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schwede
openstructure
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1037dbb6
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1037dbb6
authored
1 week ago
by
Xavier Robin
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doc: clarify conda setup
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README.md
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README.md
examples/scoring/README.md
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@@ -15,24 +15,37 @@ Please do not hesitate to contact us for feedback or troubleshooting:
## OpenStructure Installation
For a simple and portable setup, we recommend using a conda or a containerized
solution. OpenStructure provides its own Docker container registry,
making deployment easier. Deploying a docker image just needs a
docker pull which typically finishes in about a minute depending
on your local hardware and internet connection. Singularity
containers bootstrap from the docker container but must be built
by the user.
### Conda
OpenStructure is available as a
[
conda package on
Bioconda
](
https://bioconda.github.io/recipes/openstructure/README.html
)
for a simple and portable setup.
You can install it with the following command:
```
conda install bioconda::openstructure
```
Tested with
[
miniforge
](
https://conda-forge.org/miniforge/
)
.
You can then run a test script:
```
wget https://git.scicore.unibas.ch/schwede/openstructure/-/raw/master/docker/test_docker.py -O test_ost.py
ost test_ost.py
```
### Containers
For a fully portable setup, we provide containerized solutions.
OpenStructure provides its own Docker container registry,
making deployment easier. Deploying a docker image just needs a
docker pull which typically finishes in about a minute depending
on your local hardware and internet connection. Singularity
containers bootstrap from the docker container but must be built
by the user. Both solutions require root permissions.
### Docker
#### Docker
For complete documentation on using Docker with OpenStructure,
[
click here
](
https://git.scicore.unibas.ch/schwede/openstructure/tree/master/docker
)
.
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...
@@ -51,7 +64,8 @@ And run a test script:
wget https://git.scicore.unibas.ch/schwede/openstructure/-/raw/master/docker/test_docker.py -O test_ost.py
docker run --rm -v $(pwd):/home registry.scicore.unibas.ch/schwede/openstructure:latest test_ost.py
```
### Singularity
#### Singularity
For complete documentation on using Singularity with OpenStructure,
[
click here
](
https://git.scicore.unibas.ch/schwede/openstructure/tree/master/singularity
)
.
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examples/scoring/README.md
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@@ -20,8 +20,8 @@ unzip -j example.zip
The example commands here assume an OpenStructure installation
(
[
compile instructions
](
https://openstructure.org/docs/install/
)
).
Running the computations in conda or containers provide a considerably easier
setup than compiling
OpenStructure from source. Instructions for setup and
To simplify the setup, we recommend Conda or containers instead of compiling
OpenStructure from source. Instructions for setup and
running equivalent computations are available below for
*
[
Conda
](
#conda
)
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@@ -90,6 +90,8 @@ PDB format, ligands must be provided in SDF format.
# Conda
OpenStructure is available as a
[
conda package on
Bioconda
](
https://bioconda.github.io/recipes/openstructure/README.html
)
Installing OpenStructure in Conda is as easy as:
```
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