Re: Nextflow - have just used it on our HPC cluster and liked it

2023-05-10 Thread olivier sallou
On Tue, 2023-05-09 at 22:24 +0200, Pierre Gruet wrote: > Hi Andreas, > > Le 09/05/2023 à 18:36, Andreas Tille a écrit : > > Hi Pierre, > > > > Am Mon, May 08, 2023 at 10:50:54PM +0200 schrieb Pierre Gruet: > > > > > > It is very nice to hear from you on Nextflow, this is a > > > motivation

Re: Nextflow - have just used it on our HPC cluster and liked it

2023-05-09 Thread Pierre Gruet
Hi Andreas, Le 09/05/2023 à 18:36, Andreas Tille a écrit : Hi Pierre, Am Mon, May 08, 2023 at 10:50:54PM +0200 schrieb Pierre Gruet: It is very nice to hear from you on Nextflow, this is a motivation booster for the packaging! +1 I have indeed packaged many dependencies, and if I

Re: Nextflow - have just used it on our HPC cluster and liked it

2023-05-09 Thread Andreas Tille
Hi Pierre, Am Mon, May 08, 2023 at 10:50:54PM +0200 schrieb Pierre Gruet: > > It is very nice to hear from you on Nextflow, this is a motivation booster > for the packaging! +1 > I have indeed packaged many dependencies, and if I remember correctly I had > two issues at this step: > - kryo

Re: Nextflow - have just used it on our HPC cluster and liked it

2023-05-08 Thread Pierre Gruet
Hi Steffen, Le 05/05/2023 à 22:16, Steffen Möller a écrit : Hello, I must admit that I am rather impressed - a series of images were auto-downloaded to function together with singularity and this then worked on a test data collection of the workflow. So, with singularity (or docker) in

Aw: Re: Nextflow - have just used it on our HPC cluster and liked it

2023-05-08 Thread Steffen Möller
> Gesendet: Montag, 08. Mai 2023 um 08:45 Uhr > Von: "Charles Plessy" > An: debian-med@lists.debian.org > Betreff: Re: Nextflow - have just used it on our HPC cluster and liked it > > Hi Steffen and everybody, > > I also use Nextflow at work, and in

Re: Nextflow - have just used it on our HPC cluster and liked it

2023-05-08 Thread Tony Travis
On 08/05/2023 07:45, Charles Plessy wrote: [...] In bioconda you have no idea whether sed is from GNU of from busybox unless you try it or dig for a package recipe in GitHub... Hi, Charles. In fact, an Anaconda/Bioconda 'env' is little more than defined shell environment variables and a

Re: Nextflow - have just used it on our HPC cluster and liked it

2023-05-08 Thread Charles Plessy
Hi Steffen and everybody, I also use Nextflow at work, and indeed, it makes it very easy to run a pipeline many times. Also, Nextflow is a single Java executable, which makes it easy to deploy anywhere Java is already installed. You probably also saw the nf-core repository of modules and