Conda installation of trim_galore uses really old version of cutadapt

FelixKrueger / TrimGalore

A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data

GNU General Public License v3.0

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Conda installation of trim_galore uses really old version of cutadapt #172

Closed vkkodali closed 1 year ago

vkkodali commented 1 year ago

Installing trim_galore using conda installs v1.18 of cutadapt when the latest version is 4.4:

cutadapt           bioconda/linux-64::cutadapt-1.18-py37h14c3975_1

Can you please update the conda recipe to install a more up-to-date version of cutadapt?

FelixKrueger commented 1 year ago

As far as I can see the version of Cutadapt has nothing to do with the Trim Galore recipe on bioconda:

https://github.com/bioconda/bioconda-recipes/blob/master/recipes/trim-galore/meta.yaml

Indeed, when running mamba install trim-galore into a brand new environment I just got the following:

trim_galore: version 0.6.10
...
Cutadapt version: 4.4
single-core operation.
igzip command line interface 2.30.0
igzip detected. Using igzip for decompressing

What did you do?

vkkodali commented 1 year ago

Thanks, apparently the conda installation on our work machines is ancient (4.8.2). That's the reason why it was defaulting to an older version of cutadapt. I was able to fix it by using the latest version of miniconda.