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Addition of various biotool docker container APIs to the BioTools project #40

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kMutagene opened this issue Feb 12, 2019 · 1 comment
Open
12 tasks

Addition of various biotool docker container APIs to the BioTools project #40

kMutagene opened this issue Feb 12, 2019 · 1 comment
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@kMutagene
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priority-medium project-BioContainers Issues regarding the BioFSharp.BioTools project up-for-grabs
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@kMutagene
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kMutagene commented Feb 12, 2019 •
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Tools with the highest priority (feel free to suggest more):
Toolname | biocontainer available?

  • FASTA | ?
  • EMBOSS | YES
  • InterProScan | YES
  • GenScan | ?
  • BLAT | ?
  • Sim4 | YES
  • Spidey | ?
  • MEME | ?
  • MUSCLE | YES
  • MAFFT | YES
  • T-Coffee | YES
  • ProbCons | YES
@kMutagene kMutagene added up-for-grabs priority-high high priority - CSBiology members actively work on this project-BioContainers Issues regarding the BioFSharp.BioTools project labels Feb 12, 2019
@kMutagene kMutagene added this to the 1.0.0 Release milestone Feb 12, 2019
@kMutagene kMutagene self-assigned this Feb 12, 2019
kMutagene referenced this issue Feb 16, 2019
@kMutagene
Add hmmemit API to HMMER biocontainer API
3004d2e
kMutagene referenced this issue Feb 16, 2019
@kMutagene
Add hmmpress and hmmconvert APIs to HMMER biocontainer API
955398a
kMutagene referenced this issue Feb 16, 2019
@kMutagene
Add HMMscan API for HMMER biocontainer API
5670658
kMutagene referenced this issue Feb 16, 2019
@kMutagene
Add HMMsearch API to HMMER biocontainer API
60b8e51
kMutagene referenced this issue Feb 16, 2019
@kMutagene
Add HMMER API library for HMMER biocontainer.
371357a 
- Add hmmbuild API to HMMER biocontainer API
kMutagene referenced this issue Feb 16, 2019
@kMutagene
Add API for clustal-omega biocontainer
37fa7a4
kMutagene referenced this issue Feb 16, 2019
@kMutagene
Add biocontainers/blast docker API acces:
bbdcab1 
- Add windows/unix path conversions and subpath matching to MounInto in BioContainer.fs
- Add execReturnAsync (returns stdout of docker container) and execAsync (redirects stdout/stderr of container) to BioContainer.fs
- Add Blast parameter wrapping and command generation for blast container
@kMutagene kMutagene mentioned this issue Jun 21, 2019
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Essential tools moved to #55 , track only additional tools here

@kMutagene kMutagene removed this from the 1.0.0 Release milestone Jun 21, 2019
@kMutagene kMutagene added priority-medium and removed priority-high high priority - CSBiology members actively work on this labels Jun 21, 2019
@kMutagene kMutagene added this to the Backlog milestone Feb 20, 2020
@kMutagene kMutagene pinned this issue Feb 20, 2020
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