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DiltheyLab / HLA-LA

Fast HLA type inference from whole-genome data
GNU General Public License v3.0
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How to get help? #4

Closed serge2016 closed 7 years ago

serge2016 commented 7 years ago

How to get help from the program? I have tried:

root@5f5e7a4b6c25:/outputs/PRG_MHC_GRCh38_withIMGT# /soft/HLA-PRG-LA/bin/HLA-PRG-LA --help
terminate called after throwing an instance of 'std::out_of_range'
  what():  vector::_M_range_check
Aborted (core dumped)
root@5f5e7a4b6c25:/outputs/PRG_MHC_GRCh38_withIMGT# /soft/HLA-PRG-LA/bin/HLA-PRG-LA -h
terminate called after throwing an instance of 'std::runtime_error'
  what():  Please specify arguments --bwa_bin
Aborted (core dumped)
root@5f5e7a4b6c25:/outputs/PRG_MHC_GRCh38_withIMGT# /soft/HLA-PRG-LA/bin/HLA-PRG-LA help
terminate called after throwing an instance of 'std::runtime_error'
  what():  Please specify arguments --bwa_bin
Aborted (core dumped)
root@5f5e7a4b6c25:/outputs/PRG_MHC_GRCh38_withIMGT# /soft/HLA-PRG-LA/bin/HLA-PRG-LA
terminate called after throwing an instance of 'std::runtime_error'
  what():  Please specify arguments --bwa_bin
Aborted (core dumped)

What is wrong?

colindaven commented 7 years ago

Not the dev, but at a guess it wants the path to the bwa_bin eg bwa binary ?

serge2016 commented 7 years ago

@colindaven sorry, it doesn't help.

./bin/HLA-PRG-LA --bwa_bin /soft/bwa.kit/bwa --samtools_bin /soft/samtools/bin/samtools help

It starts processing something! But doesn't show help message!

AlexanderDilthey commented 7 years ago

The binary is designed to be controlled by HLA-PRG-LA.pl.

Usage is described here: https://github.com/AlexanderDilthey/HLA-PRG-LA

You need to supply the path to bwa and some other programs - see section "Modifying paths.ini" from https://github.com/AlexanderDilthey/HLA-PRG-LA

serge2016 commented 7 years ago

I think it would be great if:

  1. Indexing process is also available through HLA-PRG-LA.pl.
  2. HLA-PRG-LA prints something like "Start me using HLA-PRG-LA.pl!".

The pl script doesn't have help also!

root@5f5e7a4b6c25:/outputs/soft/HLA-PRG-LA# ./src/HLA-PRG-LA.pl --help
Unknown option: help
Use of uninitialized value $sampleID in pattern match (m//) at ./src/HLA-PRG-LA.pl line 85.
Please use only alphanumeric characters - \w+ - for --sampleID at ./src/HLA-PRG-LA.pl line 87.
root@5f5e7a4b6c25:/outputs/soft/HLA-PRG-LA# ./src/HLA-PRG-LA.pl -h
Unknown option: h
Use of uninitialized value $sampleID in pattern match (m//) at ./src/HLA-PRG-LA.pl line 85.
Please use only alphanumeric characters - \w+ - for --sampleID at ./src/HLA-PRG-LA.pl line 87.