Fix broken formulae

[tmozgach]

The Bold forlmulae is a forlmulae that exists in the old ORCA and absents in the new ORCA (brew list)

• [x] cufflinks
• [ ] libdivsufsort
• [ ] perl518
• [ ] swig
• [ ] texinfo
• [ ] masurca (new version, https://github.com/Homebrew/homebrew-science/pull/5772)
• [ ] pbsuite (conflict, bedtools: because Both install bin/bamToFastq)
• [ ] meraculous (Not current version, tricky to fix for current version)
• [x] igv
• [x] igvtools
• [x] kat
• [x] kmerstream
• [x] orthofinder
• [x] quast (is influenced by gubbins (numpy diff python),https://github.com/Homebrew/homebrew-science/issues/5752)
• [x] samtools-0.1
• [ ] smrtanalysis (can't read /home/linuxbrew/.cache/Homebrew/smrtanalysis--patch-5.run: No such file or directory)
• [x] snap
• [x] trans-abyss
• [x] wiggletools
• [ ] quake (dependency with amos)
• [ ] gubbins (https://github.com/Homebrew/homebrew-science/issues/5752)
• [x] adapterremoval
• [x] amos
• [x] anvio (uses python 3 and library from python 2.7, tricky)
• [x] augustus
• [ ] bpipe
• [x] biopieces
• [x] blat
• [x] bless
• [x] cegma
• [x] augustus
• [ ] corset
• [ ] delly
• [ ] discovardenovo
• [x] edirect
• [ ] ensembl-tools (! No formulae)
• [x] gaemr
• [ ] garli (Error: Failure while executing: patch -g 0 -f -p1)
• [x] gatk
• [x] genewise
• [x] genometools
• [x] gfatools (! No formulae)
• [x] gmap-gsnap
• [x] graphlan
• [ ] harvest-tools
• [x] maker
• [x] meme
• [x] metaphlan
• [ ] mira
• [x] mlst
• [x] mothur
• [x] musket (! No formulae)
• [x] ncbi-c++-toolkit (It is freezing up for 1-2 hours and after that Last 15 lines from /home/linuxbrew/.cache/Homebrew/Logs/ncbi-c++-toolkit/03.make: /usr/bin/install: failed to extend ‘/home/linuxbrew/.linuxbrew/Cellar/ncbi-c++-toolkit/12.0.0/bin/sff-dump’: No space left on device /usr/bin/install: error writing ‘/home/linuxbrew/.linuxbrew/Cellar/ncbi-c++-toolkit/12.0.0/bin/soap_client_sample’: No space left on device!)
• [ ] ogdraw (Image::Magick perl module, can't install)
• [x] pagan (! No formulae)
• [x] pbh5tools (! No formulae)
• [x] platanus (! No formulae)
• [ ] plink2 (plink_ld.c:10094:3: note: in expansion of macro 'LOGPRINTFWW')
• [ ] populations (qt problem)
• [ ] poretools (error is similar anvio)
• [x] prokka
• [ ] quaff
• [ ] r8s (make: *** No rule to make target /usr/include/sys/errno.h', needed by memory.o'. Stop.)
• [x] rampart
• [x] ray
• [ ] reapr
• [x] simulate-pcr
• [x] sortmerna works after c-letter
• [ ] sparseassembler (! No formulae)
• [x] sspace (! No formulae)
• [x] sspace-longread (! No formulae)
• [ ] trans_proteomic_pipeline
• [ ] ucsc-genome-browser
• [x] velvetoptimiser
• [x] MLR(planning)

Libraries:

• [x] HTSeq
• [x] pandas
• [x] pip
• [x] pysam
• [x] PyVCF
• [x] virtualenv

[sjackman]

Higher priority

• delly (https://github.com/Homebrew/homebrew-science/pull/5412)
• discovardenovo (https://github.com/bcgsc/orca/issues/19)
• gubbins (Homebrew/homebrew-science#5752)
• masurca (Homebrew/homebrew-science#5772)
• mira https://github.com/bcgsc/orca/issues/20
• mlr
• pbsuite (https://github.com/Homebrew/homebrew-science/pull/5685 + conflict, bedtools: because Both install bin/bamToFastq)
• plink2
• poretools (https://github.com/bcgsc/orca/issues/21)

Middle priority

• anvio
• corset
• ensembl-tools
• garli
• harvest-tools
• quaff
• quake
• r8s
• reapr
• trans_proteomic_pipeline

Lower priority

• meraculous
• ogdraw
• populations
• smrtanalysis
• ucsc-genome-browser

Remove if nothing depends on it

• libdivsufsort
• perl518
• swig
• texinfo

Remove

• gfatools
• musket
• ncbi-c++-toolkit
• pagan
• pbh5tools
• platanus
• sspace
• sspace-longread