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tseemann / barrnap

:microscope: :leo: Bacterial ribosomal RNA predictor
GNU General Public License v3.0
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Can not find required 'nhmmer' #44

Open Lcornet opened 4 years ago

Lcornet commented 4 years ago

Hello,

I would like to install barrnap in a singularity container but I have the following issue :

./barrnap --quiet examples/small.fna [barrnap] ERROR: Can not find required 'nhmmer' in PATH

But nhmmer is in the path : Singularity centos8.img:/opt/barrnap/bin> nhmmer -h nhmmer :: search a DNA model, alignment, or sequence against a DNA database HMMER 3.3.1 (Jul 2020); http://hmmer.org/

Could you help me to understand the problem, please ?

Singularity centos8.img:/opt/barrnap/bin> ./barrnap [barrnap] This is barrnap 0.9 [barrnap] Written by Torsten Seemann [barrnap] Obtained from https://github.com/tseemann/barrnap [barrnap] Detected operating system: linux [barrnap] Adding /opt/barrnap/bin/../binaries/linux to end of PATH [barrnap] Checking for dependencies: [barrnap] ERROR: Can not find required 'nhmmer' in PATH

Singularity centos8.img:/opt/barrnap/bin> ls ../binaries/linux/ nhmmer

jamiemcg commented 4 years ago

@Lcornet I also ran into this issue when installing barrnap in a singularity container.

By default, Centos does not include the which command. Without it barrnap cannot find the nhmmer or bedtools dependencies. For me, making sure which was installed fixed any issues.