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 11 months ago

vkkodali commented 11 months 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 11 months 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 11 months 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.