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GeneDx / pgr-tk

PGR-TK: Pangenome Research Tool Kit
MIT License
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RUST error in Conda stable version #21

Closed TanXinjiang closed 1 year ago

TanXinjiang commented 1 year ago

Hello, Thanks for the excellent toolkit and congratulations for the publication. I have installed pgr-tk v0.3.6 as introduced in README.md, and tried to create pgr minimizer database with HPRC-yr1.agc with: pgr-mdb HPRC-yr1.agc HPRC-yr1 but it raised an error as : thread 'main' panicked at 'called 'Result::unwrap()' on an 'Err' value: Error { kind: InvalidData, message: "stream did not contain valid UTF-8" src/bin/pgr-mdb.rs:47:25 note: run with 'RUST_BACKTRACE=1' environment variable to display a backtrace Same error when trying to pip install as #1 Thanks! Xinjiang Tan

cschin commented 1 year ago

@TanXinjiang thank. you should create a file containing the path to the "HPRC-yr1.agc" as the first argument of the pgr-mdb command. It don't take the "HPRC-yr1.agc" as input directly.

cschin commented 1 year ago

@TanXinjiang, I just have to do this, this is an example:

agc create human_GRCh38_no_alt_analysis_set.fasta -i file_list -o test.agc
echo test.agc > input
pgr-mdbinput test
pgr-fetch-seqs  test --list

the file_list contains the pangenome assemblies that I am interested in using

TanXinjiang commented 1 year ago

@cschin Thanks a lot! I've managed to create the index from command line, but the other functions seem to only work in the python environment ? (I only found pgr-mdb under ~/anaconda3/envs/pgr-tk/bin/)