./arcasHLA reference --update fires an error

[OrielResearchCure]

Hello all,

I would like to try the arcas-HLA tool. I hope that you will be able to help me with the installation/execution.
I am working with the following OS on a cloud machine: Debian GNU/Linux 10 (buster).
I tried to install it with Conda and it didn’t work for me (https://anaconda.org/bioconda/arcas-hla)
The following error is after manually installing the dependencies and running: git clone https://github.com/roseorenbuch/arcasHLA.git

when running the reference --update command. this is the error

Traceback (most recent call last):
  File "/home/../../../../../../STEP_4_HLA_TYPING/arcasHLA/scripts/reference.py", line 482, in <module>
    build_fasta()
  File "/home/../../../../../..//STEP_4_HLA_TYPING/arcasHLA/scripts/reference.py", line 371, in build_fasta
    utrs, exons, final_exon_length) = process_hla_dat()
  File "/home/../../../../../..//STEP_4_HLA_TYPING/arcasHLA/scripts/reference.py", line 131, in process_hla_dat
    with open(hla_dat, 'r', encoding='UTF-8') as file:
FileNotFoundError: [Errno 2] No such file or directory: '/home/../../../../../../STEP_4_HLA_TYPING/arcasHLA/scripts/../dat/IMGTHLA/hla.dat'

under dat folder, I see the following folders:

ls ./dat/
info  ref

under the ref folder, I see:

ls ./dat/ref/
GRCh38.chr6.HLA.fasta  GRCh38.chr6.fasta  GRCh38.chr6.noHLA.fasta  allele_groups.p  cDNA.p  cDNA.single.p  hla_transcripts.json

how to include the IMGTHLA folder?

Many thanks for your help,
Eila

[OrielResearchCure]

Based on previous issues that were reported, I reinstalled the git-lfs package.
The issue was not resolved by that.
Please let me know if you have any other idea how to resolve that.
Thanks,
Eila

[tpereachamblee]

Thank you for using our tool. We cannot replicate the issue you are posting here. We tested the conda environment using the following commands which worked as expected:

conda install -c bioconda arcas-hla
git lfs install 
arcasHLA reference --update -v

Please try these commands and copy the exact output of each here if there are any outstanding issues.

Moreover, as per the most recent tagged release v0.4.0 there is no longer any need to use the code base located here https://github.com/roseorenbuch/arcasHLA.git

Please clone and use this repository as such: git clone https://github.com/RabadanLab/arcasHLA.git

[tpereachamblee]

Closing issue due to inactivity.

[OrielResearchCure]

Thank you.
I was able to install it with conda.
I gad to make sure to use the python 3.6 and follow the commands that you listed