm making TRF open source with an AGPL license. Hopefully this > will be completed in a week or two. > > I'll send a link to the github repository when it's ready. > > Sincerely, > Gary Benson > > On 5/8/20 1:18 PM, Étienne Mollier wrote: > > Greetings Mr. Gary Benson and Yözen Hernández, > > > > I'm in the process of giving a hand to the Debian Med Team with > > maintaining several applications for the Debian project. In the > > context of the Covid-19 pandemic, the need for easing access to > > applications related to the medical field, notably virology, has > > become dire, and there is a list of projects that has been > > established by the Debian Med Team which is considered a > > priority work, see: > > > > > > https://salsa.debian.org/med-team/community/2020-covid19-hackathon/-/wikis/COVID-19-Hackathon-packages-needing-work > > > > So in this context, I've begun packaging VirusSeeker, initially > > written in the Washington University in St. Louis, and this > > program makes use of RepeatMasker for one of its processing > > steps. This program, in turn, depends on Tandem Repeats Finder. > > However, the current licensing terms are making TRF incompatible > > with integration into the main Debian repository, thus render > > RepeatMasker and VirusSeeker both ineligible to it as well. > > > > I was wondering if it were possible to open the source code of > > TRF, and choose licensing terms that would be compatible with an > > integration into Debian main repository, for instance by using > > the GPL-3 or the MIT license, or whichever terms suits your > > taste among the ones considered DFSG compatible: > > > > https://wiki.debian.org/DFSGLicenses#DFSG-compatible_Licenses > > > > In hope your licensing change will help us all moving forward, > > Kind Regards, signature.asc Description: PGP signature
Re: Tandem Repeats Finder License Terms
Hi, thanks also from me for the really good news. We'll do our best to get it packaged quickly. This will open another set of important packages. Kind regards Andreas. On Sun, May 10, 2020 at 01:26:08PM +0200, Étienne Mollier wrote: > Dear Gary, > > This is amazing! Thank you so much for your decision! > Yes please, let us know once the source code is available, so > the packaging of Tandem Repeats Finder can start. > > Kind Regards, > Étienne Mollier > for the Debian Med Team > > Gary Benson, on 2020-05-09 16:32:03 -0400: > > Dear Étienne, > > > > I'm making TRF open source with an AGPL license. Hopefully this > > will be completed in a week or two. > > > > I'll send a link to the github repository when it's ready. > > > > Sincerely, > > Gary Benson > > > > On 5/8/20 1:18 PM, Étienne Mollier wrote: > > > Greetings Mr. Gary Benson and Yözen Hernández, > > > > > > I'm in the process of giving a hand to the Debian Med Team with > > > maintaining several applications for the Debian project. In the > > > context of the Covid-19 pandemic, the need for easing access to > > > applications related to the medical field, notably virology, has > > > become dire, and there is a list of projects that has been > > > established by the Debian Med Team which is considered a > > > priority work, see: > > > > > > > > > https://salsa.debian.org/med-team/community/2020-covid19-hackathon/-/wikis/COVID-19-Hackathon-packages-needing-work > > > > > > So in this context, I've begun packaging VirusSeeker, initially > > > written in the Washington University in St. Louis, and this > > > program makes use of RepeatMasker for one of its processing > > > steps. This program, in turn, depends on Tandem Repeats Finder. > > > However, the current licensing terms are making TRF incompatible > > > with integration into the main Debian repository, thus render > > > RepeatMasker and VirusSeeker both ineligible to it as well. > > > > > > I was wondering if it were possible to open the source code of > > > TRF, and choose licensing terms that would be compatible with an > > > integration into Debian main repository, for instance by using > > > the GPL-3 or the MIT license, or whichever terms suits your > > > taste among the ones considered DFSG compatible: > > > > > > https://wiki.debian.org/DFSGLicenses#DFSG-compatible_Licenses > > > > > > In hope your licensing change will help us all moving forward, > > > Kind Regards, -- http://fam-tille.de
Re: Idea wanted: What is the most key open source projects to fight COVID-19?
