Running Picard as an Executable Program
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6.3 years ago
oars ▴ 200

OK, I've got the picard.jar file in my directory but I cannot get the chmod +x Picard to work? My goal is to run Picard as though it is an executable program. Here are my series of commands, I'll ** where I start having issues:

$ mkdir picard
$ cd picard
$ wget https://github.com/broadinstitute/picard/releases/download/2.8.1/picard.jar
$ java –jar /software/picard/picard.jar
#!/bin/bash
java -jar /software/picard/picard.jar $*
**$ chmod +x Picard

Hear is the error message;

$chmod +x Picard
chmod: cannot access 'Picard': No such file or directory

my next step would have been:

$sudo ln -s /software/picard/Picard /usr/local/bin

Again thinking I could run Picard as though it were an executable program:

$Picard

Is there a better way to simply make Picard an executable?

Picard • 2.9k views
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3
Entering edit mode
6.3 years ago
h.mon 35k

Picard is a java program, you need to run it with the java virtual machine.

java -jar /software/picard/picard.jar [options]

is how most people run Picard. You may want to create a wrapper script:

sudo echo 'java -jar /software/picard/picard.jar $@' /usr/local/bin/picard
sudo chmod +x /usr/local/bin/picard

Then you can just call picard [options].

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Many thanks! This worked like a charm.

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