Problems with samtools versions (1.10)

[a-lapin]

Hi, I've recently upgraded samtools to version 1.10 via linuxbrew. Since this update snippy is broken, probably it presumes that v.1.10 < v.1.7

[11:40:06] Found vt - /home/linuxbrew/.linuxbrew/bin/vt
[11:40:06] Found snippy-vcf_to_tab - /home/linuxbrew/.linuxbrew/Cellar/snippy/4.4.5/bin/snippy-vcf_to_tab
[11:40:06] Found snippy-vcf_report - /home/linuxbrew/.linuxbrew/Cellar/snippy/4.4.5/bin/snippy-vcf_report
[11:40:06] Need samtools --version >= 1.7 but you have 1.10 - please upgrade it.

[tseemann]

Yes, it is a floating point comparison bug.

Please runbrew switch samtools 1.9 until I can fix it.

[andersgs]

Remember to run brew switch htslib 1.9 and brew switch bcftools 1.9_1 too.

[chienchi]

I tried to fix it by switching to a dotted-decimal $VERSION for comparison using "version" module. But not sure it is the correct way.

use version;

97 err("Need $cmd >= $min but you have $ver - please upgrade it.") if version->declare($ver) < version->declare($min);

[tseemann]

@chienchi that is a great core perl solution! i was thinking i would need SymVer.pm but your method is better. Might need to use version->parse() though - not sure.

[luciagrami]

Hello, I have the same issue but
$ samtools --version
throws:

samtools 1.9
Using htslib 1.9
Copyright (C) 2018 Genome Research Ltd.

And $brew switch samtools 1.9 gives an error:

Error: samtools not found in the Cellar.

[Abgarmar]

Same issue too after installing snippy via conda:

conda install -c conda-forge -c bioconda -c defaults snippy

Need samtools --version >= 1.7 but you have 1.10 - please upgrade it

samtools 1.10
Using htslib 1.10.1
Copyright (C) 2019 Genome Research Ltd.

[quocviet0908]

Hi everyone,

I just got stuck in this problem as well and I think this solution can help.
After installing snippy v4.4.5, this version should come along with samtools and bcftools 1.10. You can downgrade samtools to 1.9 easily by running "conda install -c bioconda samtools=1.9" inside the snippy environment.

Cheer!

[a-lapin]

Hi!
I encountered a similar error with prokka and makeblastdb:

(base) argive@argive-PC:~/Desktop$ prokka --setupdb
[13:37:41] Appending to PATH: /home/linuxbrew/.linuxbrew/Cellar/prokka/1.14.0/bin
[13:37:41] Cleaning databases in /home/linuxbrew/.linuxbrew/Cellar/prokka/1.14.0/db
[13:37:41] Cleaning complete.
[13:37:41] Looking for 'makeblastdb' - found /home/linuxbrew/.linuxbrew/bin/makeblastdb
[13:37:41] Determined makeblastdb version is 2.10
[13:37:41] Prokka needs makeblastdb 2.8 or higher. Please upgrade and try again.

[tseemann]

This bug will be fixed in snippy 4.5.0