Hi Scott,<br>which Galaxy release are you using?<br>This is a bug which should be fixed in an updated release_15.07 git branch. <br><br>Cheers, <br>Nicola <br><br>---- Scott Szakonyi ha scritto ----<br><br><div dir="ltr"><div>Hello all,</div><div><br></div><div>I&#39;m having issues installing Trimmomatic and Picard tools from the toolshed. The errors are of the following form (Trimmomatic used for the example).</div><div><br></div><div>Trimmomatic 0.32 package shows an installation error.</div><div><br></div><div>Error details:</div><div><font size="1"><span style="color:rgb(0,0,0);font-family:&#39;Lucida Grande&#39;,verdana,arial,helvetica,sans-serif;line-height:17.1429px">  File &quot;/vectorbase/web/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py&quot;, line 142, in install_and_build_package_via_fabric</span><br style="color:rgb(0,0,0);font-family:&#39;Lucida Grande&#39;,verdana,arial,helvetica,sans-serif;line-height:17.1429px"><span style="color:rgb(0,0,0);font-family:&#39;Lucida Grande&#39;,verdana,arial,helvetica,sans-serif;line-height:17.1429px">    tool_dependency = self.install_and_build_package( tool_shed_repository, tool_dependency, actions_dict )</span><br style="color:rgb(0,0,0);font-family:&#39;Lucida Grande&#39;,verdana,arial,helvetica,sans-serif;line-height:17.1429px"><span style="color:rgb(0,0,0);font-family:&#39;Lucida Grande&#39;,verdana,arial,helvetica,sans-serif;line-height:17.1429px">  File &quot;/vectorbase/web/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py&quot;, line 136, in install_and_build_package</span><br style="color:rgb(0,0,0);font-family:&#39;Lucida Grande&#39;,verdana,arial,helvetica,sans-serif;line-height:17.1429px"><span style="color:rgb(0,0,0);font-family:&#39;Lucida Grande&#39;,verdana,arial,helvetica,sans-serif;line-height:17.1429px">    dir = tmp_dir</span><br style="color:rgb(0,0,0);font-family:&#39;Lucida Grande&#39;,verdana,arial,helvetica,sans-serif;line-height:17.1429px"><span style="color:rgb(0,0,0);font-family:&#39;Lucida Grande&#39;,verdana,arial,helvetica,sans-serif;line-height:17.1429px">  File &quot;/usr/lib64/python2.6/contextlib.py&quot;, line 34, in __exit__</span><br style="color:rgb(0,0,0);font-family:&#39;Lucida Grande&#39;,verdana,arial,helvetica,sans-serif;line-height:17.1429px"><span style="color:rgb(0,0,0);font-family:&#39;Lucida Grande&#39;,verdana,arial,helvetica,sans-serif;line-height:17.1429px">    self.gen.throw(type, value, traceback)</span><br style="color:rgb(0,0,0);font-family:&#39;Lucida Grande&#39;,verdana,arial,helvetica,sans-serif;line-height:17.1429px"><span style="color:rgb(0,0,0);font-family:&#39;Lucida Grande&#39;,verdana,arial,helvetica,sans-serif;line-height:17.1429px">  File &quot;/vectorbase/web/Galaxy/galaxy-dist/eggs/Fabric-1.7.0-py2.6.egg/fabric/context_managers.py&quot;, line 142, in _setenv</span><br style="color:rgb(0,0,0);font-family:&#39;Lucida Grande&#39;,verdana,arial,helvetica,sans-serif;line-height:17.1429px"><span style="color:rgb(0,0,0);font-family:&#39;Lucida Grande&#39;,verdana,arial,helvetica,sans-serif;line-height:17.1429px">    yield</span><br style="color:rgb(0,0,0);font-family:&#39;Lucida Grande&#39;,verdana,arial,helvetica,sans-serif;line-height:17.1429px"><span style="color:rgb(0,0,0);font-family:&#39;Lucida Grande&#39;,verdana,arial,helvetica,sans-serif;line-height:17.1429px">  File &quot;/vectorbase/web/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py&quot;, line 100, in install_and_build_package</span><br style="color:rgb(0,0,0);font-family:&#39;Lucida Grande&#39;,verdana,arial,helvetica,sans-serif;line-height:17.1429px"><span style="color:rgb(0,0,0);font-family:&#39;Lucida Grande&#39;,verdana,arial,helvetica,sans-serif;line-height:17.1429px">    initial_download=True )</span><br style="color:rgb(0,0,0);font-family:&#39;Lucida Grande&#39;,verdana,arial,helvetica,sans-serif;line-height:17.1429px"><span style="color:rgb(0,0,0);font-family:&#39;Lucida Grande&#39;,verdana,arial,helvetica,sans-serif;line-height:17.1429px">  