How do I install Boost and the bjam build engine for Cufflinks
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8 months ago
giusdalt95 ▴ 10

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?

RNA-Seq rna-seq next-gen • 428 views
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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 conda package 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?

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I would stress the last point. Don't use cufflinks in 2021.

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I know, but for a long story I have to use it

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use Bioconda

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I tried to install conda; however, the terminal gives me this error when I try to run conda even for setting up channels:

-bash: /usr/local/bin/conda: No such file or directory

I thus located it it in the PATH, both physically and symbolically (ln -s), and the terminal "tells" me:

-bash: /Users/admin/Tools/miniconda3/condabin/conda: /usr/local/bin/miniconda3/bin/python: bad interpreter: No such file or directory

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I did download it, but when I try to test it as in the tutorial:

cufflinks ./test_data.sam

I achieve this error:

dyld: lazy symbol binding failed: Symbol not found: __ZN5boost6system16generic_categoryEv Referenced from: /usr/local/bin/cufflinks Expected in: /opt/local/lib/libboost_system-mt.dylib

dyld: Symbol not found: __ZN5boost6system16generic_categoryEv
Referenced from: /usr/local/bin/cufflinks Expected in: /opt/local/lib/libboost_system-mt.dylib

Abort trap: 6

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Entering edit mode
8 months ago
giusdalt95 ▴ 10

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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