<div dir="ltr"><div class="gmail_default" style="font-family:arial,helvetica,sans-serif">Thanks Tony and Tim. </div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><br></div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif">Yes, I had installed new version of samtools recently (after un-installing the older one through Ubuntu Software Center), so I will leave those three files in the /usr/local/bin/.</div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><br></div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif">I first tried Tony's suggestions of using "sudo debsums -ac" command to find out if there are any missing files in my "/bin".</div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif">I got the following output. I understand the lines related to Brother printer which I once tried to install (un-successfully). I also have chromium browser installed. Do I have to install any of these missing files and how do I do that?</div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><br></div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><div class="gmail_default"><font color="#0000ff">:~$ sudo debsums -ac</font></div><div class="gmail_default">debsums: missing file /etc/firefox/profile/localstore.rdf (from bio-linux-themes-v8 package)</div><div class="gmail_default">debsums: missing file /etc/firefox/profile/bookmarks.html (from bio-linux-themes-v8 package)</div><div class="gmail_default">debsums: missing file /etc/firefox/profile/prefs.js (from bio-linux-themes-v8 package)</div><div class="gmail_default">debsums: missing file /etc/default/chromium-browser (from chromium-browser package)</div><div class="gmail_default">/etc/default/cups</div><div class="gmail_default">/etc/grub.d/10_linux</div><div class="gmail_default">/usr/local/Brother/Printer/HL2270DW/inf/brHL2270DWrc</div><div class="gmail_default">/usr/local/Brother/Printer/HL2270DW/inf/brHL2270DWfunc</div><div class="gmail_default">debsums: missing file /usr/share/doc/hl2270dwlpr/copyright (from hl2270dwlpr package)</div><div class="gmail_default">debsums: missing file /usr/share/doc/hl2270dwlpr/changelog.Debian.gz (from hl2270dwlpr package)</div><div class="gmail_default">debsums: missing file /usr/share/doc/ia32-libs-multiarch/changelog.gz (from ia32-libs-multiarch package)</div><div class="gmail_default">/boot/vmlinuz-3.13.0-43-generic</div><div class="gmail_default">/etc/NetworkManager/NetworkManager.conf</div><div class="gmail_default"><br></div><div class="gmail_default">I really appreciate your help.</div><div class="gmail_default"><br></div><div class="gmail_default">Best</div><div class="gmail_default"><br></div><div class="gmail_default">Tauqeer</div><div class="gmail_default"><br></div></div><div class="gmail_default" style><br></div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Apr 13, 2015 at 10:28 AM, Tony Travis <span dir="ltr"><<a href="mailto:tony.travis@minke-informatics.co.uk" target="_blank">tony.travis@minke-informatics.co.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">On 13/04/15 14:12, Tim Booth wrote:<br>
> [...]<br>
<span class="">> As for the files you listed, /usr/bin/formatrpsdb is part of the BLAST<br>
> package, so reinstall 'blast2' just to be sure. I don't recognise the<br>
> others, and I'd not expect any .jar file to be living in either /usr/bin<br>
> or /usr/local/bin.<br>
</span>> [...]<br>
<br>
Hi, Tim.<br>
<br>
These are from Samtools.<br>
<br>
<a href="http://seq_cache_populate.pl" target="_blank">seq_cache_populate.pl</a>:<br>
<br>
> <a href="https://github.com/samtools/samtools/blob/b7ac1e2819ab85d5950eb2ce02434aa422fe39ed/misc/seq_cache_populate.pl" target="_blank">https://github.com/samtools/samtools/blob/b7ac1e2819ab85d5950eb2ce02434aa422fe39ed/misc/seq_cache_populate.pl</a><br>
<br>
htsjdk-1.119.jar:<br>
<br>
> <a href="https://github.com/samtools/htsjdk/tree/1.119" target="_blank">https://github.com/samtools/htsjdk/tree/1.119</a><br>
<br>
[A version of Samtools could have been installed manually]<br>
<span class="im HOEnZb"><br>
HTH,<br>
<br>
Tony.<br>
<br>
--<br>
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</div></div></blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature"><div dir="ltr"><div>*********************************************<br>Md Tauqeer Alam, Ph.D<br>Division of Infectious Diseases</div><div>Emory University School of Medicine</div><div>615 Michael Street, Atlanta, GA 30322, USA</div><div><a href="mailto:tauqeer9@gmail.com" target="_blank">tauqeer9@gmail.com</a><br></div></div></div>
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