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chrishah / maker-docker

Docker image as base for building full MAKER image
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Perl errors after following install instructions #2

Open conchoecia opened 5 years ago

conchoecia commented 5 years ago

I followed the install instructions and ran into the following error when I ran the command: docker run -it -v $(pwd):/in/ -w /in/ --rm your-maker-plus:version RepeatModeler -pa 8 -engine ncbi -database mydbname:

Can't locate WUBlastSearchEngine.pm in @INC (you may need to install the WUBlastSearchEngine module) (@INC contains: /usr/local/RepeatMasker /usr/local/bin/RepeatModeler /usr/src/bioperl-live-release-1-7-2 /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.26.1 /usr/local/share/perl/5.26.1 /usr/lib/x86_64-linux-gnu/perl5/5.26 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.26 /usr/share/perl/5.26 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at /usr/local/bin/RepeatModeler/RepeatUtil.pm line 78.
BEGIN failed--compilation aborted at /usr/local/bin/RepeatModeler/RepeatUtil.pm line 78.
Compilation failed in require at /usr/local/bin/RepeatModeler/RepeatModeler line 114.
BEGIN failed--compilation aborted at /usr/local/bin/RepeatModeler/RepeatModeler line 114

I used maker 2.31.10 and the 2017 repbase database when I followed your install instructions in the README.md.

chrishah commented 5 years ago

Hi, Sorry, wasn't watching the issues. Didn't expect anybody to raise any since I was assuming I am the only one using this.

Your error is surprising. When building the image you did everything as I suggested in the instructions, except for using the different repbase repeatlibrary release?

Can you enter the container, please:

docker run -it --rm your-maker-plus:version /bin/bash

Then please tell me what the following returns:

ls -hl /usr/local/RepeatMasker/WUBlastSearchEngine.pm

cheers, Christoph