search

RabadanLab / arcasHLA

Fast and accurate in silico inference of HLA genotypes from RNA-seq
GNU General Public License v3.0
121 stars 50 forks source link

Command reference --version fails for specific versions #97

Open christopher-mohr opened 1 year ago

christopher-mohr commented 1 year ago

Hi,

The command arcasHLA reference --version fails for specific versions (it seems like every reference > 3.34.0).

arcasHLA reference --version 3.35.0 -v

--------------------------------------------------------------------------------
[reference] Checking out IMGT/HLA:

    git -C /opt/miniconda3/envs/test_arcas/share/arcas-hla-0.5.0-1/scripts/../dat/IMGTHLA/ checkout -f 870e39341592de0113c530f471098490a246ac24

    Previous HEAD position was af8f6da IPD-IMGT/HLA Release 3.36.0
    HEAD is now at 870e393 Moving to hml subdir in ihiw

[reference] IMGT/HLA database version:

870e39341592de0113c530f471098490a246ac24

[reference] Processing IMGT/HLA database
[reference] Error: dat/IMGTHLA/hla.dat empty or corrupted.

I installed arcasHLA using conda (bioconda/noarch::arcas-hla-0.5.0-hdfd78af_1).

Best regards Christopher

tdfy commented 1 year ago

@christopher-mohr any luck resolving this? Having the same issue.

tdfy commented 1 year ago

this sorted me out: https://github.com/RabadanLab/arcasHLA/issues/42

christopher-mohr commented 1 year ago

this sorted me out: https://github.com/RabadanLab/arcasHLA/issues/42

@tdfy Since I installed it using conda I would expect that this is not necessary. I guess the recipe might need an update then.