<div dir="ltr">Hi Tony, <div><br></div><div>thank you for your advice. I have run all your adviced commnads</div><div><br></div><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><p class=""><font color="#0000ff">:~$ apt search sickle</font></p></div></blockquote><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><p class="">Sorting... Done</p></div></blockquote><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><p class="">Full Text Search... Done</p></div></blockquote><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><p class="">r-cran-phtt/trusty 3.1.2-1cran1ppa0trusty0 all</p></div></blockquote><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><p class=""> GNU R package
"Panel Data Analysis with Heterogeneous Time</p></div></blockquote><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><p class=""> </p></div></blockquote><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><p class="">sickle/trusty 1.33-1biolinux1 amd64</p></div></blockquote><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><p class=""> windowed adaptive
trimming tool for FASTQ files using quality</p></div></blockquote><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><p class=""> </p></div></blockquote><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><p class="">flafla@biolinux:~$</p></div></blockquote><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><p class=""> </p></div></blockquote><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><p class="">flafla@biolinux:<font color="#0000ff">~$ apt show sickle</font></p></div></blockquote><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><p class="">Package: sickle</p></div></blockquote><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><p class="">Priority: optional</p></div></blockquote><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><p class="">Section: science</p></div></blockquote><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><p class="">Installed-Size: 74.8 kB</p></div></blockquote><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><p class="">Maintainer: Debian Med Packaging Team <<a href="mailto:debian-med-packaging@lists.alioth.debian.org">debian-med-packaging@lists.alioth.debian.org</a>></p></div></blockquote><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><p class="">Version: 1.33-1biolinux1</p></div></blockquote><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><p class="">Depends: libc6 (>= 2.14), zlib1g (>= 1:1.1.4)</p></div></blockquote><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><p class="">Download-Size: 17.3 kB</p></div></blockquote><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><p class="">APT-Sources: <a href="http://ppa.launchpad.net/nebc/bio-linux/ubuntu/">http://ppa.launchpad.net/nebc/bio-linux/ubuntu/</a>
trusty/main amd64 Packages</p></div></blockquote><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><p class="">Description: windowed adaptive trimming tool for FASTQ
files using quality Most modern
sequencing technologies produce reads that have deteriorating quality towards the 3'-end. Incorrectly
called bases here negatively impact
assembles, mapping, and downstream bioinformatics analyses.</p></div></blockquote><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><p class=""> .</p></div></blockquote><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><p class=""> Sickle is a tool
that uses sliding windows along with quality and length thresholds to determine when quality is
sufficiently low to trim the 3'-end of
reads. It will also discard reads based upon the length threshold. It
takes the quality values and slides a
window across them whose length is 0.1 times
the length of the read. If this length is less than 1, then the window
is set to be equal to the length of the
read. Otherwise, the window slides along the
quality values until the average quality in the window drops below
the threshold. At that point the
algorithm determines where in the window the drop occurs and cuts both the read and quality
strings there. However, if the cut point
is less than the minimum length threshold, then the read is discarded entirely.</p></div></blockquote><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><p class=""> .</p></div></blockquote><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><p class=""> Sickle supports
