Thank you so much for your video and tutorial, Mr. Vincent.
I was about to prepare the whole environment however this error showed up as follow, after " conda env create --quiet -f environment.yaml"
Channels:
- conda-forge
- bioconda
- defaults
- r
Platform: osx-arm64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... failed
Channels:
- conda-forge
- bioconda
- defaults
- r
Platform: osx-arm64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... failed
LibMambaUnsatisfiableError: Encountered problems while solving:
- nothing provides requested sra-tools
- nothing provides requested spades
- nothing provides requested sickle-trim
- nothing provides requested samtools
- nothing provides requested roary
- nothing provides blast needed by quast-4.6.3-py27pl526h3727419_2
- nothing provides requested porechop
- nothing provides requested perl-padwalker
- nothing provides requested perl-db-file
- nothing provides requested mummer
- nothing provides requested minimap2
- nothing provides requested mash
- nothing provides requested mafft
- nothing provides requested bwa
- nothing provides pysam needed by ragtag-1.0.0-pyh5ca1d4c_0
- nothing provides aragorn >=1.2 needed by prokka-1.13.7-pl526_0
- nothing provides blast >=2.7.1 needed by mlst-2.16.2-0
- nothing provides blast >=2.7 needed by abricate-0.9.3-h1341992_0
Could not solve for environment specs
The following packages are incompatible
├─ abricate is not installable because it requires
│ └─ blast >=2.7 , which does not exist (perhaps a missing channel);
├─ bwa does not exist (perhaps a typo or a missing channel);
├─ mafft does not exist (perhaps a typo or a missing channel);
├─ mash does not exist (perhaps a typo or a missing channel);
├─ minimap2 does not exist (perhaps a typo or a missing channel);
├─ mlst is not installable because there are no viable options
│ ├─ mlst [2.16.2|2.16.4] would require
│ │ └─ blast >=2.7.1 , which does not exist (perhaps a missing channel);
│ └─ mlst [2.17.6|2.18.0|...|2.23.0] would require
│ └─ blast >=2.9.0 , which does not exist (perhaps a missing channel);
├─ mummer does not exist (perhaps a typo or a missing channel);
├─ perl-db-file does not exist (perhaps a typo or a missing channel);
├─ perl-padwalker does not exist (perhaps a typo or a missing channel);
├─ porechop does not exist (perhaps a typo or a missing channel);
├─ prokka is not installable because it requires
│ └─ aragorn >=1.2 , which does not exist (perhaps a missing channel);
├─ quast is not installable because it requires
│ └─ blast, which does not exist (perhaps a missing channel);
├─ ragtag is not installable because there are no viable options
│ ├─ ragtag [1.0.0|1.0.1] would require
│ │ └─ pysam, which does not exist (perhaps a missing channel);
│ └─ ragtag [1.0.1|1.0.2|...|2.1.0] would require
│ └─ minimap2, which does not exist (perhaps a missing channel);
├─ roary does not exist (perhaps a typo or a missing channel);
├─ samtools does not exist (perhaps a typo or a missing channel);
├─ sickle-trim does not exist (perhaps a typo or a missing channel);
├─ spades does not exist (perhaps a typo or a missing channel);
└─ sra-tools does not exist (perhaps a typo or a missing channel).
As I am still new to this whole thing, my initiate thought was to install the missing package. I had used brew previously, so I did install spade pysam and above mentioned packages through brew. But it seems like the conda environment wouldnt be able to access it? I face problem to instal each of it through conda with an error saying that the package is not available.
Do you have any idea to solve such issue? Thank you!
Thank you so much for your video and tutorial, Mr. Vincent.
I was about to prepare the whole environment however this error showed up as follow, after " conda env create --quiet -f environment.yaml"
Channels:
Platform: osx-arm64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... failed
Channels:
Platform: osx-arm64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... failed
LibMambaUnsatisfiableError: Encountered problems while solving:
Could not solve for environment specs
The following packages are incompatible
├─ abricate is not installable because it requires
│ └─ blast >=2.7 , which does not exist (perhaps a missing channel);
├─ bwa does not exist (perhaps a typo or a missing channel);
├─ mafft does not exist (perhaps a typo or a missing channel);
├─ mash does not exist (perhaps a typo or a missing channel);
├─ minimap2 does not exist (perhaps a typo or a missing channel);
├─ mlst is not installable because there are no viable options
│ ├─ mlst [2.16.2|2.16.4] would require
│ │ └─ blast >=2.7.1 , which does not exist (perhaps a missing channel);
│ └─ mlst [2.17.6|2.18.0|...|2.23.0] would require
│ └─ blast >=2.9.0 , which does not exist (perhaps a missing channel);
├─ mummer does not exist (perhaps a typo or a missing channel);
├─ perl-db-file does not exist (perhaps a typo or a missing channel);
├─ perl-padwalker does not exist (perhaps a typo or a missing channel);
├─ porechop does not exist (perhaps a typo or a missing channel);
├─ prokka is not installable because it requires
│ └─ aragorn >=1.2 , which does not exist (perhaps a missing channel);
├─ quast is not installable because it requires
│ └─ blast, which does not exist (perhaps a missing channel);
├─ ragtag is not installable because there are no viable options
│ ├─ ragtag [1.0.0|1.0.1] would require
│ │ └─ pysam, which does not exist (perhaps a missing channel);
│ └─ ragtag [1.0.1|1.0.2|...|2.1.0] would require
│ └─ minimap2, which does not exist (perhaps a missing channel);
├─ roary does not exist (perhaps a typo or a missing channel);
├─ samtools does not exist (perhaps a typo or a missing channel);
├─ sickle-trim does not exist (perhaps a typo or a missing channel);
├─ spades does not exist (perhaps a typo or a missing channel);
└─ sra-tools does not exist (perhaps a typo or a missing channel).
As I am still new to this whole thing, my initiate thought was to install the missing package. I had used brew previously, so I did install spade pysam and above mentioned packages through brew. But it seems like the conda environment wouldnt be able to access it? I face problem to instal each of it through conda with an error saying that the package is not available.
Do you have any idea to solve such issue? Thank you!