Hi Marcel,
We tend to be reluctant to distribute something like this for the
following reasons:
* It increases support burden;
* It's hard to create something that satisfies everyone's needs;
* Since it doesn't require changes to the Java source, anyone can do this.
If you have wrappers that you think would be useful for the community,
perhaps you could distribute them somewhere (github?).
I should also note that in the not-to-distant future the Picard
command-line tools will be moving to the samtools model, i.e. a single
executable to which you specify which program you want to run. I think
in that case a single script will do, and you can easily create one that
is appropriate for your needs.
-Alec
On 7/1/14, 2:40 AM, Marcel Martin wrote:
On 2014-06-30 22:42, Alec Wysoker wrote:
It wouldn't do you any good to put these on your path, because the
Picard jars are not directly executable on most OSs, including (at least
for me) OS X. I.e. the program to be executed is 'java', not the Picard
jar.
Perhaps this is the right time for a suggestion for the Picard
developers: Debian/Ubuntu provides with its picard-tools package a
simple shell wrapper script that it installs as /usr/bin/picard-tools.
You can then run picard like this:
picard-tools FastqToSam
I find this extremely convenient. Even when I'm not on Ubuntu, I often
add such a wrapper script to my PATH. Would it be an idea to make this
or something like it part of the official Picard distribution?
Marcel
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Open source business process management suite built on Java and Eclipse
Turn processes into business applications with Bonita BPM Community Edition
Quickly connect people, data, and systems into organized workflows
Winner of BOSSIE, CODIE, OW2 and Gartner awards
http://p.sf.net/sfu/Bonitasoft
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