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RabadanLab / arcasHLA

Fast and accurate in silico inference of HLA genotypes from RNA-seq
GNU General Public License v3.0
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Deprecation of kallisto pseudo #109

Closed huzuner closed 7 months ago

huzuner commented 1 year ago

Dear developers,

Since the version update of kallisto ==0.46.2, the usage of kallisto pseudo is deprecated and in the latest versionv0.50.0, it is now completely removed. Hence,arcashla genotype cannot be executed any longer with conda installation since it currently downloads the latest version of kallisto due to having kallisto >=0.44.0 as a dependency.

deve105 commented 1 year ago

I would like to know if there is any solution for this problem? Thank you

huzuner commented 1 year ago

I would like to know if there is any solution for this problem? Thank you

For now you can install arcasHLA via conda and use it without a problem, since the version of kallisto in Bioconda recipe was fixed to a previous version.

abuendia commented 7 months ago

Thanks. conda env with bioconda install of kallisto added in #120.