Skip to content

Commit 89daebb

Browse files
author
Kai Waldrant
authored
add base image reference to doc (#282)
* add base image reference to doc * update changelog * add type and image * fix typo
1 parent 1f061f4 commit 89daebb

5 files changed

Lines changed: 67 additions & 17 deletions

File tree

CHANGELOG.md

Lines changed: 2 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -6,6 +6,8 @@
66

77
* Remove old hero image (PR #280).
88

9+
* Reference base-images in `create-component` pages (PR #282)
10+
911
## BUG FIXES
1012

1113
* Updated the openproblems-v2 submodule (PR #280).
Lines changed: 62 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,62 @@
1+
Each component has it's own set of dependencies, because different components might have conflicting dependencies.
2+
3+
For your convenience we have created 2 base images that can be used for python or R scripts. These images can be found in the OpenProblems github repo [base-images](https://github.com/openproblems-bio/base-images).
4+
Click on the packages to view the url you need to use. You are not required to use these images but make sure the required packages are installed to make sure OpenProblems works properly.
5+
6+
Update the `setup` definition in the `platforms` section of the config file.
7+
This section describes the packages that need to be installed in the Docker image and are required for your method to run.
8+
9+
If you're using a custom image use the following minimum setup:
10+
11+
::: {.panel-tabset}
12+
## Python
13+
```{yaml}
14+
platforms:
15+
- type: docker
16+
Image: your custom image
17+
setup:
18+
- type: apt
19+
packages:
20+
- procps
21+
- type: python
22+
packages:
23+
- anndata~=0.8.0
24+
- scanpy
25+
- pyyaml
26+
- requests
27+
- jsonschema
28+
```
29+
30+
## R
31+
32+
```{yaml}
33+
platforms:
34+
- type: docker
35+
Image: your custom image
36+
setup:
37+
- type: apt
38+
packages:
39+
- procps
40+
- libhdf5-dev
41+
- libgeos-dev
42+
- python3
43+
- python3-pip
44+
- python3-dev
45+
- python-is-python3
46+
- type: python
47+
packages:
48+
- rpy2
49+
- anndata~=0.8.0
50+
- scanpy
51+
- pyyaml
52+
- requests
53+
- jsonschema
54+
- type: r
55+
packages:
56+
- anndata
57+
- BiocManager
58+
```
59+
60+
:::
61+
62+
Please check out this [guide](https://viash.io/guide/component/add-dependencies.html) for more information on how to add extra package dependencies.

documentation/create_component/add_a_control.qmd

Lines changed: 1 addition & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -146,11 +146,7 @@ The file specified in this field contains information regarding the input and ou
146146

147147
## Step 3: Add dependencies
148148

149-
Each component has it's own set of dependencies, because different components might have conflicting dependencies.
150-
151-
In the platforms section of the config file update the `setup` definition that describes the packages that need to be installed in the Docker image and are required for your method to run. Note that both `anndata~=0.8.0` and `pyyaml` are necessary Python package dependencies.
152-
153-
Please check out this [guide](https://viash.io/guide/component/add-dependencies.html) for more information on how to add extra package dependencies.
149+
{{< include _include/_add_dependencies.qmd >}}
154150

155151
:::{.callout-note}
156152
**Tip:** After making changes to the components dependencies, you will need to rebuild the docker container as follows:

documentation/create_component/add_a_method.qmd

Lines changed: 1 addition & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -160,13 +160,7 @@ The file specified in this field contains information regarding the input and ou
160160

161161
## Step 3: Add dependencies
162162

163-
Each component has it's own set of dependencies, because different components might have conflicting dependencies.
164-
165-
Update the `setup` definition in the `platforms` section of the config file.
166-
This section describes the packages that need to be installed in the Docker image and are required for your method to run.
167-
Note that both `anndata~=0.8.0` and `pyyaml` are necessary Python package dependencies.
168-
169-
Please check out this [guide](https://viash.io/guide/component/add-dependencies.html) for more information on how to add extra package dependencies.
163+
{{< include _include/_add_dependencies.qmd >}}
170164

171165
:::{.callout-note}
172166
**Tip:** After making changes to the components dependencies, you will need to rebuild the docker container as follows:

documentation/create_component/add_a_metric.qmd

Lines changed: 1 addition & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -150,11 +150,7 @@ The file specified in this field contains information regarding the input and ou
150150

151151
## Step 3: Add dependencies
152152

153-
Each component has it's own set of dependencies, because different components might have conflicting dependencies.
154-
155-
In the platforms section of the config file update the `setup` definition that describes the packages that need to be installed in the Docker image and are required for your metric to run. Note that both `anndata~=0.8.0` and `pyyaml` are necessary Python package dependencies.
156-
157-
Please check out this [guide](https://viash.io/guide/component/add-dependencies.html) for more information on how to add extra package dependencies.
153+
{{< include _include/_add_dependencies.qmd >}}
158154

159155
:::{.callout-note}
160156
**Tip:** After making changes to the components dependencies, you will need to rebuild the docker container as follows:

0 commit comments

Comments
 (0)