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jpuritz / dDocent

a bash pipeline for RAD sequencing
ddocent.com
MIT License
53 stars 41 forks source link

Conda dDocent recipe has incorrect FreeBayes #48

Closed pdimens closed 4 years ago

pdimens commented 4 years ago

A fresh conda install of dDocent with conda install -c bioconda ddocent installs this version of freebayes:

 freebayes          bioconda/linux-64::freebayes-0.9.21.7-0

such that when dDocent is invoked, this error appears and dDocent exits:

/home/pdimens/.conda/envs/ddocent2/bin/dDocent: line 6: export: `2.7.8': not a valid identifier
dDocent 2.7.8 

Contact jpuritz@uri.edu with any problems 

Checking for required software
The version of FreeBayes installed in your $PATH is not optimized for dDocent.
Please install at least version 1.0.0

The problem is easily fixed with conda update freebayes though.

jpuritz commented 4 years ago

Hey Pavel, conda install actually attempts to match your downloaded resources. The best way to get the most up-to-date version of everything is to create a new conda environment conda create -n ddocent -c bioconda ddocent