Re: Nanoplot - ORCA -> kaleido
Hi Étienne, Am 24.05.21 um 19:39 schrieb Étienne Mollier: > Steffen Möller, on 2021-05-24: >> Nanoplot was blocked by the tricky-to-package orca extension of plotly. >> Orca seems to be substituted by kaleido, which is also tricky to package. >> >> The idea is to use some magic of chromium that is made available via >> docker to craft an executable that can transform SVGs in web outputs. I >> am tempted to think that this of general interest. They say that pypi >> and conda can just install this as a one-liner, well, so can Debian once >> it is packaged, but I have no clue how to get there. > Having filed the RFP for plotly-orca, I consider your finding > interesting. Is that the kaleido hosted on the following > location? > > https://github.com/plotly/Kaleido > > (I would guess so, just confirming.) That is what I thought - the error message was just that there is a "kaleido" module missing and pypi points the URL you found on https://pypi.org/project/kaleido/. Many thanks for having a look at this. Best, Steffen
Nanoplot - ORCA -> kaleido
Nanoplot was blocked by the tricky-to-package orca extension of plotly. Orca seems to be substitute by kaleido, which is also tricky to package. The idea is to use some magic of chromium that is made available via docker to craft an executable that can transform SVGs in web outputs. I am tempted to think that this of general interest. They say that pypi and conda can just install this a a one-liner, well, so can Debian once it is packaged, but I have no clue how to get there. Steffen
Re: ORCA
On 03.11.20 08:06, Andreas Tille wrote: > Hi Steffen, > > On Tue, Nov 03, 2020 at 01:36:00AM +0100, Steffen Möller wrote: >> I had a second look. Impressive. Seems like linuxbrew has evolved >> enormously. > If you had a look could you please give a short summary? For me it > sounds like another packaging system (like Conda). Yes. homebrew (https://brew.sh/) is some bread and butter for all MacOS users (like me). Linuxbrew uses the same technology to spread across Linux. > Would you mind doing > some comparison? Hm. We kind of did: https://link.springer.com/article/10.1007/s41019-017-0050-4 The list of packages they provide for Bioinformatics has much improved since I last looked at it. I added the brew packages referenced by the ORCA dockerfiles in the "Others" tab. But that seems wrong. Instead these should become a column "brew" next to Conda. The other column we are missing is for Guix ... but with limited hours per day, we can either add references or package something. Missing anyway. > Would anybody consider contacting ORCA developers and > invite them to join our list? I'm wondering whether a docker container > featuring Debian Med packages might have advantages or disadvantages and > I'm keen on learning what those disadvantages might be. You can install the latest that brew/conda/guix is offering on Debian stable and Debian unstable alike. And have different versions of the same tool. And changes are as quick as a pull request. Best, Steffen > >> On 02.11.20 17:07, Steffen Möller wrote: >>> Hi Tony, >>> >>> On 01.11.20 22:25, Tony Travis wrote: >>>> Hi, >>>> >>>> Has anyone looked at ORCA? >>>> >>>>> https://academic.oup.com/bioinformatics/article/35/21/4448/5475597 >>>> It has recently been promoted on Cyverse-UK: >>>> >>>>> https://cyverseuk.org/ >>>> Came to my attention because of the reference to Bio-Linux, which I've >>>> used a lot on the University of Arizona iPlant/Cyverse training cluster. >>> I added a column for ORCA on >>> >>> https://docs.google.com/spreadsheets/d/1tApLhVqxRZ2VOuMH_aPUgFENQJfbLlB_PFH_Ah_q7hM/edit#gid=853602383 >>> >>> with the packages it installs via brew in their dockerfile. >>> >>> Hail to all the whale-lovers out there >>> >>> Steffen >>> >>> >>> >>
Re: ORCA
