Bioconda package for kent

[jayramr]

Bioconda package for kent

[galt]

Yes they are available on bioconda as individual programs rather than a group of utilities. I see someone has separately made a pblat and pblat-cluster in addition to blat, but we are not involved in them. Please note that commercial use of BLAT requires a license from Kent Informatics.

[jayramr]

@galt thanks for your update.

But here you are referring to pblat package. I'm mainly looking for kent package. Please confirm both kent and pblat are same?

I searched in bioconda for kent package and unable to find anything. So I'm planning to include in bioconda if it is not available. please let me know

[galt]

all the kent utilities in bioconda are listed as individual packages.

Here is a list of utilities that you can also just download and use for linux
http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/
or mac here
http://hgdownload.soe.ucsc.edu/admin/exe/macOSX.x86_64/

You can use those directly by just downloading them.
You could also try to install with bioconda using the same utility name.

Here is one example I found:
https://anaconda.org/bioconda/blat
which says you can just do this:
conda install -c bioconda blat

We do not maintain the bioconda packages.

[AngieHinrichs]

pblat is separate from kent / UCSC. @galt was pointing out that it exists, but is not the same as blat or UCSC Genome Browser utils despite having a similar name.

Over 250 separate utils from the kent package are already in bioconda. If there is a util from the kent package that you want to use, there is a good chance that it is already in bioconda. For example, here are some popular kent utils and their corresponding bioconda packages:

• axtChain: ucsc-axtchain
• bedToBigBed: ucsc-bedtobigbed
• chainFilter: ucsc-chainfilter

In general, if you want to find a kent util in bioconda, prepend "ucsc-" to the util name, and search for it on https://anaconda.org/bioconda/ .