TestNirvana.sh

[camtorbri]

Love Nirvana annotation and the TestNirvana.sh makes the installation totally painless....!

[Installing in Win10] The very last command in the script:

analyze it with Nirvana

dotnet $NIRVANA_BIN -c $CACHE_DIR/Both --sd $SA_DIR -r $REF_TEST -i HiSeq.10000.vcf -o HiSeq.10000.annotated

hits an error that is related to a "tab" that should not be there after NA12878 [Line 36 of the HiSeek.1000.vcf]. The extra character maskes it appear as if there is a second sample to follow triggering the error.

ERROR: Inconsistent number of sample fields in line: chr1 109 ..........

Remove the extra tab at the end of this line and the command would run fine.

camilo

[jerryliu2005]

Unrelated to the above issue but I want to point out a minor bug with TestNirvana.sh. Between line #80 and #81 you need to add a cd $NIRVANA_ROOT statement for git checkout $NIRVANA_TAG to work. Otherwise the test script will always run the master branch instead of the release tag.

Another trivial thing is I do not see where the download() function is used in the test bash script but this doesn't affect anything.

-Jerry

[camtorbri]

Thanks...!

On Tue, Aug 11, 2020 at 3:23 PM Jerry Liu notifications@github.com wrote:

Unrelated to the above issue but I want to point out a minor bug with TestNirvana.sh. Between line #80 and #81 you need to add a cd $NIRVANA_ROOT statement for git checkout $NIRVANA_TAG to work. Otherwise the test script will always run the master branch instead of the release tag.

Another trivial thing is I do not see where the download() function is used in the test bash script but this doesn't affect anything.

-Jerry

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[MichaelStromberg]

Ah yes, TestNirvana.sh needs some TLC. I'll update that today and ping this thread when complete.

[MichaelStromberg]

TestNirvana.sh finally received some TLC today. Thank you for the heads up! Here's the new page: https://illumina.github.io/NirvanaDocumentation/introduction/getting-started