Failed to install Cufflinks using linuxbrew

Question

[taoi2]

After I used cufflinks which was installed to my older PC via Linuxbrew 2 years ago, I tried to installed to my new PC in the same way. However, I failed as the followed. Boost was installed using brew before installing cufflinks. Now, doesn't Homebrew/Linuxbrew support cufflinks?

$ brew install cufflinks Error: No available formula with the name "cufflinks" ==> Searching for a previously deleted formula (in the last month)... Warning: homebrew/core is shallow clone. To get complete history run: git -C "$(brew --repo homebrew/core)" fetch --unshallow

Error: No previously deleted formula found. ==> Searching for similarly named formulae... ==> Searching local taps... Error: No similarly named formulae found. ==> Searching taps... ==> Searching taps on GitHub... Error: No formulae found in taps.

[taoi2]

Thanks for your quick reply.

As you wrote, I don't use HISAT2/StringTie/Ballgown RNA-seq pipeline in this time.

I try to run a software package that uses cufflinks in its process.

I will use the binary according to your advice.

Sincerely yours,

[cpad0112]

Cufflinks brew official formula is either removed or not available at the time of your installation. Try conda/bioconda. Conda 4.5.0 (bioconda) has cufflinks 2.2.1 version. As some one suggested here, move to a better one.

[taoi2]

Thanks, cpad0112 !

I am also familiar with anaconda, and Conda has only ver2.2.1 for py27. A developer of the software package I will use, however, recommends use of the version Cufflinks 2.1.0 (or lower version). So, I will use the binary in the Conda env.

Sincerely yours,

Answer 1

[Devon Ryan]

There's no reason to use cufflinks any more, it has been superseded by stringTie. If you need cufflinks for consistency with an older project, then download a precompiled binary.