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run.sh doesn't produce usable file, last line deleted in old commit #5

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martiliasf opened this issue Jan 16, 2020 · 0 comments
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@martiliasf
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I finally figured out why I couldn't run Pharmcat from the output created by the pipeline. The last line of run.sh was deleted in an old commit, so no usable file was created.

02966ce#diff-1b0c2b516b83393edb7200ad5ff12181L114

also, the file that the line references was also deleted in the same commit:
pgkb-ngs-pipeline/external_data/grc38_pgx.tight.list

For anyone else coming across this issue, you can manually enter this line back and replace the .tight.list file in that directory and then pharmcat will run.

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