EMBOSS tools needs an update

[bgruening]

We need a new version of all EMBOSS tools. We should write a converter from EMBOSS ACD files to Galaxy xml files.

Please get in touch with us if you are interested in this project.

[hexylena]

I had one somewhere at one point. Crap. It's probably gone now. Willing to help though :)

[hexylena]

Nope, gone now. I remember the main problem with my automatic conversion was that there were a bunch of "unlisted" arguments like "seqNformat" (or something like that)

[bgruening]

Binaries can be build with: https://github.com/natefoo/docker-build/pull/2

[hexylena]

+1 for prebuilt binaries!

[hexylena]

Depends on https://github.com/galaxyproject/docker-build/issues/10

[nsoranzo]

:+1:

[innovate-invent]

Emboss 6 piece-meal update:

• ALIGNMENT
  • [ ] extractalign
• ALIGNMENT CONSENSUS
  • [ ] cons
  • [ ] consambig
  • [ ] megamerger
  • [ ] merger
• ALIGNMENT DIFFERENCES
  • [ ] diffseq
• ALIGNMENT DOT PLOTS
  • [ ] dotmatcher
  • [ ] dotpath
  • [ ] dottup
  • [ ] polydot
• ALIGNMENT GLOBAL
  • [ ] est2genome
  • [ ] needle
  • [ ] needleall
  • [ ] stretcher
• ALIGNMENT LOCAL
  • [ ] matcher
  • [ ] seqmatchall
  • [ ] supermatcher
  • [ ] water
  • [ ] wordfinder
  • [ ] wordmatch
• ALIGNMENT MULTIPLE
  • [ ] edialign
  • [ ] emma
  • [ ] infoalign
  • [ ] plotcon
  • [ ] prettyplot
  • [ ] showalign
  • [ ] tranalign
• DATA RESOURCES
  • [ ] dbtell
  • [ ] servertell
  • [ ] showdb
  • [ ] showserver
• DATA RETRIEVAL
  • [ ] codcopy
  • [ ] seqret
• DATA RETRIEVAL CHEMISTRY DATA
  • [ ] infobase
  • [ ] inforesidue
• DATA RETRIEVAL FEATURE DATA
  • [ ] featcopy
  • [ ] featmerge
• DATA RETRIEVAL ONTOLOGY DATA
  • [ ] edamdef
  • [ ] edamhasinput
  • [ ] edamhasoutput
  • [ ] edamisformat
  • [ ] edamisid
  • [ ] edamname
  • [ ] godef
  • [ ] goname
  • [ ] ontoget
  • [ ] ontogetcommon
  • [ ] ontogetdown
  • [ ] ontogetobsolete
  • [ ] ontogetroot
  • [ ] ontogetsibs
  • [ ] ontogetup
  • [ ] ontoisobsolete
  • [ ] ontotext
• DATA RETRIEVAL RESOURCE DATA
  • [ ] drfinddata
  • [ ] drfindformat
  • [ ] drfindid
  • [ ] drfindresource
  • [ ] drget
  • [ ] drtext
• DATA RETRIEVAL SEQUENCE DATA
  • [ ] abiview
  • [ ] coderet
  • [ ] entret
  • [ ] extractalign
  • [ ] infoalign
  • [ ] infoseq
  • [ ] refseqget
  • [ ] seqxref
  • [ ] seqxrefget
  • [ ] showalign
  • [ ] variationget
  • [ ] whichdb
• DATA RETRIEVAL SEQUENCE DATA ASSEMBLY DATA
  • [ ] assemblyget
  • [ ] infoassembly
• DATA RETRIEVAL TEXT DATA
