Hello all,<div>I get troubles installing Picard.</div><div>In short is there a dedicated link with precise instructions on how to install it on Galaxy?</div><div>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 picard tool.</div>
<div><br></div><div>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.</div><div>(1) create the &#39;dict&#39; file from your reference fasta file by using the following picard tool:</div>
<div>java -jar CreateSequenceDictionary.jar -R=&lt;ref-genome.fa&gt; -O=&lt;ref-genome.dict&gt;</div><div><br></div><div>(2) modify the picard.loc index file to point to the correct location</div><div><br></div><div>(3) -- the step that took me hours to find --  modify the all-fasta.loc file to point to the correct location.</div>
<div><br></div><div>Second -and still unsolved- problem: When i try to run a picard tool, I get the following exception:</div><div><span class="Apple-style-span" style="color: rgb(48, 48, 48); font-family: &#39;Lucida Grande&#39;, verdana, arial, helvetica, sans-serif; font-size: 12px; line-height: 14px; background-color: rgb(255, 255, 255); "><pre style="font-family: monospace; line-height: 10px; background-image: initial; background-attachment: initial; background-origin: initial; background-clip: initial; background-color: white; color: black; border-top-style: dotted; border-right-style: dotted; border-bottom-style: dotted; border-left-style: dotted; border-top-color: black; border-right-color: black; border-bottom-color: black; border-left-color: black; border-top-width: 1px; border-right-width: 1px; border-bottom-width: 1px; border-left-width: 1px; overflow-x: auto; overflow-y: auto; padding-top: 10px; padding-right: 10px; padding-bottom: 10px; padding-left: 10px; background-position: initial initial; background-repeat: initial initial; ">
 File &quot;/home/hg/Galaxy/galaxy-dist/tools/picard/picard_wrapper.py&quot;, line 40
    class PicardBase():
                     ^
SyntaxError: invalid syntax</pre></span></div><div>I downloaded the last release of picard (picard-tools-1.48) and put all the jars file in tool-data/shared/jars/</div><div>permission of the files are : -rw-r--r-- 1 apache      adm  </div>
<div><br></div><div>I suspect that galaxy can&#39;t find the jars file (i get the same error if I remove them from that location). Am I missing something?</div><div>Should I precise something about the classpath in galaxY?</div>
<div><br></div><div>Thank you for your help,</div><div>Colin</div><div><br></div><div><br></div><div><br></div>