I had considered cat, but from what I have read, not all readers understand it, 
or understand it as a single compressed stream. Since the resulting file would 
differ from a block gzipped file (embedded gzip headers with filenames, 
embedded per-file trailers, and the final CRC/size not matching the entire 
contents) I worry cat would be a brittle solution.

Also, single AFAIK gzjoin is not part of any installable package (more of an 
example program) I don't know if it's something that can be addressed by a 
dependency installation system, unless you host the installations.

There is stuff that happens on first start, such as copying *example files. 
Would it be far-fetched to compile the program at that stage?


________________________________________
From: James Taylor [ja...@jamestaylor.org]
Sent: Tuesday, May 24, 2011 11:51 PM
To: Duddy, John
Cc: galaxy-...@bx.psu.edu Dev
Subject: Re: [galaxy-dev] Getting binary programs into Galaxy distribution?

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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