four types of quality values: Illumina, Solexa, Phred, and Sanger. Note that the Solexa quality setting
is an approximation (the actual
conversion is a non-linear transformation). The end approximation is
close.</p></div></blockquote><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><p class=""> .</p></div></blockquote><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><p class=""> Sickle also
supports gzipped file inputs.</p></div></blockquote><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><p class=""> </p></div></blockquote></blockquote><div><p class=""></p>
<p class=""></p>
<p class=""></p>
<p class=""></p>
<p class=""></p>
<p class=""></p>
<p class=""></p>
<p class=""></p>
<p class=""></p>
<p class=""></p>
<p class=""></p>
<p class=""></p>
<p class=""></p>
<p class=""></p>
<p class=""></p>
<p class=""></p>
<p class=""></p>
<p class=""></p>
<p class=""></p>
<p class=""></p>
<p class=""></p>
<p class=""></p>
<p class=""></p>
<p class=""></p>
<p class=""></p>
</div><div><br></div><div><br></div><div> BUT in the last command I get this : </div><div><br></div><div><div><font color="#0000ff">~$ apt-cache policy sickle</font></div><div>sickle:</div><div> Installed: (none)</div><div> Candidate: 1.33-1biolinux1</div><div> Version table:</div><div> 1.33-1biolinux1 0</div><div> 500 <a href="http://ppa.launchpad.net/nebc/bio-linux/ubuntu/">http://ppa.launchpad.net/nebc/bio-linux/ubuntu/</a> trusty/main amd64 Packages</div></div><div><br></div><div><br></div><div>So it seems that it's there but not installed. Can you advise me on how to fix this? </div><div><br></div><div>thank you so much in advance, </div><div><br></div><div>Regards </div><div><br></div><div>Flavia </div></div><div class="gmail_extra"><br><div class="gmail_quote">2016-06-10 18:24 GMT+01:00 Tony Travis <span dir="ltr"><<a href="mailto:tony.travis@minke-informatics.co.uk" target="_blank">tony.travis@minke-informatics.co.uk</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><span class="">On 10/06/16 17:07, Flavia Flaviani wrote:<br>
> Hi everyone,<br>
><br>
> I have been asked to installed sickle on our biolinux machine and before<br>
> installing something that was already installed I've visited the<br>
> biolinux page <a href="http://environmentalomics.org/bio-linux-software-list/" rel="noreferrer" target="_blank">http://environmentalomics.org/bio-linux-software-list/</a><br>
><br>
> Here I can see that sicke should be available directly in biolinux:<br>
><br>
><br>
> sickle 1.33 windowed adaptive trimming tool for FASTQ files using quality<br>
><br>
><br>
> When we type in the terminal sickle we get the message :"No command<br>
> 'sickle' found, "<br>
><br>
><br>
><br>
> so I have tried:<br>
><br>
> $ dpkg -s sickle<br>
><br>
><br>
> and I got this message:<br>
><br>
> $dpkg-query: package 'sickle' is not installed and no information is<br>
> available<br>
> Use dpkg --info (= dpkg-deb --info) to examine archive files,<br>
> and dpkg --contents (= dpkg-deb --contents) to list their contents.<br>
><br>
><br>
> Would you advise me to install the program from github or is there<br>
> something I am missing for which I cannot access the preinstalled one?<br>
<br>
</span>Hi, Flavia.<br>
<br>
You should only use "dpkg" for low-level tasks when you really have to.<br>
For example to fix things that are broken and for installing downloaded<br>
.deb packages manually (although "gdebi" is easier to use). You would be<br>
better using the high-level "apt" command instead. First update the<br>
"apt" database:<br>
<br>
> root@wildcat:~# apt update<br>
> Ign <a href="http://extras.ubuntu.com" rel="noreferrer" target="_blank">http://extras.ubuntu.com</a> trusty InRelease<br>
> Ign <a href="http://archive.ubuntu.com" rel="noreferrer" target="_blank">http://archive.ubuntu.com</a> precise InRelease<br>
> [...]<br>
<br>
Then search for e.g. the "sickle" package in the repositories:<br>
<br>
> root@wildcat:~# apt search sickle<br>
> Sorting... Done<br>
> Full Text Search... Done<br>
> r-cran-phtt/trusty 3.1.2-1cran1ppa0trusty0 all<br>
> GNU R package "Panel Data Analysis with Heterogeneous Time<br>
><br>
> sickle/trusty,now 1.33-1biolinux1 amd64 [installed]<br>
