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EMBOSS tools needs an update #65

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bgruening opened this issue Feb 27, 2015 · 7 comments
Open

EMBOSS tools needs an update #65

bgruening opened this issue Feb 27, 2015 · 7 comments

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

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

@hexylena
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+1 for prebuilt binaries!

@hexylena
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hexylena commented Apr 6, 2015

Depends on galaxyproject/starforge#10

hexylena pushed a commit that referenced this issue May 8, 2015
Built using LEX/YACC as it's non-trivial to parse in a non-hacky fashion otherwise

If anyone can remove the stupid freaking spaces from the text values, I'll buy
you two tasty beverages. I've tried coercing $3 into an std::string, I've
tried %unions, I've tried modifying the regex, nothing has worked thusfar.

CC @bgruening

Starts work on #65
@nsoranzo
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👍

bgruening pushed a commit that referenced this issue Aug 19, 2019
@innovate-invent
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innovate-invent commented Feb 9, 2022

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
  • 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
  • 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

#131 (comment)
#4347 (review)

@bernt-matthias bernt-matthias mentioned this issue Jan 19, 2024
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