Closed conmeehan closed 2 months ago
pmenzel
commented
3 months ago I encountered the same issue, and just adding libboost==1.85.0 to the used conda env containing TB-Profiler worked fine. I guess one could just add this the tb-profiler recipe itself?
jodyphelan
commented
3 months ago Yeah I think it is due to the delly recipe having boost-cpp >=1.85.0 in its the dependancies. It was build and packaged when only v1.85 was out but that v1.86 is out it breaks the install. I'll see if I can fix the issue at the root (the delly recipie!)
jodyphelan
commented
3 months ago Pinned boost-cpp to 1.78 I think this has fixed the issue now. @conmeehan @pmenzel would you mind checking on your side if that has resolved?
conmeehan
commented
2 months ago Thats working now from a fresh conda install. Thanks!
kapsakcj
commented
4 weeks ago Hey Jody, I know this is closed but we ran into this issue when trying to install tb-profiler 6.4.0 in a docker image using micromamba (see mention to the PR above)
We (@sage-wright and I) tried pinning libboost==1.85.0 (did not work)
We also tried pinning boost-cpp==1.78.0 (did not work)
What did work was pinning to a slightly older version of delly==1.2.6, which allowed the conda environment to resolve successfully and allow for usher 0.6.3 to be installed. tb-profiler ran successfully on some test data using this conda environment
The 6.4.0 bioconda recipe does not pin a delly version to use, and so it automatically grabs delly 1.3.1 (latest as of this writing), which does not have the boost-cpp version pinned, like it was for v1.2.6 of delly.
Not sure if you wanted to update the bioconda recipe for tb-profiler or perhaps in the recipe for delly itself, but wanted to let you know.
jodyphelan
commented
4 weeks ago Thanks @kapsakcj , I'll pin delly v1.2.6 in the recipie for now.
I still don't fully understand the delly/usher/boost imcompatibility issue so happy to go with any reccomendations.
Curiously - when I try to install tb-profile 6.4.0 it seemt to resolve to delly 1.2.6 correctly:
(base) jody@s10:~$ mamba create -n test tb-profiler=6.4.0
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mamba (1.1.0) supported by @QuantStack
GitHub: https://github.com/mamba-org/mamba
Twitter: https://twitter.com/QuantStack
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Looking for: ['tb-profiler=6.4.0']
bioconda/noarch 5.3MB @ 6.6MB/s 1.0s
bioconda/linux-64 5.6MB @ 5.5MB/s 1.2s
pkgs/r/noarch No change
pkgs/r/linux-64 No change
pkgs/main/noarch 876.5kB @ 607.1kB/s 0.4s
pkgs/main/linux-64 7.6MB @ 3.9MB/s 2.2s
conda-forge/noarch @ 6.6MB/s 3.5s
conda-forge/linux-64 @ 6.6MB/s 8.6s
warning libmamba Invalid package cache, file '/mnt/storage10/jody/miniconda3/pkgs/freebayes-1.3.6-hb0f3ef8_7/bin/freebayes-parallel' has incorrect size
warning libmamba Invalid package cache, file '/mnt/storage10/jody/miniconda3/pkgs/snpeff-5.2-hdfd78af_1/share/snpeff-5.2-1/snpEff.config' has incorrect size
Transaction
Prefix: /mnt/storage10/jody/miniconda3/envs/test
Updating specs:
- tb-profiler=6.4.0
Package Version Build Channel Size
───────────────────────────────────────────────────────────────────────────────────────────────────
Install:
───────────────────────────────────────────────────────────────────────────────────────────────────
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+ xorg-libxau 1.0.11 hb9d3cd8_1 conda-forge/linux-64 Cached
+ xorg-libxdmcp 1.1.5 hb9d3cd8_0 conda-forge/linux-64 Cached
+ xorg-libxext 1.3.6 hb9d3cd8_0 conda-forge/linux-64 Cached
+ xorg-libxfixes 6.0.1 hb9d3cd8_0 conda-forge/linux-64 Cached
+ xorg-libxi 1.8.2 hb9d3cd8_0 conda-forge/linux-64 Cached
+ xorg-libxrender 0.9.11 hb9d3cd8_1 conda-forge/linux-64 Cached
+ xorg-libxtst 1.2.5 hb9d3cd8_3 conda-forge/linux-64 Cached
+ xorg-xorgproto 2024.1 hb9d3cd8_1 conda-forge/linux-64 Cached
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+ zstandard 0.23.0 py312hef9b889_1 conda-forge/linux-64 Cached
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Summary:
Install: 208 packages
Total download: 12MB
───────────────────────────────────────────────────────────────────────────────────────────────────
Confirm changes: [Y/n]Interesting... Not sure why yours resolved to delly 1.2.6 and our micromamba environment resolved to delly 1.3.1 but it happened.
In that we used micromamba 1.5.8 & installed with this command:
micromamba install --yes --name base --channel conda-forge --channel bioconda \
tb-profiler=6.4.0🤷 Hopefully this will be resolved upon pinning to delly 1.2.6 in the tb-profiler pathogen-profiler recipe 🤞
Hi,
Similar to https://github.com/jodyphelan/TBProfiler/issues/390 a fresh install of TBProfiler has a failure with Delly because it is hardcoded to use libboost v1.85.0. This got updated to v1.86.0 in the past week or so and now TBProfiler won't complete. Downgrading to v1.85.0 fixes it but likely a problem going forward.
Cheers, Con