I get troubles installing Picard.
In short is there a dedicated link with precise instructions on how to
install it on Galaxy?
I spent hours trying to install it and if I made a subtle step forward in
the installation, I am still stuck with exceptions when trying to run any
My first problem was to have a link to a built-in reference genome. I
finally fixed it. I explain my solution here for interested persons.
(1) create the 'dict' file from your reference fasta file by using the
following picard tool:
java -jar CreateSequenceDictionary.jar -R=<ref-genome.fa>
(2) modify the picard.loc index file to point to the correct location
(3) -- the step that took me hours to find -- modify the all-fasta.loc file
to point to the correct location.
Second -and still unsolved- problem: When i try to run a picard tool, I get
the following exception:
File "/home/hg/Galaxy/galaxy-dist/tools/picard/picard_wrapper.py", line 40
SyntaxError: invalid syntax
I downloaded the last release of picard (picard-tools-1.48) and put all the
jars file in tool-data/shared/jars/
permission of the files are : -rw-r--r-- 1 apache adm
I suspect that galaxy can't find the jars file (i get the same error if I
remove them from that location). Am I missing something?
Should I precise something about the classpath in galaxY?
Thank you for your help,
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