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wurmlab / flo

Same species annotation lift over pipeline.
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Not processing gff #8

Closed pgonzale60 closed 7 years ago

pgonzale60 commented 7 years ago

Hi!

The lift over chaining works like a charm, however it crashes when trying to process_gff. The issue seems to come from line 62 in the rakefile: require 'bio/db/gff' I don't know if I need to install something in order to make this work.

Error shows: liftOver -gff dwil_flybase.gff3 run/liftover.chn dwil_flybase-liftover-dwil_JR/lifted.gff3 dwil_flybase-liftover-dwil_JR/unlifted.gff3 Reading liftover chains Mapping coordinates WARNING: -gff is not recommended. Use 'ldHgGene -out=<file.gp>' and then 'liftOver -genePred <file.gp>' rake aborted! LoadError: cannot load such file -- bio/db/gff /home/pgonzale/Programs/flo/Rakefile:62:inprocess_gff' /home/pgonzale/Programs/flo/Rakefile:234:in block (2 levels) in <top (required)>' /home/pgonzale/Programs/flo/Rakefile:223:ineach' /home/pgonzale/Programs/flo/Rakefile:223:in block in <top (required)>' Tasks: TOP => default (See full trace by running task with --trace)

Greetings!

yeban commented 7 years ago

Hey. If you could just run gem install bio and rerun flo, that should do it.

(run sudo gem install bio if gem install bio doesn't work)

yeban commented 7 years ago

closing note - added BioRuby to dependencies section in README