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jorvis / biocode

Bioinformatics code libraries and scripts
MIT License
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Conda based install #65

Open nhartwic opened 5 years ago

nhartwic commented 5 years ago

For those who don't have admin privileges and avoid apt-get, you should be able to use conda to manage the install of the biocode dependencies. You can use the following commands...

# create a new conda environment named 'misc3' with needed dependencies and install biocode
conda create -n misc3 -c conda-forge python==3.6.8 pip zlib libblas liblapack libxml2
conda activate misc3
pip install biocode

I haven't fully tested my install but have used several of the gff scripts and it all seems to work fine.

Assuming this installation method actually works (I don't see why it wouldn't) it may be worth adding these commands to the biocode README

jorvis commented 5 years ago

I don't use conda but will happily accept a pull request with this added to the README if you're interested in doing it. My only suggestions to change would be the 'misc3' to something like 'biocode' (why not?) and accepting any Python 3.4 or higher.

mikemc commented 4 years ago

I just installed Biocode via this method and have one minor suggestion if these instructions are added to the README. I came here looking for a way to convert Genbank files to GFF3 files, and in addition to the above I had to install Biopython to the conda environment before I could use the gff/convert_genbank_to_gff3.py script. If Biopython is a common requirement for Biocode scripts then it might be worth adding it to the conda create call or mentioning it as an optional dependency.