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@@ -75,7 +75,7 @@ All files are prefixed (`<prefix>`) as the input genome fasta file. | |
Platon can be installed/used in 2 different ways. | ||
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In all cases, the custom database must be downloaded which we provide for download: | ||
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3349652.svg)](https://doi.org/10.5281/zenodo.3349652) | ||
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3349651.svg)](https://doi.org/10.5281/zenodo.3349651) | ||
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### GitHub | ||
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@@ -85,7 +85,7 @@ In all cases, the custom database must be downloaded which we provide for downlo | |
Example: | ||
``` | ||
$ git clone [email protected]:oschwengers/platon.git | ||
$ wget https://zenodo.org/record/3349652/files/db.tar.gz | ||
$ wget https://zenodo.org/record/3358926/files/db.tar.gz | ||
$ tar -xzf db.tar.gz | ||
$ rm db.tar.gz | ||
$ platon/bin/platon --db ./db genome.fasta | ||
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@@ -96,7 +96,7 @@ Platon will automatically recognise it and thus, the database path doesn't need | |
to be specified: | ||
``` | ||
$ git clone [email protected]:oschwengers/platon.git | ||
$ wget https://zenodo.org/record/3349652/files/db.tar.gz | ||
$ wget https://zenodo.org/record/3358926/files/db.tar.gz | ||
$ tar -xzf db.tar.gz | ||
$ rm db.tar.gz | ||
$ mv db/ platon | ||
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@@ -110,7 +110,7 @@ $ platon/bin/platon genome.fasta | |
Example: | ||
``` | ||
$ conda install -c conda-forge -c bioconda -c defaults platon | ||
$ wget https://zenodo.org/record/3349652/files/db.tar.gz | ||
$ wget https://zenodo.org/record/3358926/files/db.tar.gz | ||
$ tar -xzf db.tar.gz | ||
$ rm db.tar.gz | ||
$ platon --db ./db genome.fasta | ||
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@@ -124,7 +124,7 @@ $ platon --db ./db genome.fasta | |
Platon/database (1./2.): | ||
``` | ||
$ pip3 install cb-platon | ||
$ wget https://zenodo.org/record/3349652/files/db.tar.gz | ||
$ wget https://zenodo.org/record/3358926/files/db.tar.gz | ||
$ tar -xzf db.tar.gz | ||
$ rm db.tar.gz | ||
$ platon --db ./db genome.fasta | ||
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@@ -181,8 +181,8 @@ Platon depends on a custom database based on MPS, RDS, RefSeq Plasmid database, | |
PlasmidFinder db as well as custom HMM models. This database based on | ||
RefSeq release 95 can be downloaded here: | ||
(zipped 1.8 Gb, unzipped 2.6 Gb) | ||
- [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3349652.svg)](https://doi.org/10.5281/zenodo.3349652) | ||
- [https://zenodo.org/record/3349652/files/db.tar.gz](https://zenodo.org/record/3349652/files/db.tar.gz) | ||
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3349651.svg)](https://doi.org/10.5281/zenodo.3349651) | ||
- [https://zenodo.org/record/3358926/files/db.tar.gz](https://zenodo.org/record/3358926/files/db.tar.gz) | ||
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## Dependencies | ||
Platon was developed and tested in Python 3.5 and depends on BioPython (>=1.71). | ||
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