Interproscan from Seqera Containers fails to build

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1

This is not wave, but container related, and I didn’t know if there was a more appropriate channel, or where to post a bug report.

I want to make a make a container for interproscan:5.59_91.0 since the biocontainers one has can’t use ps in the expected way.

When searching for interproscan:5.59_91.0, seqera containers only brings up interproscan:5.59_STUB, which then causes a subsequent build error as it can’t find a package by that name.

Container build details:
build id: 2cd7150970073846_1

name:

oras://community.wave.seqera.io/library/interproscan:5.59_STUB--2cd7150970073846

conda:

channels:
- conda-forge
- bioconda
dependencies:
- bioconda::interproscan=5.59_STUB

singularity file:

BootStrap: docker
From: mambaorg/micromamba:1.5.8-lunar
%files
    {{wave_context_dir}}/conda.yml /scratch/conda.yml
%post
    micromamba install -y -n base -f /scratch/conda.yml
    micromamba install -y -n base conda-forge::procps-ng
    micromamba clean -a -y
%environment
    export PATH="$MAMBA_ROOT_PREFIX/bin:$PATH"

build log:

INFO:    Starting build...
Getting image source signatures
Copying blob sha256:6360b371721185fefbbad6763ab745900f1b2f7714570234473232dd575fc07f
Copying blob sha256:2ec3f7ad9b3ca7370ae62c6bdb36e3575239b5b0942163d36814c87efb3ff90d
Copying blob sha256:4f4fb700ef54461cfa02571ae0db9a0dc1e0cdb5577484a6d75e68dc38e8acc1
Copying blob sha256:03dae77ff45c4b21a524fe292d91a7704d870b528d3e03c3624a4d48e7733d65
Copying blob sha256:8c61d418774c0c5a7be0036dd042add78077c4195d904abdba1080bad2539797
Copying blob sha256:7716ca30060043d1c1ba35c09e8eb2fda19788fc0d5ec491d85e866306207cc9
Copying blob sha256:aab7f787139dee8557ebf54563c3e9e57c28d98e41e98f997c8af42c15b78b09
Copying blob sha256:4f4fb700ef54461cfa02571ae0db9a0dc1e0cdb5577484a6d75e68dc38e8acc1
Copying blob sha256:837d55536720ebdfd52a582cc6333019e0cfe430ef7c24fb17333f8d0fb9e7ec
Copying blob sha256:897362c12ca72fae6ca70474a9f2e9ced3a57c82f11f13033d4c3c73aae320a8
Copying blob sha256:3893cbe24e910b5f4aa84fde0aedaf93c0cd7fbd66a423c39cb1077d420753e8
Copying blob sha256:d1b61e94977bd32162b9537fa73b2bde0c0e866044bf3b973c7a20501102e11d
Copying config sha256:77165e42cdbb8e7d7ceaba550c333c88eb20b2463d45247197390b43b2588c48
Writing manifest to image destination
Storing signatures
2024/06/05 11:11:46  info unpack layer: sha256:6360b371721185fefbbad6763ab745900f1b2f7714570234473232dd575fc07f
2024/06/05 11:11:48  info unpack layer: sha256:2ec3f7ad9b3ca7370ae62c6bdb36e3575239b5b0942163d36814c87efb3ff90d
2024/06/05 11:11:48  info unpack layer: sha256:7716ca30060043d1c1ba35c09e8eb2fda19788fc0d5ec491d85e866306207cc9
2024/06/05 11:11:48  info unpack layer: sha256:4f4fb700ef54461cfa02571ae0db9a0dc1e0cdb5577484a6d75e68dc38e8acc1
2024/06/05 11:11:48  info unpack layer: sha256:8c61d418774c0c5a7be0036dd042add78077c4195d904abdba1080bad2539797
2024/06/05 11:11:48  info unpack layer: sha256:03dae77ff45c4b21a524fe292d91a7704d870b528d3e03c3624a4d48e7733d65
2024/06/05 11:11:48  info unpack layer: sha256:aab7f787139dee8557ebf54563c3e9e57c28d98e41e98f997c8af42c15b78b09
2024/06/05 11:11:48  info unpack layer: sha256:4f4fb700ef54461cfa02571ae0db9a0dc1e0cdb5577484a6d75e68dc38e8acc1
2024/06/05 11:11:48  info unpack layer: sha256:837d55536720ebdfd52a582cc6333019e0cfe430ef7c24fb17333f8d0fb9e7ec
2024/06/05 11:11:48  info unpack layer: sha256:897362c12ca72fae6ca70474a9f2e9ced3a57c82f11f13033d4c3c73aae320a8
2024/06/05 11:11:48  info unpack layer: sha256:3893cbe24e910b5f4aa84fde0aedaf93c0cd7fbd66a423c39cb1077d420753e8
2024/06/05 11:11:48  info unpack layer: sha256:d1b61e94977bd32162b9537fa73b2bde0c0e866044bf3b973c7a20501102e11d
INFO:    Copying /efs/wave/build/2cd7150970073846_1/context/conda.yml to /scratch/conda.yml
INFO:    Running post scriptlet
+ micromamba install -y -n base -f /scratch/conda.yml
error    libmamba Could not solve for environment specs
    The following package could not be installed
    └─ interproscan 5.59_STUB*  does not exist (perhaps a typo or a missing channel).
critical libmamba Could not solve for environment specs
FATAL:   While performing build: while running engine: exit status 1
2

Thanks @mahesh.binzerpanchal - so the issue here is that the web front-end is showing an incorrect / non-existent version number?

Short term fix is to use the Wave CLI instead, that should support you manually requesting any version number.

Longer term we’ll look into why the web UI is returning this version string. Soon the web interface should also allow manually specifying a version string, and returning multiple version results to choose from.

Phil

3

I made one for you convenience

» wave --conda bioconda::interproscan=5.59_91.0 -F -s 
oras://community.wave.seqera.io/library/interproscan:5.59_91.0--c515d30aea1d4874
1 Like
4

Thank you Phil and Paolo.

Yes, the issue is the web front-end. Those sound like nice future developments.

1 Like
5

Ok apparently this has already been fixed in dev and is just awaiting deployment. So it should return the proper version v. soon.

1 Like
6

Update - this is now deployed and working as expected:

CleanShot 2024-08-14 at 00.27.06@2x
CleanShot 2024-08-14 at 00.27.06@2x1712×784 61 KB

With a version selector:

CleanShot 2024-08-14 at 00.27.12@2x
CleanShot 2024-08-14 at 00.27.12@2x828×430 52.8 KB

The method we now have for fetching available version numbers should hopefully be a lot more robust. But if you find any other cases where something similar is happening, please give us a shout!

Phil

1 Like