Hi Jun, I concur that the nanopore associated workflows are of high priority. On 09.05.20 22:10, Jun Aruga wrote: Hi Andreas, The 3 pipelines nf-core/nanoseq, https://github.com/nf-core/nanoseq Not the workflow is in Debian, but most of the tools it uses. Missing is only the optional route embracing https://github.com/lbcb-sci/graphmap2 nf-core/artic, Not in Debian, yet, but on its way on https://salsa.debian.org/med-team/fieldbioinformatics That was from during the Hackathon, no idea where this stands, now. No ITP referenced. nf-core/viralrecon That is the next-flow workflow, I understand - no, have not seen that, yet. Nextflow itself causes some problems, if I get this right. Most tools contributing to viralrecon are already in the distribution. Missing are https://github.com/andersen-lab/ivar http://snpeff.sourceforge.net/SnpEff.html http://snpeff.sourceforge.net/SnpSift.html http://cab.spbu.ru/software/meta-spades/ https://github.com/ekg/seqwish https://github.com/BU-ISCIII/plasmidID which are all in the de novo assembly section. Concerning your list below I tend to think that Debian has them all with a few exceptions (nanolyse, ...). also listed above. Ubiquitous tools aside, like R or cat, they should be listed on https://blends.debian.org/med/tasks/bio. Does that help? Best, Steffen I shared are the most applicable (= the highest priority) to COVID-19 analysis. [1]. Now I share the additional 5 pipelines that are certainly relevant (= the 2nd highest priority). [2] This is the result of my interview in the nf-core Slack channel. Could you check the packages situations in Debian? Sorry I knew information about the 5 pipelines a few weeks ago. But I took a time to summarize the list of the packages and email it. * nf-core/scrnaseq (single cell) * nf-core/smartseq2 (single cell) * nf-core/sarek (whole-genome sequencing) * nf-core/mag (meta-genomics) * nf-core/bcellmagic (immune response) https://github.com/nf-core/scrnaseq/blob/master/bin/scrape_software_versions.py bustools kallisto multiqc salmon star https://github.com/nf-core/smartseq2/blob/master/bin/scrape_software_versions.py fastqc multiqc https://github.com/nf-core/sarek/blob/master/bin/scrape_software_versions.py allelecount ascat bcftools bwa fastqc freebayes gatk htslib manta multiqc qualimap r samtools snpeff strelka tiddit vcftools vep https://github.com/nf-core/mag/blob/master/bin/scrape_software_versions.py busco cat centrifuge fastp fastqc filtlong kraken2 megahit metabat multiqc nanolyse nanoplot porechop quast spades https://github.com/nf-core/bcellmagic/blob/master/bin/scrape_software_versions.py changeo fastqc multiqc muscle presto r r-alakazam r-shazam r-tigger vsearch [1] nf-core Slack #covid19 channel https://nfcore.slack.com/archives/C0105J0J9T8/p1587480925053900 > The pipelines you listed are the ones that are/will be most applicable to COVID-19 analysis. [2] nf-core Slack #covid19 channel https://nfcore.slack.com/archives/C0105J0J9T8/p1587498948095200 > But the single cell pipelines could certainly be relevant. Also sarek for whole-genome sequencing analysis, mag for metagenomics analysis and bcellmagic for investigations into the immune response.. Thanks & Cheers, Jun
Re: undefined vdb_mbed functions in ncbi-vdb2 library - ran out of ideas
u...@debian.org (Aaron M. Ucko) writes: >> I'd be super happy if you would find some time to turn your hints into >> code in salsa. ;-) > > I'll try to find time this weekend. I didn't find as much time as I hoped, but I just pushed changes to correct sra-sdk's accidental cutover to ncbi-vdb, and will follow up with my tweaks to both packages when I get a chance. -- Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org) http://www.mit.edu/~amu/ | http://stuff.mit.edu/cgi/finger/?a...@monk.mit.edu
