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DiltheyLab / HLA-LA

Fast HLA type inference from whole-genome data
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Graph path for Conda install #39

Closed NTNguyen13 closed 3 years ago

NTNguyen13 commented 4 years ago

Hi, I have tried HLA:LA recently, I installed it through bioconda, however, I haven't seen any instruction at the end of the installation.

I downloaded the PRG_MHC_GRCh38_withIMGT graph manually, unzip them into the path ~/anaconda3/opt/hla-la/src/graphs/ (the full path is ~/anaconda3/opt/hla-la/src/graphs/PRG_MHC_GRCh38_withIMGT). However, when I run the command, it still gives error:


HLA-LA.pl --BAM $file --sampleID $sample_name --graph PRG_MHC_GRCh38_withIMGT/ --maxThreads 10 --workingDir ~/test_hlala
HLA-LA.pl

Identified paths:
        samtools_bin: ~/anaconda3/bin/samtools
        bwa_bin: ~/anaconda3/bin/bwa
        java_bin: ~/anaconda3/bin/java
        picard_sam2fastq_bin: ~/anaconda3/bin/picard
        General working directory: ~/test_hlala
        Sample-specific working directory: ~test_hlala/0411_01_01

Graph directory ~/opt/hla-la/src/../graphs/PRG_MHC_GRCh38_withIMGT/ not found - valid graph names are subdirectories of the graphs directory in the HLA-LA root at ~/anaconda3/bin/HLA-LA.pl line 198.

I checked the directory:


file "/home/nguyen/anaconda3/opt/hla-la/src/Graph/PRG_MHC_GRCh38_withIMGT/"
/home/nguyen/anaconda3/opt/hla-la/src/Graph/PRG_MHC_GRCh38_withIMGT/: directory

and the files inside

ls
extendedReferenceGenome  knownReferences  mapping  mapping_PRGonly  PRG  referenceGenomeSimulations  sampledReferenceGenomes  sequences.txt  translation

What did go wrong in my case?

davetang commented 4 years ago

The error seems to indicate that HLA-LA.pl is looking for the directory at ~/opt/hla-la/src/../graphs/PRG_MHC_GRCh38_withIMGT/, which equals ~/opt/hla-la/graphs/PRG_MHC_GRCh38_withIMGT/

However, the directory exists at ~/anaconda3/opt/hla-la/src/Graph/PRG_MHC_GRCh38_withIMGT/.

tinyheero commented 3 years ago

I ran into the same problem. The graph data needs to be downloaded and placed in a folder graphs folder that exists in the same level as the src and bin folder. So in your case, it should be placed at ~/anaconda3/opt/hla-la/graphs/PRG_MHC_GRCh38_withIMGT.

NTNguyen13 commented 3 years ago

Hi, moving the graph to opt/hla-la is correct, thank you both!