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tseemann / abricate

:mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes
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Trouble installing from source on Ubuntu 18.04 LTS #166

Open skbrimer opened 3 years ago

skbrimer commented 3 years ago

Hello Abricate team,

I have finally been able to get everything work, however I don't think the way I did it is the best so I wanted send this issue.

I currently have all the required packages, in my path, and at the list version levels or better (blast 2.7.1, perl 5.26).

When I ran the abricate --setupdb I got several errors about the individual databases not being index and I should run the same command again to set them up. I end up just using the abricate-get_db --db <db> --force for each one that it said wasn't indexed which was most of them. I am not sure what or why it didn't do this the provided db's

My other concern, and the part I don't think was a great idea, was abricate was unable to locate makeblastdb from my path. I even added it in my path explicitly (ie. /opt/ncbi-blast-2.7.1+/bin/makeblastdb) and it still couldn't located it. So my "fix" was I edited the abricate-get_db perl script and put the full location in the command to get it to work.

Is this a common error? How should I have fixed this instead?

Thank you for creating and maintaining this package!

andersgs commented 3 years ago

@skbrimer can you detail how you created the environment? Did you use conda?

In regards to makeblastdb, can you share the output of echo $PATH?

The folder with the executable should be in the path, not the full path to the executable itself. Does that make sense?

skbrimer commented 3 years ago

Thanks you for getting back so fast @andersgs! I did not use conda to create the environment. I followed the directions for installing from github.

I understand that the folder should be in the path (i.e. blast/bin) I just temperately added the path to the executable to see if that would work. Please find the requested output below. 

sean@LEN943:~$ echo $PATH
/home/sean/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/home/sean/.local/bin:/opt/:/opt/bwa:/opt/SPAdes-3.13.0-Linux/bin:/opt/miniasm:/opt/minimap2:/opt/ncbi-blast-2.7.1+/bin:/opt/prokka/bin/:/opt/ont-guppy-cpu/bin:/opt/bbmap/:/opt/kma:/opt/Harvest/:/opt/seqtk/:/opt/wtdbg2/:/opt/flu-amd
omrctnr commented 3 years ago

@skbrimer could you send your abricate version abricate --version

Maybe you can update as follows: conda update -c conda-forge -c bioconda -c defaults abricate