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
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/