Commit ecd1fc4a authored by Santiago Insua's avatar Santiago Insua
Browse files

Merge branch 'latest'

parents 9b9c81ab 39b3fcaf
build/
.idea/
.DS_Store
.vscode/
source/_build/
\ No newline at end of file
......@@ -6,7 +6,7 @@ The easy way to get access to the example Dockerfiles used in the exercises is t
```
# Clone this documentation if you haven't already done so
> git clone https://gitlab.ebi.ac.uk/TSI/tsi-ccdoc
> git clone https://gitlab.ebi.ac.uk/TSI/tsi-ccdoc.git
> cd tsi-ccdoc
```
......
......@@ -13,7 +13,7 @@ The easy way to get access to the example files used in the exercises is to clon
```
# Clone this documentation if you haven't already done so
> cd
> git clone https://gitlab.ebi.ac.uk/TSI/tsi-ccdoc
> git clone https://gitlab.ebi.ac.uk/TSI/tsi-ccdoc.git
> cd tsi-ccdoc/tsi-cc/ResOps/scripts/gitlab
```
......
......@@ -5,13 +5,13 @@
Run a real-world bioinformatics application in a docker container
### Running velvet from the bioboxes repository ###
This example is heavily abridged from the [bioboxes.org](https://bioboxes.org/) tutorial, at [http://bioboxes.org/docs/using-a-biobox/](http://bioboxes.org/docs/using-a-biobox/). Please refer to that tutorial for full details.
This example is heavily abridged from the [bioboxes.org](http://bioboxes.org/) tutorial, at [http://bioboxes.org/docs/using-a-biobox/](http://bioboxes.org/docs/using-a-biobox/). Please refer to that tutorial for full details.
I've included the **biobox.yaml** file and the input reads directly in this repository, for convenience. You only need **cd** into the **bioboxes** directory, check you have everything, and invoke **docker run** appropriately.
```
# Clone this documentation if you haven't already done so
> # git clone https://gitlab.ebi.ac.uk/TSI/tsi-ccdoc
> # git clone https://gitlab.ebi.ac.uk/TSI/tsi-ccdoc.git
> # cd tsi-ccdoc
# You need to be in the right working directory
......@@ -174,7 +174,7 @@ total 16
cd ..
```
[bioboxes.org](https://bioboxes.org/) is a really well-organized site, with excellent documentation, and is well worth exploring.
[bioboxes.org](http://bioboxes.org/) is a really well-organized site, with excellent documentation, and is well worth exploring.
### Conclusion ###
There are a lot of bioinformatics applications already wrapped up in container images. Bioboxes isn't the only site that provides them, but it's an extremely good one.
......
......@@ -9,7 +9,7 @@ You can create the dockerfiles in this exercise by cutting and pasting from the
```
# Clone this documentation if you haven't already done so
> git clone https://gitlab.ebi.ac.uk/TSI/tsi-ccdoc
> git clone https://gitlab.ebi.ac.uk/TSI/tsi-ccdoc.git
> cd tsi-ccdoc/tsi-cc/ResOps/scripts/docker/
```
......
......@@ -18,9 +18,6 @@ Implementation of Error-tracking,
https://gitlab.ebi.ac.uk/soumyadip/error-tracking-example
Deployed resource,
http://sentry.rdsds.ci-apps.tsi.ebi.ac.uk/ [sample@ebi.ac.uk/sample or Register]
Gitlab Integration
~~~~~~~~~~~~~~~~~~~
Gitlab Integration information can be found at,
......
......@@ -24,10 +24,6 @@ Implementation of tracing (Opentracing - Jaegar) can be found in,
https://gitlab.ebi.ac.uk/soumyadip/opentracing-sample-python/
The Jaegar UI is available at,
http://jaegar.rdsds.ci-apps.tsi.ebi.ac.uk/search
Gitlab Integration
~~~~~~~~~~~~~~~~~~~
......
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