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databio / bedhost

API and UI for BEDbase
http://api.bedbase.org
BSD 2-Clause "Simplified" License
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Install bigBedToBed in container #49

Closed nsheff closed 3 years ago

nsheff commented 3 years ago

http://dev1.bedbase.org/api/bed/78c0e4753d04b238fc07e4ebe5a02984/regions/chr1

{
  "detail": "ERROR: bigBedToBed is not installed."
}
nsheff commented 3 years ago

@xuebingjie1990 can you add bigBedToBed into the bedhost container?

xuebingjie1990 commented 3 years ago

can you add bigBedToBed into the bedhost container?

i'm not sure how to install bigBedToBed in the container... should I just add these lines to the docker file?

# Install bigBedToBed
ADD ./third_party/linux.x86_64/bigBedToBed /usr/local/bin/bigBedToBed
RUN chmod 755 /usr/local/bin/bigBedToBed

is /usr/local/bin the right path it should be at?

nsheff commented 3 years ago

that's the right direction.

you can do it that way; you'd need to stick the binary in this repo then. You could also download the binary from ucsc and see if that works. but then you'd need wget or curl in the container. maybe it's already there?

xuebingjie1990 commented 3 years ago

You could also download the binary from ucsc and see if that works. but then you'd need wget or curl in the container. maybe it's already there?

like this? 

RUN wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigBedToBed -P /usr/local/bin
RUN chmod 755 /usr/local/bin/bigBedToBed
nsheff commented 3 years ago

try it!