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ablab / quast

Genome assembly evaluation tool
http://quast.sf.net
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Error running QUAST with reads #217

Open fgvieira opened 2 years ago

fgvieira commented 2 years ago

Installed quast from bioconda but, when running it with some pacbio reads, got an error because it could not compile bwa:

Running Reads analyzer...
Compiling BWA (details are in ~/conda/e6259dc85fe1040d962ac085bd6454c2/lib/python3.9/site-packages/quast_libs/bwa/make.log and make.err)
WARNING: Permission denied accessing ~/conda/e6259dc85fe1040d962ac085bd6454c2/lib/python3.9/site-packages/quast_libs/bwa. Did you forget sudo?
Failed reads analysis

If quast requires bwa/bedtools/gridss/..., wouldn't it be better to include them in the bioconda recipe?

Also, is it intended that quast uses bwa to map pacbio reads? Shouldn't it use minimap2?

bebatut commented 2 years ago

Did you find a way to run the tool anyway? I got the same error when updating the Galaxy tool for quast: installation of quast from conda and no rights to on /usr/ local/lib/python3.10/site-packages/quast_libs/bwa/make.log

fgvieira commented 2 years ago

It seems QUAST checks if the binary exist before trying to install them, so I just manually installed all necessary programs in the conda environment. But it would make more sense to include them in the conda recipe.

bebatut commented 2 years ago

I thought the solution was more complex :smile: I created a PR on bioconda to update the package and add bwa and bedtools as run requirements

fgvieira commented 2 years ago

Can you also add gridss? Not sure if QUAST needs other programs, but those three for sure.

Thanks!

bebatut commented 2 years ago

I just added gridss too. Let's see if it works :smile:

KatSteinke commented 1 year ago

For me, even after explicitly adding gridss to the environment I'm running QUAST (5.2.0 installed through mamba) in, it'll try to build its own. Is anyone else still having that issue, or is it just me having overlooked something?