Re: ArrayExpressHTS ran into removed fastx-toolkit
Le Tue, Jul 27, 2021 at 12:02:00PM +0200, Steffen Möller a écrit :
>
> fastx-toolkit https://tracker.debian.org/pkg/fastx-toolkit ran into a
> bug in one of its dependencies and was removed for that reason.
> ArrayExpressHTS still depends on fasta_formatter from that library.
Hi Steffen,
I had a quick look (git grep) at the source code of ArrayExpressHTS and
although it has an option to indicate the path to fasta_formatter, it
appears to never use it.
As a control, you can git grep other external tools (samtools, mmseq,
...) and you will see that, in contrary to the search with
fasta_formatter, it returns lines of code that do construct a shell
command using the path to the tool.
So if I am not mistaken, maybe we can just drop its dependancy ?
Have a nice day,
Charles
--
Charles Plessy Nagahama, Yomitan, Okinawa, Japan
Debian Med packaging team http://www.debian.org/devel/debian-med
Tooting from work, https://mastodon.technology/@charles_plessy
Tooting from home, https://framapiaf.org/@charles_plessy
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