Good morning, I am trying to install Cufflinks for RNA-seq analysis purposes. I'm following the tutorial at the link http://cole-trapnell-lab.github.io/cufflinks/getting_started/, but I am struggling to properly download and install bjam build engine, since it's not even mentioned in the Boost tutorial (https://www.boost.org/doc/libs/1_75_0/more/getting_started/unix-variants). I tried everything - attending the tutorial, looked on the internet, manually add the BOOST_ROOT directory to my PATH etc - but nothing actually seemed to work. Does anybody struggled as well while installing Cufflinks?
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written
by
giusdalt95 •
1 answer
I solved installing with conda... The problem was that I had a "too updated" version of Python (v3.8). I had the v3.6 installed with conda:
conda create --name py36 python=3.6
and subsequently activated the environment:
conda activate py36
Thank you all for your disposability!
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Trouble getting Cufflinks to run
written by williamsbrian5064
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Cufflinks installation error
written by saj98
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Breakdancer installing problem
written by salvocamiolo •
I'd simply download the binary for your operating system, no need for building it from source: http://cole-trapnell-lab.github.io/cufflinks/install/
Or install with
condapackage manager.Actually, I would not use cufflinks at all these days, it is old, newer alternatives with better normalization techniques exist. What is your analysis goal?
I would stress the last point. Don't use cufflinks in 2021.
I know, but for a long story I have to use it
use Bioconda
I tried to install conda; however, the terminal gives me this error when I try to run
condaeven for setting up channels:I thus located it it in the PATH, both physically and symbolically (
ln -s), and the terminal "tells" me:I did download it, but when I try to test it as in the tutorial:
cufflinks ./test_data.samI achieve this error:
hello, would you tell that what is a better alternative for cufflinks?