[Date Prev][Date Next] [Thread Prev][Thread Next] [Date Index] [Thread Index]

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
>>>
>>>
>>>
>>
Reply to: