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<p class="MsoNormal">Hi All<br>
<br>
We’ve been trying to install VEP 77 (<a href="https://github.com/Ensembl/ensembl-tools/archive/release/77.zip">https://github.com/Ensembl/ensembl-tools/archive/release/77.zip</a>) in order to replicate results from a previous analysis.
<br>
<br>
<br>
<o:p></o:p></p>
<p class="MsoNormal">We’re running perl v5.10.1 on Red Hat Enterprise Linux Server release 6.6 (Santiago)<br>
<br>
<span style="font-family:"Courier New"">sh-4.1# perl -version<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Courier New""><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Courier New"">This is perl, v5.10.1 (*) built for x86_64-linux-thread-multi<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><br>
When we run Install.pl we get the error<br>
<br>
<o:p></o:p></p>
<p class="MsoNormal"><br>
<span style="font-family:"Courier New"">sh-4.1# perl INSTALL.pl<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Courier New""><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Courier New"">Hello! This installer is configured to install v77 of the Ensembl API for use by the VEP.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Courier New"">It will not affect any existing installations of the Ensembl API that you may have.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Courier New""><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Courier New"">It will also download and install cache files from Ensembl's FTP server.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Courier New""><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Courier New"">Checking for installed versions of the Ensembl API...done<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Courier New""><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Courier New"">Setting up directories<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Courier New"">Destination directory ./Bio already exists.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Courier New"">Do you want to overwrite it (if updating VEP this is probably OK) (y/n)? y<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Courier New""><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Courier New"">Downloading required files<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Courier New"">- fetching ensembl<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Courier New"">** GET https://github.com/Ensembl/ensembl/archive/release/77.zip ==> 302 Found<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Courier New"">** GET https://codeload.github.com/Ensembl/ensembl/zip/release/77 ==> 200 OK (4s)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Courier New"">- unpacking ./Bio/tmp/ensembl.zip<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Courier New"">Key 'archive' is of invalid type for Archive::Extract::new provided by main::unpack_arch at /usr/share/perl5/Archive/Extract.pm line 270.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Courier New"">Can't call method "extract" on an undefined value at INSTALL.pl line 905.<br>
<br>
</span><span style="font-family:"Cambria","serif""><br>
</span>The file ensembl.zip is downloaded and appears to be a valid zip archive and can be extracted manually.
<br>
<br>
The perl core module Archive::Extract appears to be there.<span style="font-family:"Cambria","serif"">
<br>
<br>
</span><span style="font-family:"Courier New"">Package namespace installed latest in CPAN file<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Courier New"">Algorithm::Diff 1.1903 1.1903 TYEMQ/Algorithm-Diff-1.1903.tar.gz<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Courier New"">App::cpanminus 1.7039 1.7039 MIYAGAWA/App-cpanminus-1.7039.tar.gz<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Courier New"">Archive::Extract 0.74 0.76 BINGOS/Archive-Extract-0.76.tar.gz<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Courier New"">Archive::Zip 1.51 1.53 PHRED/Archive-Zip-1.53.tar.gz<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Courier New"">Attribute::Handlers 0.85 0.99 RJBS/Attribute-Handlers-0.99.tar.gz<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Cambria","serif""><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Courier New""><br>
We also tried with the latest version of the installer to try to diagnose the problem but we got the same error.
<br>
<br>
Any ideas for what might be wrong? <br>
<br>
Regards<br>
David<o:p></o:p></span></p>
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