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update guidelines for bioconda#2194
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daler committed Aug 22, 2016
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Expand Up @@ -210,12 +210,54 @@ In some cases, there may be a name collision when writing a recipe. For example
[wget](recipes/wget) recipe is for the standard command-line tool. There is
also a Python package called `wget` [on
PyPI](https://pypi.python.org/pypi/wget). In this case, we prefixed the Python
package with `python-` (see [python-wget](recipes/python-wget)). A similiar
package with `python-` (see [python-wget](recipes/python-wget)). A similar
collision was resolved with [weblogo](recipes/weblogo) and
[python-weblogo](recipes/python-weblogo).

If in doubt about how to handle a naming collision, please submit an issue.

### Fixes for missing URLs
Sometimes, URLs to source code may disappear -- particularly with R and
Bioconductor packages, where only the very latest source code is hosted on the
Bioconductor servers. This means that rebuilding an older package version fails
because the source can't be found.

The solution to this is the [Cargo
Port](https://depot.galaxyproject.org/software/), developed and maintained by
the [Galaxy](https://galaxyproject.org/) team. The Galaxy Jenkins server
performs daily archives of the source code of packages in `bioconda`, and makes
these tarballs permanently available in Cargo Port. If you try rebuilding
a recipe and the seems to have disappeared, do the following:

- search for the package and version at https://depot.galaxyproject.org/software/
- add the URL listed in the "Package Version" column to your `meta.yaml` file
another entry in the `source: url` section.
- add the corresponding sha256 checksum displayed upon clicking the Info icon
in the "Help" column to the `source:` section.

For example, if this stopped working:

```yaml
source:
fn: argh-0.26.1.tar.gz
url: https://pypi.python.org/packages/source/a/argh/argh-0.26.1.tar.gz
md5: 5a97ce2ae74bbe3b63194906213f1184
```

then change it to this:

```yaml
source:
fn: argh-0.26.1.tar.gz
url:
- https://pypi.python.org/packages/source/a/argh/argh-0.26.1.tar.gz
- https://depot.galaxyproject.org/software/argh/argh_0.26.1_src_all.tar.gz
md5: 5a97ce2ae74bbe3b63194906213f1184
sha256: 06a7442cb9130fb8806fe336000fcf20edf1f2f8ad205e7b62cec118505510db
```



## Tests
An adequate test must be included in the recipe. An "adequate" test depends on
the recipe, but must be able to detect a successful installation. While many
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