File &quot;/vectorbase/web/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py&quot;, line 32, in execute_step</span><br style="color:rgb(0,0,0);font-family:&#39;Lucida Grande&#39;,verdana,arial,helvetica,sans-serif;line-height:17.1429px"><span style="color:rgb(0,0,0);font-family:&#39;Lucida Grande&#39;,verdana,arial,helvetica,sans-serif;line-height:17.1429px">    initial_download=initial_download )</span><br style="color:rgb(0,0,0);font-family:&#39;Lucida Grande&#39;,verdana,arial,helvetica,sans-serif;line-height:17.1429px"><span style="color:rgb(0,0,0);font-family:&#39;Lucida Grande&#39;,verdana,arial,helvetica,sans-serif;line-height:17.1429px">  File &quot;/vectorbase/web/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py&quot;, line 685, in execute_step</span><br style="color:rgb(0,0,0);font-family:&#39;Lucida Grande&#39;,verdana,arial,helvetica,sans-serif;line-height:17.1429px"><span style="color:rgb(0,0,0);font-family:&#39;Lucida Grande&#39;,verdana,arial,helvetica,sans-serif;line-height:17.1429px">    dir = self.url_download( work_dir, downloaded_filename, url, extract=True, checksums=checksums )</span><br style="color:rgb(0,0,0);font-family:&#39;Lucida Grande&#39;,verdana,arial,helvetica,sans-serif;line-height:17.1429px"><span style="color:rgb(0,0,0);font-family:&#39;Lucida Grande&#39;,verdana,arial,helvetica,sans-serif;line-height:17.1429px">  File &quot;/vectorbase/web/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py&quot;, line 223, in url_download</span><br style="color:rgb(0,0,0);font-family:&#39;Lucida Grande&#39;,verdana,arial,helvetica,sans-serif;line-height:17.1429px"><span style="color:rgb(0,0,0);font-family:&#39;Lucida Grande&#39;,verdana,arial,helvetica,sans-serif;line-height:17.1429px">    extraction_path = archive.extract( install_dir )</span><br style="color:rgb(0,0,0);font-family:&#39;Lucida Grande&#39;,verdana,arial,helvetica,sans-serif;line-height:17.1429px"><span style="color:rgb(0,0,0);font-family:&#39;Lucida Grande&#39;,verdana,arial,helvetica,sans-serif;line-height:17.1429px">  File &quot;/vectorbase/web/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py&quot;, line 89, in extract</span><br style="color:rgb(0,0,0);font-family:&#39;Lucida Grande&#39;,verdana,arial,helvetica,sans-serif;line-height:17.1429px"><span style="color:rgb(0,0,0);font-family:&#39;Lucida Grande&#39;,verdana,arial,helvetica,sans-serif;line-height:17.1429px">    os.chmod( absolute_filepath, unix_permissions )</span><br style="color:rgb(0,0,0);font-family:&#39;Lucida Grande&#39;,verdana,arial,helvetica,sans-serif;line-height:17.1429px"><br style="color:rgb(0,0,0);font-family:&#39;Lucida Grande&#39;,verdana,arial,helvetica,sans-serif;line-height:17.1429px"><span style="color:rgb(0,0,0);font-family:&#39;Lucida Grande&#39;,verdana,arial,helvetica,sans-serif;line-height:17.1429px">[Errno 2] No such file or directory: &#39;/data/galaxy/tmp/tmp-toolshed-mtdeqJvts/Trimmomatic-0.32/Trimmomatic-0.32/&#39;</span></font></div><div><font size="1"><span style="color:rgb(0,0,0);font-family:&#39;Lucida Grande&#39;,verdana,arial,helvetica,sans-serif;line-height:17.1429px"><br></span></font></div><div>I&#39;ve tried several version of the tool with no success. Any thoughts? I&#39;ve searched project website but haven&#39;t come up with anything definitive. </div><div><br></div><div>Thanks for any help you can offer,</div><div><br>-- <br><div class="gmail_signature"><div dir="ltr"><div dir="ltr"><div>Scott B. Szakonyi</div><div>Research Programmer</div><div><b><span style="font-size:8pt;font-family:Arial,sans-serif">Center for Research Computing</span></b><br><span style="font-size:8pt;font-family:Arial,sans-serif">107 Information Technology Center<br>Notre Dame, IN 46556</span><span style="font-size:8pt;font-family:Arial,sans-serif"><a href="http://crc.nd.edu/" style="color:rgb(17,85,204)" target="_blank"><br>http://crc.nd.edu</a></span><br></div><div><br></div></div></div></div>
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