Fix failed tests

[sjackman]

• [x] perl: Missing libraries: libgdbm.so.4 https://github.com/Linuxbrew/homebrew-core/pull/6328
• [x] beast: BEAST requires Java version 8
• [x] discovar: discovar cannot be built with any available compilers
• [x] gaemr: Failed executing: GAEMR.py --help https://github.com/brewsci/homebrew-science/pull/56
• [x] graphviz: Error: fontconfig: Couldn't find font.
• [x] icu4c: gendict --uchars /usr/share/dict/words dict: error opening input file: ICU Error "U_FILE_ACCESS_ERROR"
• [x] idba: idba -r 220668.reads-10: execution expired
• [x] raxml: raxmlHPC-PTHREADS: execution expired
• [x] RepeatMasker: Can't locate Text/Soundex.pm
• [x] ropebwt2: 1 expected but was 0
• [x] ruby: An error occurred while installing gemoji (3.0.0), and Bundler cannot continue.

See https://hub.docker.com/r/bcgsc/orca/builds/bkugb8zp2colunaf5ngggya/

• [x] bowtie: Can't locate Clone.pm
• [x] mlst: Can't locate List/MoreUtils.pm
• [x] prokka: Can't locate Bio/Root/Version.pm
• [x] simulate-pcr: Can't locate Bio/SeqIO.pm
• [x] trinity: execution expired
• [x] unzip: Failed executing: /usr/bin/zip
• [x] velvetoptimiser: Can't locate Bio/SeqIO.pm

See https://hub.docker.com/r/bcgsc/orca/builds/b2wrhgjdp4ijkxvns7z8zr/

[sjackman]

I cannot reproduce in Docker the test failures of…

• beast
• idba
• raxml
• ropebwt2

discovar failure is harmless. ruby failure is known, with no known solution.