hexdump is missing from lumpy container

[ernfrid]

Seeing errors like:

/opt/lumpy-sv/bin/lumpyexpress: line 15: -n: command not found
/opt/lumpy-sv/bin/lumpyexpress: line 16: [: ==: unary operator expected

in my log files.

This results from hexdump not being installed in the container. Thus, the environment variable is undefined and these errors result.

Note that I believe these to be inconsequential and thus may not fix immediately since I'd prefer not to change pipeline versions midstream.

[indraniel]

Wasn't hexdump used to identify bam vs cram filed?

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On Thu, May 18, 2017, 18:53 Dave Larson ***@***.***> wrote: Seeing errors like: /opt/lumpy-sv/bin/lumpyexpress: line 15: -n: command not found /opt/lumpy-sv/bin/lumpyexpress: line 16: [: ==: unary operator expected in my log files. Note that I believe these to be inconsequential and thus may not fix immediately. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#6>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AACm1jW0egJrTXLcswg4PM81UYrJ8MGsks5r7NnkgaJpZM4Nf7Nq> .

[ernfrid]

@indraniel - it was, but sambamba has a bug to do with CRAM so I believe we're using samtools which auto-detects if it's CRAM or BAM.