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asl / BandageNG

a Bioinformatics Application for Navigating De novo Assembly Graphs Easily
GNU General Public License v3.0
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Bandage cannot find BLAST #147

Open Adamtaranto opened 8 months ago

Adamtaranto commented 8 months ago

I have BLAST and Minimap2 installed in my base miniconda env but Bandage cannot find them when I try to build a database.

Where does Bandage search for these executables?

Adamtaranto commented 8 months ago

Adding symlinks to the programs in the BandageNG.app/MacOS dir alongside the BandageNG app does not work.

It would be useful to have an option to enter a custom PATH in the Graph Search dialogue box.

asl commented 8 months ago

Bandage-NG looks into lots of custom paths (in addition to PATH) including:

                                                                   "/usr/bin"
                                                                   "/bin"
                                                                   "/usr/sbin"
                                                                   "/sbin"
                                                                   "/opt/local/bin"
                                                                   "/usr/local/bin"
                                                                   "/opt/homebrew/bin"
                                                                   "$HOME/bin"
                                                                   "$HOME/.local/bin"
                                                                   "$HOME/miniconda3/bin"
                                                                   "/usr/local/ncbi/blast/bin"

I would suggest you for now to install into one of these paths (as you are on Mac, then just install blast via Homebrew)