package das_tool could not be installed

[s-junguy]

Hi, I set everything up and submitted with "metaphor execute". This is the error I got: Building DAG of jobs... Creating conda environment miniconda3/envs/metaphor/lib/python3.11/site-packages/metaphor/workflow/envs/das_tool.yaml... Downloading and installing remote packages. CreateCondaEnvironmentException: Could not create conda environment from /home/usr/miniconda3/envs/metaphor/lib/python3.11/site-packages/metaphor/workflow/rules/../e\ nvs/dastool.yaml: Command: mamba env create --quiet --file "/home/usr/miniconda3/envs/metaphor/lib/python3.11/site-packages/metaphor/config/conda/66309510e64ad\ c489d746221bc073a7e.yaml" --prefix "/home/usr/miniconda3/envs/metaphor/lib/python3.11/site-packages/metaphor/config/conda/66309510e\ 64adc489d746221bc073a7e_" Output: Retrieving notices: ...working... done warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY Could not solve for environment specs The following package could not be installed └─ das_tool 1.1.4** is not installable because it requires └─ r-magrittr >=2.0.1 , which conflicts with any installable versions previously reported.

Metaphor did not finish with exit code 1. Please see the error message below. An error occurred while running Metaphor. Please check the traceback below. Traceback (most recent call last): File "/home/usr/miniconda3/envs/metaphor/bin/metaphor", line 10, in sys.exit(main()) ^^^^^^ File "/home/usr/miniconda3/envs/metaphor/lib/python3.11/site-packages/metaphor/cli/cli.py", line 278, in main args.func(args) File "/home/usr/miniconda3/envs/metaphor/lib/python3.11/site-packages/metaphor/cli/execute.py", line 109, in main retcode = run_cmd(cmd) ^^^^^^^^^^^^ File "/home/usr/miniconda3/envs/metaphor/lib/python3.11/site-packages/metaphor/utils.py", line 92, in run_cmd retcode = check_call(cmd.split()) File "/home/usr/miniconda3/envs/metaphor/lib/python3.11/site-packages/metaphor/cli/cli.py", line 278, in main args.func(args) File "/home/usr/miniconda3/envs/metaphor/lib/python3.11/site-packages/metaphor/cli/execute.py", line 109, in main retcode = run_cmd(cmd) ^^^^^^^^^^^^ File "/home/usr/miniconda3/envs/metaphor/lib/python3.11/site-packages/metaphor/utils.py", line 92, in run_cmd retcode = check_call(cmd.split()) ^^^^^^^^^^^^^^^^^^^^^^^ File "/home/usr/miniconda3/envs/metaphor/lib/python3.11/subprocess.py", line 413, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['snakemake', '--snakefile', '/home/usr/miniconda3/envs/metaphor/lib/python3.11/site-package\ s/metaphor/workflow/Snakefile', '--configfile', 'metaphor_settings.yaml', '--cores', '4', '-p', '-r', '--use-conda', '--wrapper-pref\ ix', 'https://github.com/snakemake/snakemake-wrappers/raw/', '--conda-prefix', '/home/usr/miniconda3/envs/metaphor/lib/python3.11/si\ te-packages/metaphor/config/conda', '--config', 'samples=samples.csv', '--config', 'max_mb=180000']' returned non-zero exit status 1\ .

[vinisalazar]

Hi @s-junguy,

Thank you for reporting this issue. It should be fixed in the release v1.7.9 of Metaphor, which will be out soon.

Best, Vini

[vinisalazar]

@s-junguy Metaphor v1.7.9 is now available from Bioconda. I'll close this issue, but please reopen it if your problem is not solved.