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scib-pipeline #33

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boegel opened this issue Oct 3, 2022 · 6 comments
Closed

scib-pipeline #33

boegel opened this issue Oct 3, 2022 · 6 comments
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@deniskristak
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difficulty: medium software that likely require a fair amount of effort to support new new software priority: high Python R site:ugent Software installation request for UGent Tier-2 sources-only Only sources available (no conda, binaries, container)

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@boegel
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boegel commented Oct 3, 2022

@boegel boegel added difficulty: medium software that likely require a fair amount of effort to support new new software priority: high Python R site:ugent Software installation request for UGent Tier-2 labels Oct 3, 2022
@deniskristak deniskristak self-assigned this Jan 4, 2023
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starting with these 2 pages of dependencies:
https://github.com/theislab/scib-pipeline/blob/main/envs/scib-pipeline-R4.0.yml
https://github.com/theislab/scib-pipeline/blob/main/envs/scib-R4.0.yml

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turns out we need scib first - https://github.com/theislab/scib/blob/main/setup.cfg

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theislab/scib#360 - issue with deprecated dependency

@deniskristak
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deniskristak commented Jan 13, 2023 •
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rpy2 upgrade to 2022a is a bit difficult - here's an issue with test err that probably needs to be solved:
rpy2/rpy2#974

@deniskristak deniskristak mentioned this issue Jan 18, 2023
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theislab/scib-pipeline#53
opened issue at developer's repo...the software itself installs fine, but running the initial example fails immediately

@ItIsI-Orient ItIsI-Orient added the sources-only Only sources available (no conda, binaries, container) label May 18, 2023
@laraPPr
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laraPPr commented Feb 15, 2024 •
edited by boegel
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Asked the user if the installing scib-pipeline is still relevant for them. Will reopen the ticket if the user reaches out that this is still relevant for their research.

@laraPPr laraPPr closed this as completed Feb 15, 2024
PetrKralCZ added a commit that referenced this issue May 16, 2024
@PetrKralCZ
Big cleanup for closed tickets #102 #117 #119 #134 #136 #184 #187 #196 …
18b422b 
…#208 #245 #263 #280 #33 #38 #45 #53 #87 #99
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difficulty: medium software that likely require a fair amount of effort to support new new software priority: high Python R site:ugent Software installation request for UGent Tier-2 sources-only Only sources available (no conda, binaries, container)
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@boegel @deniskristak @laraPPr @ItIsI-Orient