AntiSMASH & GapMind installations give an error? #5
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Anto007
changed the title
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Hello @Anto007 , Thanks for reporting the issue. It seems like Please give it a try and let us know if the issue is still there. |
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Thanks @acarafat for getting back on this. I had tried this too but the same error persists after running |
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Hi @Anto007, It looks like similar to the with recent A possible solution is to use Conda to build |
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Hi @Anto007, Arafat is correct, it seems to be an issue with the latest nrpys conda build recipe. An easier alternative may be to try again with pip in the beav environment, but this time using the force reinstall option: python -m pip install --upgrade --force-reinstall nrpys |
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Thank you very much @alexweisberg and @acarafat for your responses. The force reinstall for nrpys worked to get AntiSMASH installed but GapMind installation still seems to fail. I have the perl-DBI module in my conda env (as running |
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Hmm, could you paste the output of the following command both before and after activating your beav environment?
Sometimes having other perl modules installed elsewhere can conflict with the conda versions. If you |
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Thank you for your feedback @alexweisberg I think this problem is due to perl library conflicts. $PERL5LIB points to a perl version outside of my conda beav. I tried setting export PERL5LIB to the perl version within the conda beav env but GapMind installation still fails. I don't wanna run unset PERL5LIB without knowing if it would have permanent consequences? There are a hundred other tools installed on my system and I wish to not break those for the purpose of merely making beav work. One of the main reasons I was interested in beav is cos' it also provided GapMind analysis but unfortunately, it seems like beav would just end up on my 'interesting but unusable tools' list. GapMind standalone version is another tool that I don't feel very motivated to install since a convenient web-server is already available for the same |
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If you run |
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Thank you very much again @alexweisberg for your patient responses. I tried I uninstalled the conda beav env and retried the above steps in a fresh conda beav env and the GapMind intallation error persisted. Strangely, antiSMASH installation also failed this time (despite making it to work in the previous conda beav env by running your recommended command-line |
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That is odd. Did you have the conda environment activated when you ran beav_db? The antismash error looks like an internet connection issue. perhaps the server hosting the antismash db is temporarily down. You might want to try rerunning it later. The GapMind error also is strange. The perl library path (@inc) doesn't seem to include any of the folders from your conda environment, which makes me think it is not activated. If it is somehow using your system perl instead, which is a different version from the one in the beav environment, then it won't be able to use the DBI library from the conda environment. |
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Thank you @alexweisberg. I agree it's strange. The conda environment is activated though. If it were not activated, there's no way the command |
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A few other things you could try would be to activate the conda environment, and then try running
and
Both of these should point to the perl files and paths in your conda environment. If not, something is odd with the setup of perl or the activation of conda on your system. |
Hi,
Beav looks interesting and I was hoping to testing it out. I installed beav via conda on my Ubuntu 20.04.6 LTS workstation but I get the below error after activating the conda beav env and running beav_db
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