[Bio-linux-list] Sickle biolinux 8

[Tony Travis]

On 10/06/16 17:07, Flavia Flaviani wrote:
> Hi everyone, 
> 
> I have been asked to installed sickle on our biolinux machine and before
> installing something that was already installed I've visited the
> biolinux page http://environmentalomics.org/bio-linux-software-list/ 
> 
> Here I can see that sicke should be available directly in biolinux: 
> 
> 
> sickle	1.33	windowed adaptive trimming tool for FASTQ files using quality
> 
> 
> When we type in the terminal sickle we get the message :"No command
> 'sickle' found, " 
> 
> 
> 
> so I have tried: 
> 
>     $ dpkg -s sickle
> 
> 
> and I got this message: 
> 
>     $dpkg-query: package 'sickle' is not installed and no information is
>     available
>     Use dpkg --info (= dpkg-deb --info) to examine archive files,
>     and dpkg --contents (= dpkg-deb --contents) to list their contents.
> 
> 
> Would you advise me to install the program from github or is there
> something I am missing for which I cannot access the preinstalled one? 

Hi, Flavia.

You should only use "dpkg" for low-level tasks when you really have to.
For example to fix things that are broken and for installing downloaded
.deb packages manually (although "gdebi" is easier to use). You would be
better using the high-level "apt" command instead. First update the
"apt" database:

> root at wildcat:~# apt update
> Ign http://extras.ubuntu.com trusty InRelease
> Ign http://archive.ubuntu.com precise InRelease                                
> [...]

Then search for e.g. the "sickle" package in the repositories:

> root at wildcat:~# apt search sickle
> Sorting... Done
> Full Text Search... Done
> r-cran-phtt/trusty 3.1.2-1cran1ppa0trusty0 all
>   GNU R package "Panel Data Analysis with Heterogeneous Time
> 
> sickle/trusty,now 1.33-1biolinux1 amd64 [installed]
>   windowed adaptive trimming tool for FASTQ files using quality

Having found that there is, indeed, a "sickle" package, you can show
details about the package and its dependencies:

> root at wildcat:~# apt show sickle
> Package: sickle
> Priority: optional
> Section: science
> Installed-Size: 74.8 kB
> Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
> Version: 1.33-1biolinux1
> Depends: libc6 (>= 2.14), zlib1g (>= 1:1.1.4)
> Download-Size: 17.3 kB
> APT-Manual-Installed: yes
> APT-Sources: http://ppa.launchpad.net/nebc/bio-linux/ubuntu/ trusty/main amd64 Packages
> 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.
>  .
>  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.
>  .
>  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.
>  .
>  Sickle also supports gzipped file inputs.

You can also see if other versions or upgrade candidates are available:

> root at wildcat:~# apt-cache policy sickle
> sickle:
>   Installed: 1.33-1biolinux1
>   Candidate: 1.33-1biolinux1
>   Version table:
>  *** 1.33-1biolinux1 0
>         500 http://ppa.launchpad.net/nebc/bio-linux/ubuntu/ trusty/main amd64 Packages
>         100 /var/lib/dpkg/status

HTH,

  Tony.

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