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Teichlab / bracer

BraCeR - reconstruction of B cell receptor sequences from single-cell RNAseq data
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IgBLAST crashes in docker container #53

Open antonkulaga opened 4 years ago

antonkulaga commented 4 years ago

When I ran the latest docker container on test fastq data it crashes with IgBLAST subprocess stdout.txt stderr.txt

Here is the command that was run:

bracer assemble --ncores 28 --species Hsap  cell_1 bracer_results /cromwell-executions/BCR_extraction/39483cc3-3a87-4370-96bb-7c7e8e4112dd/call-bracer_assemble/inputs/1726693592/cell1_1.fastq /cromwell-executions/BCR_extraction/39483cc3-3a87-4370-96bb-7c7e8e4112dd/call-bracer_assemble/inputs/1726693592/cell1_2.fastq
dcroote commented 4 years ago

This may have to do with the IGDATA environment variable being exported by a Dockerfile ENTRYPOINT script: https://github.com/Teichlab/bracer/blob/131c2b9a90cef87ea7afd7c47227852d822537a9/Dockerfile#L72

Try exporting IGDATA prior to running bracer assemble: 

export IGDATA=/ncbi-igblast-1.4.0/bin && bracer assemble ...