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jpuritz / dDocent

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

Error in install_dDocent_requirements #14

Closed jerowe closed 8 years ago

jerowe commented 8 years ago

Starting on line 54 there is a chunk of code that looks like it should install vcflib, but instead installs freebayes instead.

echo "Checking for vcflib" if which vcfcombine &>/dev/null; then echo "FreeBayes is already installed" else echo "Downloading and installing FreeBayes" git clone --recursive git://github.com/ekg/freebayes.git cd freebayes

jpuritz commented 8 years ago

vcflib is packaged as part of freebayes if you use the --recursive option. The next line of code changes the directory into the vcflib. Freebayes is needed for the pipeline anyway, so I just stuck with that repository. It's no different than going directly to the vcflib github.