[Date Prev][Date Next] [Thread Prev][Thread Next] [Date Index] [Thread Index]

Packaging Ray for Debian Med

[I posted this already, but before confirming my subscription]

Hello Tim,

Thank you for your wise guidance regarding Debian package preparation.

I successfully created a Debian package for Ray 2.1.0.

You will find packages here in a git repository:

https://github.com/sebhtml/ray-debian-package

I installed my .deb with dpkg -i, tested it with some data,
checked what's in it with dpkg -L ray|less, and finally removed it
from my virtual machines (i386 and amd64).

I will add a sparc package tomorrow.

Can you review what I did ?

          Sébastien

--
Sent from my IBM Blue Gene/Q


On 11/01/2012 08:10 AM, Tim Booth wrote:

Hi Sébastien,

Firstly, do you have regular access to a Debian/Ubuntu machine apart
from CloudBioLinux?  If so, what exactly is it running (for example,
Ubuntu 12.04 "Precise" 64-bit)?

Then you could start by reading this documentation:

http://developer.ubuntu.com/packaging/html/packaging-new-software.html

Do have a go at following it if you're keen, but don't be surprised if
you quickly get stuck as there is is a lot to take in.  What you're
aiming for is to construct a "debian" directory of assorted files that
tell the "debuild" system how build a .deb package file from the
original tarball, as well as what other packages it depends on, how it
should be indexed in the package archive, etc.  If your source already
supports "make; sudo make install" then the build rules are trivial but
you still need to get the other meta-data in order.

Here's an example:

https://launchpad.net/~nebc/+archive/bio-linux/+sourcepub/2753076/+listing-archive-extra

The packaging work is in the "debian.tar.gz" file; the "orig.tar.gz"
file is the upstream source; the ".dsc" file is an auto-generated header
file, and the two .deb files are compiled packages, made by the
Launchpad auto-builders and ready to install.

Once you have the "debian" directory in order, you can run the build on
your local machine to make an installable .deb package.  You can also
generate the requisite ".dsc" file to initiate an upload to Launchpad.

If you want me to make an initial package for you I'm happy to do that,
or if you want to have a go yourself feel free to fire any questions my
way.  It's probably best to take further discussion of packaging details
off the CloudBioLinux mailing list.

Cheers,

TIM

On Thu, 2012-11-01 at 11:13 +0000, Sébastien Boisvert wrote:

I am surely interested in that.

Where do I start ?

On 11/01/2012 06:21 AM, Tim Booth wrote:

Dear Sébastien,

Thanks for your contribution of Ray to Bio-Linux.  I just wondered if
you were interested in making Ray into a .deb package that could be
hosted on Launchpad.net?  This is slightly more effort in the first
place but has several benefits:

        * The .deb package will be usable by every user of Debian, Ubuntu
          and derivatives
        * The .deb package could, in future, be submitted to the main
          Debian archive via Debian-Med so it would start appearing in the
          Software Centre etc.
        * CloudBioLinux will be able to add Ray without the patch to
          bio-nextgen.py, and will also see updates automatically rather
          than being hard-coded to 2.1.0
        * The Launchpad auto-build system will build binaries for multiple
          architectures, run unit tests, and check for build issues after
          any dependency updates

Making a package from scratch is a very steep learning curve, as there
are so many factors to consider, but once you have one working it's
pretty easy to maintain, so I'd be happy to get you started.  Let me
know if you are interested.

Cheers,

TIM

On Thu, 2012-11-01 at 02:23 +0000, Sébastien Boisvert wrote:

Hello,

I am delighted that you are interested in my patchwork.

I edited my work to address your concerns:

       git://github.com/sebhtml/cloudbiolinux.git  ray-v2.1.0-in-CloudBioLinux-edited-for-brad

You will find my pull request at

       https://github.com/chapmanb/cloudbiolinux/pull/56

at your convenience.


---
$ git diff --stat master..ray-v2.1.0-in-CloudBioLinux-edited-for-brad
    cloudbio/custom/bio_nextgen.py | 13 +++++++++++++
    config/custom.yaml             |  1 +
    2 files changed, 14 insertions(+)


               Sébastien

On 10/31/2012 10:17 PM, Sébastien Boisvert wrote:

Sebastian;
This is brilliant, thank you for adding the Ray build. We'd be happy to
include this, please do send a pull request on GitHub and I'll merge it
in. A couple of quick changes:

- manifest/custom-packages.yaml does not need to be manually edited.
      This is automatically populated via a script when we build new
      releases, so ray will be included when we roll the next AMI.
- contrib/flavor/cloudman/tools.yaml should also not be edited. This is
      John's work on a minimal Galaxy/CloudMan instance, so has items that
      have Galaxy wrappers. Longer term, I'd love to include it there as
      well.

Thanks again for doing this, looking forward to rolling in the pull
request,
Brad
- show quoted text -

Sébastien Boisvert (1):
          The Ray distributed genome assembled was added



Let me know if I must edit my work before it is accepted in the mainline tree of
CloudBioLinux.


              Sébastien

--
You received this message because you are subscribed to the Google Groups "cloudbiolinux" group.
To post to this group, send email to cloudb...@googlegroups.com.
To unsubscribe from this group, send email to cloudbiolinu...@googlegroups.com.
For more options, visit this group at http://groups.google.com/group/cloudbiolinux?hl=en.



--
***
Sébastien Boisvert
http://boisvert.info
Sent from a PC (Linux panic 3.6.2-4.fc17.x86_64).
Reply to: