Open bluefox18010139 opened 7 months ago
vappiah
commented
7 months ago Hi @bluefox18010139 It appears the software version for macos is unavailable in conda. Here are some possible workarounds.
Alternatively you can create a docker image that has all the tools and you can run that. Or Create a Virtual Linux Environment on your system and use that.
bluefox18010139
commented
7 months ago Dear Mr. Vincent,
Thank you for your quick response. I have installed other packages using brew but I'm not really sure of how you meant by download binaries and compile from source.
I tried the virtual linux environment but still receiving the same missing packages. I tried to install the missing packages through conda at linux virtual environment but the same error showed as follow.
"Retrieving notices: ...working... done Channels:
PackagesNotFoundError: The following packages are not available from current channels:
Current channels:
To search for alternate channels that may provide the conda package you're looking for, navigate to
https://anaconda.organd use the search bar at the top of the page."
I faced the same error when I tried to install blast using conda at my own terminal. I think back again to my operating system sadly, maybe I should have linux x86 instead.. If you have any ideas, kindly drop your opinion. It will be highly appreciated.
Really wish can try using your established method. Thank you!
vappiah
commented
7 months ago I have some tutorials on conda which can help you setup your linux system. Here are the links
https://www.youtube.com/playlist?list=PLe1-kjuYBZ070ZEjX3MulaMGcQPhU8KQY https://www.youtube.com/playlist?list=PLe1-kjuYBZ070ZEjX3MulaMGcQPhU8KQY
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:
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!