basic steps for customizing packages for CloudBioLinux.

[Jianwu Wang]

Hi Brad,

    I followed the "fab -f fabfile.py -H localhost install_biolinux " step at https://github.com/chapmanb/cloudbiolinux/ to install cloudbiolinux on an openstack ubuntu instance. The whole process took a long time, but it finished correctly in the end. Great tool!

    I want to customize the package (add and remove some packages/data) for our project. I'm studying the source code right now. I wonder whether there is a document/webpage about the basic steps for it? For instance, if I want to install several new packages and their data, which files I should modify or implement? I'm sure such documents will speedup my work. Thanks.

-- 
Best wishes

Sincerely yours

Jianwu Wang
wangj...@gmail.com 

[Brad Chapman]

Jianwu;
Glad to hear that CloudBioLinux was useful for bootstrapping a system on
OpenStack. To configure exact sets of packages or libraries to install
you can use CloudBioLinux flavors:

https://github.com/chapmanb/cloudbiolinux#customization-with-flavors

This allows you to adjust the configuration files to install specific
targets of interest. For example, here is a flavor for our nextgen
pipeline that uses system libraries to bootstrap the system then
installs a specific set of custom tools:

https://github.com/chapmanb/cloudbiolinux/tree/master/contrib/flavor/ngs_pipeline_minimal

For adding new tools, you have choices. CloudBioLinux wraps packaging
systems (debian/RPM packages, Homebrew and Nix) so you could create a
package/recipe on any of those and then use CloudBioLinux to pull it in.
That's the preferred approach since it makes the tool useful to a
community outside of CloudBioLinux. We also have a `custom` build system
that provides a Python-based build API on top of Fabric for installations.
There are a ton of example tools in the custom directory:

https://github.com/chapmanb/cloudbiolinux/blob/master/cloudbio/custom/bio_nextgen.py

Hope this is helpful for getting started. Thanks much for the feedback,
Brad

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[Jianwu Wang]

Hi Brad,

    Thanks a lot. I added the script to install biokepler following the way of bio_nextgen. It works for me. Now, I can run 'fab -f fabfile.py -H localhost install_biolinux:flavor=biokepler' to install tools for biokepler.

    I also tried to include biokepler as a package as a default package when user runs 'fab -f fabfile.py -H localhost install_biolinux'. I changed the config/main.yaml and config/custom.yaml added the info for 'bio_kepler' package. But this command doesn't actually install the bio_kepler package when I ran it on a bare ubuntu machine. Please help. Thanks.

     You can find my changes at https://github.com/jianwuwang/cloudbiolinux/commits/master

Jianwu

[Brad Chapman]

Jianwu;
Great work getting this setup. Everything in your configuration looks
right to me, and it works on my local machine. As a test, I commented
everything out but bio_kepler in the main.yaml, then ran:

fab -H localhost install_biolinux:custom

and it started installing all of your configured custom packages.
So.. it should work great as is. If you replicate the setup and command
I describe above, what behavior do you see from CloudBioLinux?

Brad