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Merge pull request #251 from HadrienG/dockerfile-fix
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Fixed the Dockerfile
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HadrienG authored Feb 22, 2024
2 parents e335ca9 + 49bc793 commit 418c92b
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10 changes: 0 additions & 10 deletions Dockerfile

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2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -37,7 +37,7 @@ _Note:_ Insilicoseq requires python >= 3.5
Alternatively, with docker:

```shell
docker pull hadrieng/insilicoseq:latest
docker pull quay.io/biocontainers/insilicoseq:2.0.0--pyh7cba7a3_0
```

For more installation options, please refer to the full [documentation](http://insilicoseq.readthedocs.io)
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5 changes: 3 additions & 2 deletions doc/iss/install.rst
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Expand Up @@ -63,15 +63,16 @@ If you wish to use InSilicoSeq using docker

.. code-block:: bash
docker pull hadrieng/insilicoseq:latest
docker pull docker pull quay.io/biocontainers/insilicoseq:<tag>
Where <tag> should be chosen amongst the tags available on `quay.io <https://quay.io/repository/biocontainers/insilicoseq?tab=tags>`_ .
To use InSilicoSeq with docker, you need to provide a `volume` to the ``docker run`` command.
Given with the ``-v`` option, the volume is your way of exchanging data (in this case, your input and output files) with the docker container.

.. code-block:: bash
docker run -v /Users/hadrien/data:/mnt/data -it --rm \
hadrieng/insilicoseq iss generate \
quay.io/biocontainers/insilicoseq:<tag> iss generate \
--genomes /mnt/data/genomes.fasta -m miseq \
-o /mnt/data/reads
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