<span class="">> windowed adaptive trimming tool for FASTQ files using quality<br>
<br>
</span>Having found that there is, indeed, a "sickle" package, you can show<br>
details about the package and its dependencies:<br>
<br>
> root@wildcat:~# apt show sickle<br>
> Package: sickle<br>
> Priority: optional<br>
> Section: science<br>
> Installed-Size: 74.8 kB<br>
> Maintainer: Debian Med Packaging Team <<a href="mailto:debian-med-packaging@lists.alioth.debian.org">debian-med-packaging@lists.alioth.debian.org</a>><br>
> Version: 1.33-1biolinux1<br>
> Depends: libc6 (>= 2.14), zlib1g (>= 1:1.1.4)<br>
> Download-Size: 17.3 kB<br>
> APT-Manual-Installed: yes<br>
> APT-Sources: <a href="http://ppa.launchpad.net/nebc/bio-linux/ubuntu/" rel="noreferrer" target="_blank">http://ppa.launchpad.net/nebc/bio-linux/ubuntu/</a> trusty/main amd64 Packages<br>
> Description: windowed adaptive trimming tool for FASTQ files using quality<br>
> Most modern sequencing technologies produce reads that have deteriorating<br>
> quality towards the 3'-end. Incorrectly called bases here negatively impact<br>
> assembles, mapping, and downstream bioinformatics analyses.<br>
> .<br>
> Sickle is a tool that uses sliding windows along with quality and length<br>
> thresholds to determine when quality is sufficiently low to trim the 3'-end<br>
> of reads. It will also discard reads based upon the length threshold. It takes<br>
> the quality values and slides a window across them whose length is 0.1 times<br>
> the length of the read. If this length is less than 1, then the window is set<br>
> to be equal to the length of the read. Otherwise, the window slides along the<br>
> quality values until the average quality in the window drops below the<br>
> threshold. At that point the algorithm determines where in the window the drop<br>
> occurs and cuts both the read and quality strings there. However, if the cut<br>
> point is less than the minimum length threshold, then the read is discarded<br>
> entirely.<br>
> .<br>
> Sickle supports four types of quality values: Illumina, Solexa, Phred, and<br>
> Sanger. Note that the Solexa quality setting is an approximation (the actual<br>
> conversion is a non-linear transformation). The end approximation is close.<br>
> .<br>
> Sickle also supports gzipped file inputs.<br>
<br>
You can also see if other versions or upgrade candidates are available:<br>
<br>
> root@wildcat:~# apt-cache policy sickle<br>
> sickle:<br>
> Installed: 1.33-1biolinux1<br>
> Candidate: 1.33-1biolinux1<br>
> Version table:<br>
> *** 1.33-1biolinux1 0<br>
> 500 <a href="http://ppa.launchpad.net/nebc/bio-linux/ubuntu/" rel="noreferrer" target="_blank">http://ppa.launchpad.net/nebc/bio-linux/ubuntu/</a> trusty/main amd64 Packages<br>
> 100 /var/lib/dpkg/status<br>
<br>
HTH,<br>
<br>
Tony.<br>
<span class="HOEnZb"><font color="#888888"><br>
--<br>
Minke Informatics Limited, Registered in Scotland - Company No. SC419028<br>
Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK)<br>
tel. <a href="tel:%2B44%280%2919755%2063548" value="+441975563548">+44(0)19755 63548</a> <a href="http://minke-informatics.co.uk" rel="noreferrer" target="_blank">http://minke-informatics.co.uk</a><br>
mob. <a href="tel:%2B44%280%297985%20078324" value="+447985078324">+44(0)7985 078324</a> mailto:<a href="mailto:tony.travis@minke-informatics.co.uk">tony.travis@minke-informatics.co.uk</a><br>
_______________________________________________<br>
Bio-Linux-list mailing list<br>
<a href="mailto:Bio-Linux-list@bioinformatics.org">Bio-Linux-list@bioinformatics.org</a><br>
<a href="http://www.bioinformatics.org/mm/listinfo/bio-linux-list" rel="noreferrer" target="_blank">http://www.bioinformatics.org/mm/listinfo/bio-linux-list</a><br>
</font></span></blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr">Flavia Flaviani<div><br></div><div><b>PhD student</b> </div><div>Department of Molecular and Cell Biology</div><div>University of Cape Town, South Africa </div><div style="text-align:left">In collaboration with </div><div>The marine Biological Association of the UK (Plymouth, UK) </div><div><a href="mailto:flvfla001@myuct.ac.za" target="_blank">flvfla001@myuct.ac.za</a></div><div><a href="mailto:flafla@mba.ac.uk" target="_blank">flafla@mba.ac.uk</a></div><div><br></div></div></div>
</div>