  • [ ] drtext
  • [ ] entret
  • [ ] ontotext
  • [ ] textget
  • [ ] textsearch
  • [ ] xmltext
• DATA RETRIEVAL URL DATA
  • [ ] urlget
• DATA RETRIEVAL XML DATA
  • [ ] xmlget
• DISPLAY
  • [ ] abiview
  • [ ] cirdna
  • [ ] iep
  • [ ] lindna
  • [ ] pepinfo
  • [ ] pepnet
  • [ ] pepwheel
  • [ ] plotorf
  • [ ] prettyplot
  • [ ] prettyseq
  • [ ] remap
  • [ ] showfeat
  • [ ] showpep
  • [ ] sixpack
• DOCUMENTATION
  • [ ] seealso
  • [ ] tfm
  • [ ] wossdata
  • [ ] wossinput
  • [ ] wossname
  • [ ] wossoperation
  • [ ] wossoutput
  • [ ] wossparam
  • [ ] wosstopic
• EDIT
  • [ ] aligncopy
  • [ ] aligncopypair
  • [ ] biosed
  • [ ] codcopy
  • [ ] cutseq
  • [ ] degapseq
  • [ ] descseq
  • [ ] entret
  • [ ] extractalign
  • [ ] extractfeat
  • [ ] extractseq
  • [ ] featcopy
  • [ ] featmerge
  • [ ] featreport
  • [ ] feattext
  • [ ] listor
  • [ ] makenucseq
  • [ ] makeprotseq
  • [ ] maskambignuc
  • [ ] maskambigprot
  • [ ] maskfeat
  • [ ] maskseq
  • [ ] newseq
  • [ ] nohtml
  • [ ] noreturn
  • [ ] nospace
  • [ ] notab
  • [ ] notseq
  • [ ] nthseq
  • [ ] nthseqset
  • [ ] pasteseq
  • [ ] revseq
  • [ ] seqcount
  • [ ] seqret
  • [ ] seqretsetall
  • [ ] seqretsplit
  • [ ] sizeseq
  • [ ] skipredundant
  • [ ] skipseq
  • [ ] splitsource
  • [ ] splitter
  • [ ] trimest
  • [ ] trimseq
  • [ ] trimspace
  • [ ] union
  • [ ] vectorstrip
  • [ ] yank
• ENZYME KINETICS
  • [ ] findkm
• FEATURE TABLES
  • [ ] extractfeat
  • [ ] maskfeat
  • [ ] showfeat
  • [ ] twofeat
• NUCLEIC 2D STRUCTURE
  • [ ] banana
  • [ ] btwisted
  • [ ] einverted
  • [ ] sirna
• NUCLEIC CODON USAGE
  • [ ] cai
  • [ ] chips
  • [ ] codcmp
  • [ ] codcopy
  • [ ] cusp
  • [ ] syco
• NUCLEIC COMPOSITION
  • [ ] banana
  • [ ] btwisted
  • [ ] chaos
  • [ ] compseq
  • [ ] dan
  • [ ] density
  • [ ] freak
  • [ ] isochore
  • [ ] wordcount
• NUCLEIC CPG ISLANDS
  • [ ] cpgplot
  • [ ] cpgreport
  • [ ] geecee
  • [ ] newcpgreport
  • [ ] newcpgseek
• NUCLEIC FUNCTIONAL SITES
  • [ ] marscan
  • [ ] sirna
  • [ ] trimest
• NUCLEIC GENE FINDING
  • [ ] checktrans
  • [ ] getorf
  • [ ] marscan
  • [ ] plotorf
  • [ ] showorf
  • [ ] sixpack
  • [ ] syco
  • [ ] tcode
  • [ ] wobble
• NUCLEIC MOTIFS
  • [ ] dreg
  • [x] fuzznuc #4347
  • [ ] fuzztran
• NUCLEIC MUTATION
  • [ ] msbar
  • [ ] shuffleseq
• NUCLEIC PRIMERS
  • [ ] eprimer3
  • [ ] eprimer32
  • [ ] primersearch
  • [ ] stssearch
• NUCLEIC PROFILES
  • [ ] profit
  • [ ] prophecy
