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marbl / parsnp

Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can be both draft assemblies and finished genomes, and output includes variant (SNP) calls, core genome phylogeny and multi-alignments. Parsnp leverages contextual information provided by multi-alignments surrounding SNP sites for filtration/cleaning, in addition to existing tools for recombination detection/filtration and phylogenetic reconstruction.
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conda and pip install don't install the latest version #90

Closed tiagocabralborelli closed 3 years ago

tiagocabralborelli commented 3 years ago

Recently I had to reinstall parsnp and I realized that neither conda nor pip are downloading version 1.5.4. Instead, they download version 1.2 which presented some bugs even for genomes that I have successfully used before. I tried to replace only the parsnp file available on this repository but I'm my Linux abilities are that good. Please can someone give me a hint? Thanks.

bkille commented 3 years ago

Hi, this seems to be a symptom of not setting up the Bioconda channels. The documentation for setting up Bioconda can be found here. Please let me know if conda still can't find the newest version of Parsnp after you've set up the channels.

tiagocabralborelli commented 3 years ago

I tried set bioconda channel and the version problem remains but with the conda-forge channel, everything seems to be ok and working well.

Thanks, guys. <3