Hi Dannon,<div><br></div><div>I tried to run Bowtie2 and Tophat using a reference from history and these are the errors I got:<div><br></div><div><div><i>An error occurred running this job: Error indexing reference sequence /bin/sh: bowtie2-build: command not found.</i></div>
<div><i><br></i></div><div><i><br></i></div><div><i>An error occurred running this job: Could not determine Tophat version /bin/sh: tophat: command not found Error indexing reference sequence /bin/sh: bowtie-build: command not found cp: /Users/abebe/tabix-0.2.6/python/galaxy-dist/database/job_working_directory/000/65/tophat_out/insertions.b</i></div>
<div><i><br></i></div><div>I also tried to run eXpress on data mapped using Bowtie and this error came:</div><div><br></div><div><i>An error occurred running this job: /bin/sh: express: command not found cp: /Users/abebe/tabix-0.2.6/python/galaxy-dist/database/job_working_directory/000/63/params.xprs: No such file or directory cp: /Users/abebe/tabix-0.2.6/python/galaxy-dist/database/job_working_directory/000/63/results. </i></div>
<div><br></div>External dependencies might be the problem. We didn&#39;t do anything to install NGS tools or others for that matter. How do we install dependencies?</div><div><br></div><div><br></div><div>Thanks for your help.</div>
<div><br></div><div>Tilahun</div><div>--------------------------</div><div><br><div class="gmail_quote">On Tue, Dec 18, 2012 at 10:32 AM, Dannon Baker <span dir="ltr">&lt;<a href="mailto:dannonbaker@me.com" target="_blank">dannonbaker@me.com</a>&gt;</span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">What specific errors are you seeing?  Some tools have external dependencies that need to be installed.<br>
<br>
-Dannon<br>
<div><div class="h5"><br>
On Dec 18, 2012, at 11:29 AM, Tilahun Abebe &lt;<a href="mailto:tilahun.abebe@uni.edu">tilahun.abebe@uni.edu</a>&gt; wrote:<br>
<br>
&gt; Hi,<br>
&gt;<br>
&gt; We installed a local galaxy a couple of days ago following the basic installation instruction (<a href="http://wiki.galaxyproject.org/Admin/Get%20Galaxy" target="_blank">http://wiki.galaxyproject.org/Admin/Get%20Galaxy</a>). The installation went well, all the tools are listed on the left. I can also upload data to Galaxy. However, an error occurs when I try to run RNA-seq analysis. I am thinking the tools are not configured properly. Can you give me tips to configure NGS tools? An example file with setup syntax will help as well.<br>

&gt;<br>
&gt; Thanks.<br>
&gt;<br>
&gt; Tilahun<br>
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</blockquote></div><br></div></div>