make not working on Mac OS X with current go installed

[njbowen]

make error in Mac OS X 10.14.3 command and error pasted below

G2A:2vcf-develop nbowen$ make
go build -o bin/2vcf ./cmd/2vcf/
cmd/2vcf/2vcf.go:11:2: cannot find package "github.com/briandowns/spinner" in any of:
/usr/local/go/src/github.com/briandowns/spinner (from $GOROOT)
/Users/nbowen/go/src/github.com/briandowns/spinner (from $GOPATH)
cmd/2vcf/2vcf.go:12:2: cannot find package "github.com/fatih/color" in any of:
/usr/local/go/src/github.com/fatih/color (from $GOROOT)
/Users/nbowen/go/src/github.com/fatih/color (from $GOPATH)
cmd/2vcf/2vcf.go:13:2: cannot find package "github.com/plantimals/2vcf/convert" in any of:
/usr/local/go/src/github.com/plantimals/2vcf/convert (from $GOROOT)
/Users/nbowen/go/src/github.com/plantimals/2vcf/convert (from $GOPATH)
cmd/2vcf/2vcf.go:14:2: cannot find package "github.com/plantimals/2vcf/genomicsuploader" in any of:
/usr/local/go/src/github.com/plantimals/2vcf/genomicsuploader (from $GOROOT)
/Users/nbowen/go/src/github.com/plantimals/2vcf/genomicsuploader (from $GOPATH)
cmd/2vcf/2vcf.go:16:2: cannot find package "gopkg.in/alecthomas/kingpin.v2" in any of:
/usr/local/go/src/gopkg.in/alecthomas/kingpin.v2 (from $GOROOT)
/Users/nbowen/go/src/gopkg.in/alecthomas/kingpin.v2 (from $GOPATH)
make: *** [2vcf] Error 1
G2A:2vcf-develop nbowen$

[njbowen]

used go get command to pull all the packages listed in error, now error is
go build -o bin/2vcf ./cmd/2vcf/

github.com/plantimals/2vcf/genomicsuploader

../go/src/github.com/plantimals/2vcf/genomicsuploader/genomicsuploader.go:95:26: c.GenomicsService.Variants undefined (type *genomics.Service has no field or method Variants)
../go/src/github.com/plantimals/2vcf/genomicsuploader/genomicsuploader.go:95:44: undefined: genomics.ImportVariantsRequest
../go/src/github.com/plantimals/2vcf/genomicsuploader/genomicsuploader.go:113:41: undefined: genomics.Dataset
../go/src/github.com/plantimals/2vcf/genomicsuploader/genomicsuploader.go:115:27: c.GenomicsService.Datasets undefined (type *genomics.Service has no field or method Datasets)
../go/src/github.com/plantimals/2vcf/genomicsuploader/genomicsuploader.go:130:25: c.GenomicsService.Datasets undefined (type *genomics.Service has no field or method Datasets)
../go/src/github.com/plantimals/2vcf/genomicsuploader/genomicsuploader.go:130:43: undefined: genomics.Dataset
../go/src/github.com/plantimals/2vcf/genomicsuploader/genomicsuploader.go:141:44: undefined: genomics.Dataset
../go/src/github.com/plantimals/2vcf/genomicsuploader/genomicsuploader.go:141:64: undefined: genomics.VariantSet
../go/src/github.com/plantimals/2vcf/genomicsuploader/genomicsuploader.go:143:27: c.GenomicsService.Variantsets undefined (type *genomics.Service has no field or method Variantsets)
../go/src/github.com/plantimals/2vcf/genomicsuploader/genomicsuploader.go:143:48: undefined: genomics.SearchVariantSetsRequest
../go/src/github.com/plantimals/2vcf/genomicsuploader/genomicsuploader.go:143:48: too many errors
make: *** [2vcf] Error 2

[plantimals]

Hi @njbowen,

I see you closed the issue here, were you able to get the project built? If you're still having trouble, please let me know, I'd be happy to help.

