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SciLifeLab / bcbb

Useful bioinformatics code, primarily in Python and R
http://bcbio.wordpress.com
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Picard issues with the pipeline #235

Closed guillermo-carrasco closed 11 years ago

guillermo-carrasco commented 11 years ago

Debian-med team has packaged the new version of picard-tools, which is not compatible with our pipeline when installing "normally". Our pipeline needs all individual .jar files, which are not installed in the normal way (a single picard-tools wrapper script is installed). As debian-med version is higher than ours, and we're using their repository to download other dependencies, apt is getting their picard-tools version.

I've pointed to our specific version of picard-tools by the moment, but maybe we can take a look at this fact.

As @chapmanb is making a few changes in the pipeline now, maybe he can advise us with this matter?

Thank you very much!

chapmanb commented 11 years ago

Guillermo; Thanks for the heads up on this. I checked in some changes which should allow the pipeline to work with either the picard-tools script provided by Debian, or the directory of jars approach:

https://github.com/chapmanb/bcbb/commit/64b6b83f9c15e79184beba1c1c89860104264b81

The only downside with picard-tools is that I don't see a way to set java options without modifying their custom shell script.

Hope this works for what you need. I'm happy to adjust as needed, Brad

guillermo-carrasco commented 11 years ago

Hi Brad,

Thanks a lot for this change. I'll test it and let you know how it goes.

A few months ago I was also trying to use the default Debian installation but I also realized that there doesn't seems to be a way of setting the java options without modifying their script.

Thanks again!