Hi all,
I installed metaDMG with the recommended conda installation remotely on linux (and some suggested tweaks from past issues on the page), environment file:
name: metaDMG
channels:
- conda-forge
- bioconda
- defaults
dependencies:
- python==3.9
- pip
- pip:
- metaDMG[all]
- logger-tt==1.7.0
- htslib==1.15
- cxx-compiler
- c-compiler
- eigen
- gcc_linux-64
- samtools
It initially seemed to work. However, when running metaDMG config, I need to specify a --metaDMG-cpp to point to the location of this file. It doesn't seem to exist in the conda environment (find /my/conda/env/location -maxdepth 6 -type f -name "*ccp" returns no hits).
Do I need to separately install and build metaDMG-cpp from the sister github page? This feels counterintuitive, given the metaDMG cli is working on my end already.
Here's the command I ran:
metaDMG config ../S30455.Y1.E1.L1.nohuman.fastq.subgenomesaa.fna.e2e.bam \
> --names ../ncbi_taxonomy/names.dmp \
> --nodes ../ncbi_taxonomy/nodes.dmp \
> --acc2tax ../ncbi_taxonomy/nucl_wgs.accession2taxid.gz \
> --custom-database \
> --bayesian
And the error:
Usage: metaDMG config [OPTIONS] SAMPLES...
Try 'metaDMG config --help' for help.
╭─ Error
│ Invalid value for '--metaDMG-cpp' / '-m': The file metaDMG-cpp does not exists. │
Thanks in advance,
Carly
Hi all,
I installed metaDMG with the recommended conda installation remotely on linux (and some suggested tweaks from past issues on the page), environment file:
It initially seemed to work. However, when running metaDMG config, I need to specify a --metaDMG-cpp to point to the location of this file. It doesn't seem to exist in the conda environment (find /my/conda/env/location -maxdepth 6 -type f -name "*ccp" returns no hits).
Do I need to separately install and build metaDMG-cpp from the sister github page? This feels counterintuitive, given the metaDMG cli is working on my end already.
Here's the command I ran:
And the error:
Thanks in advance,
Carly