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Description
Bug report
Expected behavior and actual behavior
Expected:
- If a Conda lock file works locally, we should be able to supply it by http.
- We should also have clear documentation around required naming/ file extensions for lock files.
Observed
Here is a conda lockfile produced with micromamba like micromamba env export --explicit > env.txt:
This works:
#!/usr/bin/env nextflow
process FOO {
debug true
conda 'env.txt'
script:
"""
R --version
"""
}
workflow {
FOO()
}We would expect the same file hosted remotely to work:
...
conda 'https://gist.githubusercontent.com/pinin4fjords/e8cdca9521586f667ed1c5bcd33598d9/raw/550f0f4ed17f5d2741552a2b9f1d625239e499ec/env.txt'
...... but it does not:
Nextflow 24.09.2-edge is available - Please consider updating your version to it
N E X T F L O W ~ version 24.02.0-edge
┃ Launching `main.nf` [cheesy_marconi] DSL2 - revision: 510b3a1397
[- ] FOO -
[- ] FOO -
Creating env using conda: https://gist.githubusercontent.com/pinin4fjords/e8cdca9521586f667ed1c5bcd33598d9/raw/550f0f4ed17f5d2741552a2b9f1d625239e499ec/env.txt [cache /workspace/gitpod/hello-nextflow/foo/work/conda/env-eeddd0960df503db901cc9c3644e607a]
ERROR ~ Error executing process > 'FOO'
Caused by:
[- ] FOO -
Creating env using conda: https://gist.githubusercontent.com/pinin4fjords/e8cdca9521586f667ed1c5bcd33598d9/raw/550f0f4ed17f5d2741552a2b9f1d625239e499ec/env.txt [cache /workspace/gitpod/hello-nextflow/foo/work/conda/env-eeddd0960df503db901cc9c3644e607a]
ERROR ~ Error executing process > 'FOO'
Caused by:
Failed to create Conda environment
command: conda create --mkdir --yes --quiet --prefix /workspace/gitpod/hello-nextflow/foo/work/conda/env-eeddd0960df503db901cc9c3644e607a --file /workspace/gitpod/hello-nextflow/foo/https\:/gist.githubusercontent.com/pinin4fjords/e8cdca9521586f667ed1c5bcd33598d9/raw/550f0f4ed17f5d2741552a2b9f1d625239e499ec/env.txt
status : 1
message:
/opt/conda/lib/python3.12/site-packages/conda/cli/conda_argparse.py:248: FutureWarning: `--mkdir` is deprecated and will be removed in 25.3. Redundant argument.
super().__call__(parser, namespace, values, option_string)
CondaFileIOError: '/workspace/gitpod/hello-nextflow/foo/https:/gist.githubusercontent.com/pinin4fjords/e8cdca9521586f667ed1c5bcd33598d9/raw/550f0f4ed17f5d2741552a2b9f1d625239e499ec/env.txt'. [Errno 2] No such file or directory: '/workspace/gitpod/hello-nextflow/foo/https:/gist.githubusercontent.com/pinin4fjords/e8cdca9521586f667ed1c5bcd33598d9/raw/550f0f4ed17f5d2741552a2b9f1d625239e499ec/env.txt'
-- Check '.nextflow.log' file for details
Naming the file with .lock, even locally does not work:
...
conda 'env.lock'
...(i.e renaming env.txt to env.lock):
Nextflow 24.09.2-edge is available - Please consider updating your version to it
N E X T F L O W ~ version 24.02.0-edge
┃ Launching `main.nf` [awesome_dalembert] DSL2 - revision: 021eb262d1
[- ] FOO -
Creating env using conda: env.lock [cache /workspace/gitpod/hello-nextflow/foo/work/conda/env-f187ecbc64371e10748465ebfbff2242]
ERROR ~ Error executing process > 'FOO'
Caused by:
Failed to create Conda environment
command: conda create --mkdir --yes --quiet --prefix /workspace/gitpod/hello-nextflow/foo/work/conda/env-f187ecbc64371e10748465ebfbff2242 env.lock
status : 1
message:
/opt/conda/lib/python3.12/site-packages/conda/cli/conda_argparse.py:248: FutureWarning: `--mkdir` is deprecated and will be removed in 25.3. Redundant argument.
super().__call__(parser, namespace, values, option_string)
Channels:
- conda-forge
- bioconda
- defaults
Platform: linux-64
[- ] FOO -
Creating env using conda: env.lock [cache /workspace/gitpod/hello-nextflow/foo/work/conda/env-f187ecbc64371e10748465ebfbff2242]
ERROR ~ Error executing process > 'FOO'
Caused by:
Failed to create Conda environment
command: conda create --mkdir --yes --quiet --prefix /workspace/gitpod/hello-nextflow/foo/work/conda/env-f187ecbc64371e10748465ebfbff2242 env.lock
status : 1
message:
/opt/conda/lib/python3.12/site-packages/conda/cli/conda_argparse.py:248: FutureWarning: `--mkdir` is deprecated and will be removed in 25.3. Redundant argument.