Rob

[plantimals]

If your troubles are coming from the Google Genomics package, I'm working on a newer version that removes the deprecated package.

[njbowen]

Not sure, think it was one of the .go calls. I’ll wait for your update and try again later, thanks.

[plantimals]

@njbowen I've got a branch that builds with the Google Genomics integrations removed. I'll push it tonight and let you know. Thank you for your patience.

[plantimals]

@njbowen ok, you should be able to pull the latest commits and build. I'm also working on including some pre-built binaries so people who just want to use the tool will be able to.

[njbowen]

got it to make, command is in 2vcf-develop/bin/2vcf
not sure of basic command, but issued this from the 2vcf-develop folder

nbowen$ bin/./2vcf conv ancestry X.zip -o X.vcf.zip

vcf output at: X.vcf.zip

however, don't think it ran, can't find output. in --help found a few pointers, but still need assistance. thanks,

[njbowen]

even though I installed go using brew. I still had errors with the make in the 2vcf-develop/ . It presented errors that it was looking for go directories or packages and couldn't find them. I installed each as the errors were returned using go get GitHub.com/xyz until finally no errors were returned. is this how it should make? or is there something wrong with my go installation maybe?
thanks,

[plantimals]

@njbowen yeah, when you build a new project you need to go get any packages you don't already have. I just added a dependency manager called dep. If you check out the latest commits, brew install dep, then run dep ensure, it should download all the required packages.

in any case, you managed to build the executable, so let's see if we can get it working for you. I think you might be missing the reference data path. if you run from the root of the repo that you checked out, it should work automatically, otherwise you can specify a path to the reference. try:

./bin/2vcf conv ancestry path/to/my-genotypes.zip

You may have noticed that the reference/ directory holds a VCF containing the reference data, and the binary needs to be able to load that. if you don't run it from the root directory, you can use the --vcf-ref parameter to specify a path to that reference file.

[plantimals]

@njbowen if you have any future problems with building the binary, now you can download a pre-built binary https://github.com/plantimals/2vcf/releases/tag/v0.3.3

[njbowen]

@plantimals I was in the root directory, but tomorrow I’ll try giving it the reference path and I’ll install a pre built binary and give that a try. Thanks,

[njbowen]

@plantimals I replaced the 2vcf with the Darwin build. I run the command as in the picture below and get a line that the output is..... but there is no output file in the folder. Thanks for helping with this.

[njbowen]

@plantimals I've also run the same and pointed it to the reference file as you suggested, got same blue output line but no output file.

[plantimals]

@njbowen well, I feel pretty dumb, the ancestry path was simply not plugged in. I no longer have an example of ancestry data to test on. I've made the obvious update, but I can't test it locally. If you wouldn't mind pasting a line or two of your file here, replace the genotype calls with nonsense to protect your identity, I would greatly appreciate it. Here's the latest update: https://github.com/plantimals/2vcf/releases/tag/v0.3.5

I really appreciate that you're taking the time to help get this right. I'd be happy to help in a more direct way if you have a time crunch at all here. We could exchange emails, get on a google hangout or something. Let me know if I can be of assistance.

[njbowen]

@plantimals Ancestry_DNA_test.txt

[njbowen]

@plantimals looks like it works now, thanks.

[plantimals]

@njbowen awesome! thank you so much for your help. If you come across any more issues, I would greatly appreciate hearing about them. Especially any features that would make your use easier.

[njbowen]

hi just tried to run on a 23andme v5 raw data file and it only returned ~190K SNPs in the .vcf
do I need a different reference vcf to process v5 results from 23andMe? the v3 raw results seem to work fine.

[plantimals]

@njbowen hmmm. would it be possible for you to extract the rs_id's from your results? I'd like to intersect them with column 3 of the reference file. I really doubt there's been such a huge turnover that only ~20% of the markers would have successful observations.