installation issue for sourmash #41
Comments
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Hello Can you try just this: It just worked for me |
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Thank you for pasting your results. It seems like installation goes well but I get few packages compared to what you have. My installing output is here:
And when I try to run the test i get another error:
So can you please share the text of your "sourmash.yaml"? I think I may be missing something.
Many thanks, |
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My "sourmash.yaml" file looks like this:
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Just to confirm that the magpy_install and test commands ran to completion for me yesterday with no problems This may be a problem with your conda setup.... |
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Ok, thanks for letting me know. I am going to download a new miniconda, and start everything from scratch. Hope it would work this time. Will update you. Many thanks for your time. |
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What OS are you using?
…________________________________
From: mars188 ***@***.***>
Sent: Tuesday, November 16, 2021 4:32:11 PM
To: WatsonLab/MAGpy ***@***.***>
Cc: WATSON Mick ***@***.***>; Comment ***@***.***>
Subject: Re: [WatsonLab/MAGpy] installation issue for sourmash (Issue #41)
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Ok, thanks for letting me know. I am going to download a new miniconda, and start everything from scratch. Hope it would work this time. Will update you. Many thanks for your time.
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I'm running on HPC on commandline. |
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So linux I guess... |
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Ok, I downloaded the new miniconda, set up the new environment but get the same error again. Not sure what's wrong with my conda set up :( |
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Sometimes it is the underlying OS – if some of the libraries conda wants to install are new and the OS is really old, then it can struggle
Do you have access to a different linux OS?
From: mars188 ***@***.***>
Sent: 18 November 2021 08:15
To: WatsonLab/MAGpy ***@***.***>
Cc: WATSON Mick ***@***.***>; Comment ***@***.***>
Subject: Re: [WatsonLab/MAGpy] installation issue for sourmash (Issue #41)
This email was sent to you by someone outside the University.
You should only click on links or attachments if you are certain that the email is genuine and the content is safe.
Ok, I downloaded the new miniconda, set up the new environment but get the same error again.
Not sure what's wrong with my conda set up :(
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You are receiving this because you commented.
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The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. Is e buidheann carthannais a th’ ann an Oilthigh Dhùn Èideann, clàraichte an Alba, àireamh clàraidh SC005336.
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Hello,
I want to use MAGpy for my metagenomic data analysis but get the error at a very early stage. My command is here:
git clone https://github.com/WatsonLab/MAGpy.gitcd MAGpyconda env create -f envs/install.yamlThis succesfully creates a conda environment.
I activated the environment
conda activate maypy_installThen ran the following command:
nakemake -rp -s MAGpy --cores 24 --use-conda testBut get the following error:
`Building DAG of jobs...
Creating conda environment envs/prodigal.yaml...
Downloading and installing remote packages.
Environment for envs/prodigal.yaml created (location: .snakemake/conda/55c7ff22b092c19217e5f2ec3f9e4209)
Creating conda environment envs/bioperl.yaml...
Downloading and installing remote packages.
Environment for envs/bioperl.yaml created (location: .snakemake/conda/a38998cd23e9ca04e9db80dcbfc6e82c)
Creating conda environment envs/pfam_scan.yaml...
Downloading and installing remote packages.
Environment for envs/pfam_scan.yaml created (location: .snakemake/conda/31f109d7845f53d8b16f172a493949bd)
Creating conda environment envs/phylophlan.yaml...
Downloading and installing remote packages.
Environment for envs/phylophlan.yaml created (location: .snakemake/conda/d1d3c5ec64b4c2330ba4a92faf2e0eb3)
Creating conda environment envs/diamond.yaml...
Downloading and installing remote packages.
Environment for envs/diamond.yaml created (location: .snakemake/conda/8435cfd2ff926a9883cafbdc8d09837d)
Creating conda environment envs/sourmash.yaml...
Downloading and installing remote packages.
CreateCondaEnvironmentException:
Could not create conda environment from /scratch/gencore/ma5877/MAGs/MAGpy/envs/sourmash.yaml:
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Encountered problems while solving:
Please help in solving this issue. Many thanks in advance!
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