super().__call__(parser, namespace, values, option_string)
Channels:
- conda-forge
- bioconda
- defaults
Platform: linux-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... failed
PackagesNotFoundError: The following packages are not available from current channels:
- env.lock
Current channels:
- https://conda.anaconda.org/conda-forge
- https://conda.anaconda.org/bioconda
- defaults
- https://repo.anaconda.com/pkgs/main
- https://repo.anaconda.com/pkgs/r
To search for alternate channels that may provide the conda package you're
looking for, navigate to
https://anaconda.org
and use the search bar at the top of the page.
-- Check '.nextflow.log' file for details
Neither does supplying the .lock file by http:
...
conda 'https://gist.githubusercontent.com/pinin4fjords/c5a32673f084cdb772b03a63b9b1d118/raw/c6493bad0819bf8dff0c342af06eaeeee9c03af0/env.lock'
...Error:
N E X T F L O W ~ version 24.02.0-edge
┃ Launching `main.nf` [nasty_torvalds] DSL2 - revision: b01a400c6a
[- ] FOO -
[- ] FOO -
Creating env using conda: https://gist.githubusercontent.com/pinin4fjords/c5a32673f084cdb772b03a63b9b1d118/raw/c6493bad0819bf8dff0c342af06eaeeee9c03af0/env.lock [cache /workspace/gitpod/hello-nextflow/foo/work/conda/env-ea0ebf23bfe548bbed42e257c0d75fa4]
ERROR ~ Error executing process > 'FOO'
Caused by:
Failed to create Conda environment
command: conda create --mkdir --yes --quiet --prefix /workspace/gitpod/hello-nextflow/foo/work/conda/env-ea0ebf23bfe548bbed42e257c0d75fa4 https://gist.githubusercontent.com/pinin4fjords/c5a32673f084cdb772b03a63b9b1d118/raw/c6493bad0819bf8dff0c342af06eaeeee9c03af0/env.lock
status : 1
message:
/opt/conda/lib/python3.12/site-packages/conda/cli/conda_argparse.py:248: FutureWarning: `--mkdir` is deprecated and will be removed in 25.3. Redundant argument.
super().__call__(parser, namespace, values, option_string)
Channels:
- conda-forge
- bioconda
- defaults
Platform: linux-64
[- ] FOO -
Creating env using conda: https://gist.githubusercontent.com/pinin4fjords/c5a32673f084cdb772b03a63b9b1d118/raw/c6493bad0819bf8dff0c342af06eaeeee9c03af0/env.lock [cache /workspace/gitpod/hello-nextflow/foo/work/conda/env-ea0ebf23bfe548bbed42e257c0d75fa4]
ERROR ~ Error executing process > 'FOO'
Caused by:
Failed to create Conda environment
command: conda create --mkdir --yes --quiet --prefix /workspace/gitpod/hello-nextflow/foo/work/conda/env-ea0ebf23bfe548bbed42e257c0d75fa4 https://gist.githubusercontent.com/pinin4fjords/c5a32673f084cdb772b03a63b9b1d118/raw/c6493bad0819bf8dff0c342af06eaeeee9c03af0/env.lock
status : 1
message:
/opt/conda/lib/python3.12/site-packages/conda/cli/conda_argparse.py:248: FutureWarning: `--mkdir` is deprecated and will be removed in 25.3. Redundant argument.
super().__call__(parser, namespace, values, option_string)
Channels:
- conda-forge
- bioconda
- defaults
Platform: linux-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... failed
PackagesNotFoundError: The following packages are not available from current channels:
- //gist.githubusercontent.com/pinin4fjords/c5a32673f084cdb772b03a63b9b1d118/raw/c6493bad0819bf8dff0c342af06eaeeee9c03af0/env.lock
Current channels:
- https://conda.anaconda.org/conda-forge
- https://conda.anaconda.org/bioconda
- defaults
- https://repo.anaconda.com/pkgs/main
- https://repo.anaconda.com/pkgs/r
To search for alternate channels that may provide the conda package you're
looking for, navigate to
https://anaconda.org
and use the search bar at the top of the page.
-- Check '.nextflow.log' file for details
Environment
- Nextflow version: 24.09.2-edge
- Java version: [?]
- Operating system: Linux
- Bash version: (use the command
$SHELL --version)
Additional context
(Add any other context about the problem here)
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