https://biohackathons.github.io/ - BioHackathons Paper

Hello, This paper (coauthored by multiple-DebianMed-Sprint attendee Pjotr) Garcia L, Antezana E, Garcia A, Bolton E, Jimenez R, et al. (2020) Ten simple rules to run a successful BioHackathon. PLOS Computational Biology 16(5): e1007808. https://doi.org/10.1371/journal.pcbi.1007808

Re: RFS paml - fixed #957659

Hi, Got a reply from Ziheng Yang, the author of PAML. He said he will include the suggested changes upstream. Best, Julien. PS: does this solve the issue or is there anything else I should do :s ? On Sun, May 10, 2020 at 11:59 AM Étienne Mollier wrote: > Hi Julien, > > Andreas Tille, on 2020

Re: Idea wanted: What is the most key open source projects to fight COVID-19?

Hi Steffen, Thanks for sharing the information. > > 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 I think the nf-core/nanoseq and other nf-core pipelines the

Re: https://biohackathons.github.io/ - BioHackathons Paper

> https://biohackathons.github.io/ Wow, it's a great summarized page! Thanks for sharing! -- Jun | He - His - Him

Re: Idea wanted: What is the most key open source projects to fight COVID-19?

Hi Jun, On Mon, May 11, 2020 at 12:11:38PM +0200, Jun Aruga wrote: > > Not the workflow is in Debian, but most of the tools it uses. Missing is > > only the optional route embracing > > I think the nf-core/nanoseq and other nf-core pipelines themselves are > not in Debian. Because I think Nextflo

Re: Idea wanted: What is the most key open source projects to fight COVID-19?

> I tried to package nextflow but I stumbled upon a dependency from capsule > >https://lists.debian.org/debian-java/2020/04/msg00046.html > > my suspicion that this is not really good to have it in Debian was confirmed > here: > >https://lists.debian.org/debian-java/2020/05/msg0.html O

Re: Idea wanted: What is the most key open source projects to fight COVID-19?

Hello, On 2020-05-11 16:11, Jun Aruga wrote: >> I have no idea at all whether capsule can be avoided to package nextflow. > Sure. Maybe I will take a look at digging the code of the nextflow in > the future. I would suggest turning to Java packaging team regarding capsules. They might know how to

Re: Idea wanted: What is the most key open source projects to fight COVID-19?

Hi Jun, thanks a lot for your input which is extremely helpful. On Sat, May 09, 2020 at 10:10:33PM +0200, Jun Aruga wrote: > Hi Andreas, > > The 3 pipelines nf-core/nanoseq, nf-core/artic, nf-core/viralrecon I > shared are the most applicable (= the highest priority) to COVID-19 > analysis. [1].

Re: https://biohackathons.github.io/ - BioHackathons Paper

On Mon, May 11, 2020 at 10:20:06AM +0200, Steffen Möller wrote: > featured this URL > > https://biohackathons.github.io/ > > which apparently lacks a notion of our regular Sprint. I suggest we send > a PR :o)  I find this to be very helpful. +1 :-) Thanks for spotting, Andreas. -- http://f

Re: Idea wanted: What is the most key open source projects to fight COVID-19?

On Mon, May 11, 2020 at 03:39:41PM +0200, Andreas Tille wrote: > Hi Jun, > > thanks a lot for your input which is extremely helpful. > > On Sat, May 09, 2020 at 10:10:33PM +0200, Jun Aruga wrote: > > Hi Andreas, > > > > The 3 pipelines nf-core/nanoseq, nf-core/artic, nf-core/viralrecon I > > sha

Re: Idea wanted: What is the most key open source projects to fight COVID-19?

Andreas and Steffen. Many thanks for updating the spread sheet adding the Debian and Bio.tools status! I added the following 2 columns. It's great if we can fill it if we have a time. * Deb in Debian? arm64 * Deb in Debian? ppc64le Because I would like to know the status supporting arm64 (aarch

Re: RFS paml - fixed #957659

Hi Julien, Julien Yann Dutheil, on 2020-05-11 11:00:31 +0200: > Got a reply from Ziheng Yang, the author of PAML. He said he will include > the suggested changes upstream. Great! Thank you! > PS: does this solve the issue or is there anything else I should do :s ? I would be tempted to think t

RFS tigr-glimmer: reinforced `make` error checking

Control: tags -1 patch Good day, I had a look at the package tigr-glimmer and wrote a patch to reinforce the Makefile infrastructure where it seemed needed. The issue can be reproduced by specifying an invalid C++ compiler and attempt a build: $ CXX=invalid-cpp make -C src While the bui

Re: Idea wanted: What is the most key open source projects to fight COVID-19?

Hi Jun, On Mon, May 11, 2020 at 06:33:15PM +0200, Jun Aruga wrote: > Many thanks for updating the spread sheet adding the Debian and > Bio.tools status! You are welcome. > I added the following 2 columns. It's great if we can fill it if we have a > time. > > * Deb in Debian? arm64 > * Deb in

RFS: fitgcp

Hi, While adding autopkgtests for fitgcp, I ran into several bugs - some of which are changes that 2to3 probably missed. I've pushed a patch along with the tests. Please review and sponsor. https://salsa.debian.org/med-team/fitgcp Regards, Pranav ᐧ

Re: Idea wanted: What is the most key open source projects to fight COVID-19?

On 11.05.20 22:23, Andreas Tille wrote: Hi Jun, On Mon, May 11, 2020 at 06:33:15PM +0200, Jun Aruga wrote: Many thanks for updating the spread sheet adding the Debian and Bio.tools status! You are welcome. I added the following 2 columns. It's great if we can fill it if we have a time. *