release tarball without test and demo data

[lpantano]

Hi

I am helping to develop bcbio-nextgen: https://github.com/chapmanb/bcbio-nextgen, and we like to add you tool as part of our workflow of structural variant detection.

We have an automatic deployment for the tools we used, and would like to add this one as well. We want to avoid to add test data as part of the intallation, and we would like to know if you would think about create a release of pindel without this folder, so we can create a homebrew formula for the installation of only the tool, and not the test data?

thanks a lot!

[liangkaiye]

it is fine to remove the test and demo data for your package. I think you could do that in your installation script to only get the source code, not the test data.

For the Pindel stable release, I would prefer to keep the test data in to fullfill various needs. hope that you can understand.

On Mon, Sep 15, 2014 at 2:10 PM, Lorena notifications@github.com wrote:

Hi

I am helping to develop bcbio-nextgen: https://github.com/chapmanb/bcbio-nextgen, and we like to add you tool as part of our workflow of structural variant detection.

We have an automatic deployment for the tools we used, and would like to add this one as well. We want to avoid to add test data as part of the intallation, and we would like to know if you would think about create a release of pindel without this folder, so we can create a homebrew formula for the installation of only the tool, and not the test data?

thanks a lot!

— Reply to this email directly or view it on GitHub https://github.com/genome/pindel/issues/4.

[chapmanb]

Kai; Thanks for all your work on pindel. We're looking forward to getting this into bcbio and doing evaluations. The main installation issue is that we'd ideally like to track recent versions, like 0.2.5a7, so we can evaluate and contribute back. Unfortunately to build these we'd need to clone from GitHub, which involves a 400M download with all of the demo and test data. We were hoping to avoid creating custom tarballs, and wanted to see if it was possible to incorporate something like that into your development/release workflow. We could then plug these code-only tarballs into a homebrew recipe (https://github.com/chapmanb/homebrew-cbl) to make pindel directly installable. Happy to work with this in any way that's best with your process. Thanks again.

[liangkaiye]

hi Brad,

Please let me know whether you need my help on anything related to Pindel.

Kai

On 9/16/14, 8:52 AM, Brad Chapman wrote:

Kai; Thanks for all your work on pindel. We're looking forward to getting this into bcbio and doing evaluations. The main installation issue is that we'd ideally like to track recent versions, like 0.2.5a7, so we can evaluate and contribute back. Unfortunately to build these we'd need to clone from GitHub, which involves a 400M download with all of the demo and test data. We were hoping to avoid creating custom tarballs, and wanted to see if it was possible to incorporate something like that into your development/release workflow. We could then plug these code-only tarballs into a homebrew recipe (https://github.com/chapmanb/homebrew-cbl) to make pindel directly installable. Happy to work with this in any way that's best with your process. Thanks again.

— Reply to this email directly or view it on GitHub https://github.com/genome/pindel/issues/4#issuecomment-55745369.

[liangkaiye]

avi and travis suggested creating a branch and tag it. Please see the release without demo and test data. It is small now. Please let us know if you have any questions.

https://github.com/genome/pindel/releases

On Mon, Sep 15, 2014 at 2:10 PM, Lorena notifications@github.com wrote:

Hi

I am helping to develop bcbio-nextgen: https://github.com/chapmanb/bcbio-nextgen, and we like to add you tool as part of our workflow of structural variant detection.

We have an automatic deployment for the tools we used, and would like to add this one as well. We want to avoid to add test data as part of the intallation, and we would like to know if you would think about create a release of pindel without this folder, so we can create a homebrew formula for the installation of only the tool, and not the test data?

thanks a lot!

— Reply to this email directly or view it on GitHub https://github.com/genome/pindel/issues/4.

[chapmanb]

Kai; Thanks much for this, that tag is perfect and we put together a Homebrew recipe to build and install pindel:

https://github.com/chapmanb/homebrew-cbl/blob/master/pindel.rb

Future tags could be version specific, rather than bcbio specific since these lightweight tarballs may be useful for other folks packaging pindel for other build systems.

Really nice, thank you again.

[liangkaiye]

hi Brad,

This is great. In the future, I will package lightweight release together with the official full set.

Kai

On 9/17/14, 4:19 AM, Brad Chapman wrote:

Kai; Thanks much for this, that tag is perfect and we put together a Homebrew recipe to build and install pindel:

https://github.com/chapmanb/homebrew-cbl/blob/master/pindel.rb

Future tags could be version specific, rather than bcbio specific since these lightweight tarballs may be useful for other folks packaging pindel for other build systems.

Really nice, thank you again.

— Reply to this email directly or view it on GitHub https://github.com/genome/pindel/issues/4#issuecomment-55868790.