On 03/11/2020 07:06, Andreas Tille wrote: Hi Steffen, On Tue, Nov 03, 2020 at 01:36:00AM +0100, Steffen Möller wrote: I had a second look. Impressive. Seems like linuxbrew has evolved enormously. If you had a look could you please give a short summary? For me it sounds like another packaging system (like Conda). Would you mind doing some comparison? Would anybody consider contacting ORCA developers and invite them to join our list? I'm wondering whether a docker container featuring Debian Med packages might have advantages or disadvantages and I'm keen on learning what those disadvantages might be. Hi, Andreas. OK, I'm willing to volunteer to contact them! I've been using Docker a lot recently to run virus scanning pipelines and I have very mixed feelings about it. It's good if you understand how to use it, but presents huge opportunities to get it wrong and can be quite impenetrable if you don't know or have to motivation to use it properly. On balance, I think it is better to use Bioconda instead. Bye, Tony. -- Minke Informatics Limited, Registered in Scotland - Company No. SC419028 Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK) tel. +44(0)19755 63548http://minke-informatics.co.uk mob. +44(0)7985 078324mailto:tony.tra...@minke-informatics.co.uk
Re: ORCA
Hi Steffen, On Tue, Nov 03, 2020 at 01:36:00AM +0100, Steffen Möller wrote: > I had a second look. Impressive. Seems like linuxbrew has evolved > enormously. If you had a look could you please give a short summary? For me it sounds like another packaging system (like Conda). Would you mind doing some comparison? Would anybody consider contacting ORCA developers and invite them to join our list? I'm wondering whether a docker container featuring Debian Med packages might have advantages or disadvantages and I'm keen on learning what those disadvantages might be. Kind regards Andreas. > On 02.11.20 17:07, Steffen Möller wrote: > > Hi Tony, > > > > On 01.11.20 22:25, Tony Travis wrote: > >> Hi, > >> > >> Has anyone looked at ORCA? > >> > >>> https://academic.oup.com/bioinformatics/article/35/21/4448/5475597 > >> It has recently been promoted on Cyverse-UK: > >> > >>> https://cyverseuk.org/ > >> Came to my attention because of the reference to Bio-Linux, which I've > >> used a lot on the University of Arizona iPlant/Cyverse training cluster. > > I added a column for ORCA on > > > > https://docs.google.com/spreadsheets/d/1tApLhVqxRZ2VOuMH_aPUgFENQJfbLlB_PFH_Ah_q7hM/edit#gid=853602383 > > > > with the packages it installs via brew in their dockerfile. > > > > Hail to all the whale-lovers out there > > > > Steffen > > > > > > > > -- http://fam-tille.de
Re: ORCA
I had a second look. Impressive. Seems like linuxbrew has evolved enormously. On 02.11.20 17:07, Steffen Möller wrote: > Hi Tony, > > On 01.11.20 22:25, Tony Travis wrote: >> Hi, >> >> Has anyone looked at ORCA? >> >>> https://academic.oup.com/bioinformatics/article/35/21/4448/5475597 >> It has recently been promoted on Cyverse-UK: >> >>> https://cyverseuk.org/ >> Came to my attention because of the reference to Bio-Linux, which I've >> used a lot on the University of Arizona iPlant/Cyverse training cluster. > I added a column for ORCA on > > https://docs.google.com/spreadsheets/d/1tApLhVqxRZ2VOuMH_aPUgFENQJfbLlB_PFH_Ah_q7hM/edit#gid=853602383 > > with the packages it installs via brew in their dockerfile. > > Hail to all the whale-lovers out there > > Steffen > > >
Re: ORCA
Hi Tony, On 01.11.20 22:25, Tony Travis wrote: > Hi, > > Has anyone looked at ORCA? > >> https://academic.oup.com/bioinformatics/article/35/21/4448/5475597 > > It has recently been promoted on Cyverse-UK: > >> https://cyverseuk.org/ > > Came to my attention because of the reference to Bio-Linux, which I've > used a lot on the University of Arizona iPlant/Cyverse training cluster. I added a column for ORCA on https://docs.google.com/spreadsheets/d/1tApLhVqxRZ2VOuMH_aPUgFENQJfbLlB_PFH_Ah_q7hM/edit#gid=853602383 with the packages it installs via brew in their dockerfile. Hail to all the whale-lovers out there Steffen
ORCA
Hi, Has anyone looked at ORCA? https://academic.oup.com/bioinformatics/article/35/21/4448/5475597 It has recently been promoted on Cyverse-UK: https://cyverseuk.org/ Came to my attention because of the reference to Bio-Linux, which I've used a lot on the University of Arizona iPlant/Cyverse training cluster. Bye, Tony. -- Minke Informatics Limited, Registered in Scotland - Company No. SC419028 Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK) tel. +44(0)19755 63548http://minke-informatics.co.uk mob. +44(0)7985 078324mailto:tony.tra...@minke-informatics.co.uk
