John, I'll take a look at the program. There isn't a great way to do this until the dependency installation system is working. A thin python wrapper (using Cython) would be the usual trick we would use.

However: have you considered just using cat? This should be completely valid for gzip (at the cost of an extra 15 bytes per source file or so for duplicate headers). It looks like gzjoin does require decompression of all input data so this trade off may be worthwhile.



On May 24, 2011, at 3:13 PM, Duddy, John wrote:

There is a C program for merging Gzip files (gzjoin) that I’d love to rely on for a core Galaxy capability. Is there a standard way to get things like this included in Galaxy? Recoding it in Python would be a bit of a pain, and might be a lot slower due to the IO layer not allowing the reuse of buffers.

Thanks -

John Duddy
Sr. Staff Software Engineer
Illumina, Inc.
9885 Towne Centre Drive
San Diego, CA 92121
Tel: 858-736-3584
E-mail: jdu...@illumina.com

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