  • [ ] prophet
• NUCLEIC PROPERTIES
  • [ ] banana
  • [ ] btwisted
  • [ ] dan
• NUCLEIC REPEATS
  • [ ] einverted
  • [ ] equicktandem
  • [ ] etandem
  • [ ] palindrome
• NUCLEIC RESTRICTION
  • [ ] recoder
  • [ ] redata
  • [ ] remap
  • [ ] restover
  • [ ] restrict
  • [ ] showseq
  • [ ] silent
• NUCLEIC TRANSCRIPTION
  • [ ] jaspscan
  • [ ] marscan
  • [ ] tfscan
• NUCLEIC TRANSLATION
  • [ ] backtranambig
  • [ ] backtranseq (Needs to be migrated from #2261)
  • [ ] checktrans
  • [ ] coderet
  • [ ] plotorf
  • [ ] prettyseq
  • [ ] remap
  • [ ] showorf
  • [ ] showseq
  • [ ] sixpack
  • [ ] transeq
• ONTOLOGY
  • [ ] ontocount
  • [ ] ontoget
  • [ ] ontogetcommon
  • [ ] ontogetdown
  • [ ] ontogetobsolete
  • [ ] ontogetroot
  • [ ] ontogetsibs
  • [ ] ontogetup
  • [ ] ontoisobsolete
  • [ ] ontotext
• ONTOLOGY EDAM
  • [ ] drfinddata
  • [ ] drfindformat
  • [ ] drfindid
  • [ ] drfindresource
  • [ ] edamdef
  • [ ] edamhasinput
  • [ ] edamhasoutput
  • [ ] edamisformat
  • [ ] edamisid
  • [ ] edamname
  • [ ] wossdata
  • [ ] wossinput
  • [ ] wossoperation
  • [ ] wossoutput
  • [ ] wossparam
  • [ ] wosstopic
• ONTOLOGY GO
  • [ ] godef
  • [ ] goname
• ONTOLOGY TAXONOMY
  • [ ] taxget
  • [ ] taxgetdown
  • [ ] taxgetrank
  • [ ] taxgetspecies
  • [ ] taxgetup
• PHYLOGENY MOLECULAR SEQUENCE
  • [ ] distmat
• PROTEIN 2D STRUCTURE
  • [ ] garnier
  • [ ] helixturnhelix
  • [ ] pepcoil
  • [ ] pepnet
  • [ ] pepwheel
• PROTEIN 3D STRUCTURE
  • [ ] psiphi
• PROTEIN COMPOSITION
  • [ ] backtranambig
  • [ ] backtranseq
  • [ ] compseq
  • [ ] emowse
  • [ ] freak
  • [ ] mwcontam
  • [ ] mwfilter
  • [ ] oddcomp
  • [ ] pepdigest
  • [ ] pepinfo
  • [ ] pepstats
  • [ ] wordcount
• PROTEIN DOMAINS
  • [ ] helixturnhelix
  • [ ] pepcoil
• PROTEIN FUNCTIONAL SITES
  • [ ] sigcleave
  • [ ] tmap
• PROTEIN MOTIFS
  • [ ] antigenic
  • [ ] epestfind
  • [ ] fuzzpro
  • [ ] fuzztran
  • [ ] patmatdb
  • [ ] patmatmotifs
  • [ ] preg
  • [ ] pscan
  • [ ] sigcleave
• PROTEIN MUTATION
  • [ ] msbar
  • [ ] shuffleseq
• PROTEIN PROFILES
  • [ ] profit
  • [ ] prophecy
  • [ ] prophet
• PROTEIN PROPERTIES
  • [ ] charge
  • [ ] hmoment
  • [ ] iep
  • [ ] octanol
  • [ ] pepinfo
  • [ ] pepstats
  • [ ] pepwindow
  • [ ] pepwindowall
• UTILS
  • [ ] embossdata
  • [ ] embossversion

https://github.com/galaxyproject/tools-iuc/pull/131#issuecomment-1020923673 https://github.com/galaxyproject/tools-iuc/pull/4347#pullrequestreview-877890935