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| <!-- | ||
| Please edit this readme with some basic information about the tool and how to use this container. | ||
| - Include information about databases and additional files that are included. | ||
| - Keep it short - you don't need to recreate the documentation from the creators. | ||
| - Do not just copy and paste the readme or help for the tool. | ||
| --> | ||
| # VIGOR4 container | ||
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| # <program> container | ||
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| Main tool: [<program>](link to program) | ||
| Main tool: [vigor4](https://github.com/JCVenterInstitute/VIGOR4) | ||
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| Code repository: | ||
| Code repository: https://github.com/JCVenterInstitute/VIGOR4 | ||
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| Additional tools: | ||
| - list: version | ||
| - exonerate: 2.4.0 | ||
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| Basic information on how to use this tool: | ||
| - executable: <tool> | ||
| - help: <-h> | ||
| - version: <-v> | ||
| - description: <tool does something> | ||
| - executable: vigor4 | ||
| - help: -h | ||
| - version: --version | ||
| - description: | | ||
| > VIGOR4 (Viral Genome ORF Reader) is a Java application to predict protein sequences encoded in viral genomes. | ||
| > VIGOR4 determines the protein coding sequences by sequence similarity searching against curated viral protein databases. | ||
| Additional information: | ||
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| <Container contains X database at Y> | ||
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| Full documentation: link to documentation or wiki | ||
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| ## Example Usage | ||
| All databases in VIGOR4_DB have been downloaded to /VIGOR_DB and can be found at /VIGOR_DB/Reference_DBs. | ||
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| Currently included databases: | ||
| ```bash | ||
| <how creator of the dockerfile uses it> | ||
| antennavirus_txid2560091_db | ||
| bandavirus_txid2733256_db | ||
| beidivirus_txid2501981_db | ||
| cicadellivirus_txid2948664_db | ||
| coguvirus_txid2560118_db | ||
| dengue_GP_mp | ||
| dengue_txid12637_db | ||
| embe_db | ||
| embe_orf1a_mp | ||
| embe_orf1ab_mp | ||
| entovirus_txid2733257_db | ||
| feravirus_txid2501995_db | ||
| flua_db | ||
| flua_ha_mp | ||
| flub_db | ||
| fluc_db | ||
| goukovirus_txid1980420_db | ||
| hantaviridae_db | ||
| hartmanivirus_txid2169607_db | ||
| hibeco_db | ||
| hibeco_orf1a_mp | ||
| hibeco_orf1ab_mp | ||
| horwuvirus_txid2501976_db | ||
| hudivirus_txid2501977_db | ||
| hudovirus_txid2501978_db | ||
| inshuvirus_txid2501996_db | ||
| ixovirus_txid2733258_db | ||
| jonvirus_txid2501997_db | ||
| lassa_db | ||
| laulavirus_txid2560166_db | ||
| lentinuvirus_txid2733259_db | ||
| merbe_db | ||
| merbe_orf1a_mp | ||
| merbe_orf1ab_mp | ||
| mobuvirus_txid2501979_db | ||
| monkeypox_db | ||
| nairoviridae_db | ||
| nobeco_db | ||
| nobeco_orf1a_mp | ||
| nobeco_orf1ab_mp | ||
| orthophasmavirus_txid1980538_db | ||
| peribunyaviridae_db | ||
| phasivirus_txid1980421_db | ||
| phlebovirus_txid11584_db | ||
| pidchovirus_txid2501975_db | ||
| reptarenavirus_txid1653395_db | ||
| rsv_db | ||
| rtva_db | ||
| rtvb_db | ||
| rtvc_db | ||
| rtvf_db | ||
| rtvg_db | ||
| rubodvirus_txid2733260_db | ||
| sapo_db | ||
| sapo_mp | ||
| sarbe_db | ||
| sarbe_orf1a_mp | ||
| sarbe_orf1ab_mp | ||
| sarscov2_db | ||
| sarscov2_orf1a_mp | ||
| sarscov2_orf1ab_mp | ||
| sawastrivirus_txid2560224_db | ||
| tenuivirus_txid12329_db | ||
| uukuvirus_txid2734594_db | ||
| veev_db | ||
| veev_nsp_mp | ||
| veev_sp_mp | ||
| wenrivirus_txid2560254_db | ||
| wnvII_db | ||
| wnvI_db | ||
| wnv_GP1_mp | ||
| wnv_GP2_mp | ||
| wnv_GP3_mp | ||
| wuhivirus_txid2501998_db | ||
| zikv_db | ||
| zikv_mp | ||
| ``` | ||
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| VIGOR4_DB is up-to-date with commit [390582955049b9ddc989510672fbde90cf3387c7](https://github.com/JCVenterInstitute/VIGOR_DB/commits/master/), which was made on Dec 1, 2022. | ||
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| <!-- Example README | ||
| # pasty container | ||
| Main tool: [pasty](https://github.com/rpetit3/pasty) | ||
| Code repository: https://github.com/rpetit3/pasty | ||
| Additional tools: | ||
| - ncbi-blast+: 2.12.0 | ||
| - python: 3.10.6 | ||
| Basic information on how to use this tool: | ||
| - executable: pasty | ||
| - help: --help | ||
| - version: --version | ||
| - description: "A tool easily taken advantage of for in silico serogrouping of Pseudomonas aeruginosa isolates from genome assemblies" | ||
| Additional information: | ||
| Full documentation: [https://github.com/rpetit3/pasty](https://github.com/rpetit3/pasty) | ||
| Full documentation: [https://github.com/JCVenterInstitute/VIGOR4](https://github.com/JCVenterInstitute/VIGOR4) | ||
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| ## Example Usage | ||
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| ```bash | ||
| pasty --assembly /pasty-1.0.2/test/O1-GCF_000504045.fna.gz --prefix O1-GCF_000504045 | ||
| ``` | ||
| --> | ||
| vigor4 -i entovirus.fasta -o entovirus -d /VIGOR_DB/Reference_DBs/entovirus_txid2733257_db | ||
| ``` |