Skippy 4.0 bug (Can not find required 'vcffirstheader' in PATH)

[manuss11]

Hello, while running nullarbor it stopped and showed the following error: Can not find required 'vcffirstheader' in PATH I found that it is a bug from the 4.0 version of skippy. I tried to downgrade to 3.2v, but I am not able to run nullarbor with skippy 3.2. How could I solve this issue? Could I return the pipeline from that step?

Thanks

[stephenturner]

I ran into this issue a while back, wrote this hack years ago to fix it. Not sure if it'll still work. https://gist.github.com/stephenturner/005d4e4e322b8cf5b991d1d357527859#file-nullarbor-install-ubuntu1404-sh-L194

On Tue, Jul 3, 2018 at 3:36 PM manuss11 notifications@github.com wrote:

Hello, while running nullarbor it stopped and showed the following error: Can not find required 'vcffirstheader' in PATH I found that it is a bug from the 4.0 version of skippy. I tried to downgrade to 3.2v, but I am not able to run nullarbor with skippy 3.2. How could I solve this issue? Could I return the pipeline from that step?

Thanks

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[tseemann]

Snippy 4 is a requirement of Nullarbor 2 . Both are close to release, but not quite ready yet.

It appears you have a bad vcflib installation. Vcflib was buggy in the past but I think it's fixed now.

How did you install things? Manually, brew or conda?

[manuss11]

Mostly by using conda. I found a solution by installing 3.2v and then 4.0v (vcffirstheader remains, I don't know how). But after re-run, another bug related to snippy 4.0 appeared:

snpEff build -c reference/snpeff.config -dataDir . -gff3 ref

java.lang.RuntimeException: Error parsing property 'ref.NC_017960.codonTable'. No such codon table 'Bacterial_and_Plant_Plastid' at org.snpeff.snpEffect.Config.createCodonTables(Config.java:169) at org.snpeff.snpEffect.Config.readConfig(Config.java:650) at org.snpeff.snpEffect.Config.init(Config.java:480) at org.snpeff.snpEffect.Config.(Config.java:117) at org.snpeff.SnpEff.loadConfig(SnpEff.java:451) at org.snpeff.snpEffect.commandLine.SnpEffCmdBuild.run(SnpEffCmdBuild.java:364) at org.snpeff.SnpEff.run(SnpEff.java:1183) at org.snpeff.SnpEff.main(SnpEff.java:162)

Mr. Seemann, did you mean that we cannot run nullarbor 2 until snippy 4 will be released? Should I use Nullarbor 1 instead?

Thanks

[tseemann]

SNippy 4 in conda is a mistake. Someone added it prematurely, It does not work. You'll need to use github clone method.