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bcgsc / orca

:whale: Genomics Research Container Architecture
http://www.bcgsc.ca/services/orca
GNU General Public License v3.0
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Temporarily remove abricate, uninstall jdk #80

Closed lcoombe closed 5 years ago

lcoombe commented 5 years ago
lcoombe commented 5 years ago

abricate error:

/home/linuxbrew/.linuxbrew/Cellar/abricate/0.8.10/bin/abricate
--setupdb
Removing old BLAST indices for /home/linuxbrew/.linuxbrew/Cellar/abricate/0.8.10/libexec/bin/../db/ncbi/sequences
Making nucl BLAST index for /home/linuxbrew/.linuxbrew/Cellar/abricate/0.8.10/libexec/bin/../db/ncbi/sequences
Removing old BLAST indices for /home/linuxbrew/.linuxbrew/Cellar/abricate/0.8.10/libexec/bin/../db/plasmidfinder/sequences
Making nucl BLAST index for /home/linuxbrew/.linuxbrew/Cellar/abricate/0.8.10/libexec/bin/../db/plasmidfinder/sequences
ERROR: Database plasmidfinder is not indexed, please try: abricate --setupdb
Warning: The post-install step did not complete successfully
lcoombe commented 5 years ago

Error when building appletviewer

==> Pouring openjdk-1.8.0-181.x86_64_linux.bottle.tar.gz
Error: The `brew link` step did not complete successfully
The formula built, but is not symlinked into /home/linuxbrew/.linuxbrew
Could not symlink bin/appletviewer
Target /home/linuxbrew/.linuxbrew/bin/appletviewer
is a symlink belonging to jdk. You can unlink it:
brew unlink jdk
To force the link and overwrite all conflicting files:
brew link --overwrite openjdk
To list all files that would be deleted:
brew link --overwrite --dry-run openjdk