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BioJulia / Bio.jl

[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia
http://biojulia.dev
MIT License
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Installation of Bio.jl master branch; HttpParser fails #478

Closed weinstockj closed 7 years ago

weinstockj commented 7 years ago

I'm on Ubuntu 14.04, running Julia 0.5.2. I'm trying to use the Bio.Var module in the Bio.jl package.

Running Pkg.clone("https://github.com/BioJulia/Bio.jl.git") fails with

ERROR: HttpParser LoadError: could not spawn setenv(make -j8 C http-parser-2.7.1 library ....)

The error message includes a recommendation to run Pkg.build("HttpParser"), which fails with the same error message.

I tried earlier to install Bio.jl on Julia 0.6.0, which failed due to PairwiseListMatrices not building.

I understand that I am not using the stable release here, but I am only interested in the VCF reader. Perhaps there's a workaround for using the Bio.Var module? My apologies if this is more of an HttpParser issue than a Bio.jl issue.

TransGirlCodes commented 7 years ago

Try using the latest release of GeneticVariation.jl - it contains the VCF parser from Bio.Var. GeneticVariation is the Bio.Var module in the new non-monolithic code organisation we are moving to.

weinstockj commented 7 years ago

Thanks - that worked!