Comments (3)
I can add something like this, but it would have to be much shorter. I’m not so happy that the package name py39-cutadapt
obviously contains the Python version number, and that therefore the instructions will therefore need to be updated from time to time. I guess this is a naming convention you have to follow, but I would prefer if this weren’t necessary.
Can you verify that this would work:
FreeBSD
Cutadapt can be installed via the FreeBSD ports system. To install as a binary package, run:
pkg install py39-cutadapt
from cutadapt.
I can add something like this, but it would have to be much shorter. I’m not so happy that the package name
py39-cutadapt
obviously contains the Python version number, and that therefore the instructions will therefore need to be updated from time to time. I guess this is a naming convention you have to follow, but I would prefer if this weren’t necessary.Can you verify that this would work:
FreeBSD
Cutadapt can be installed via the FreeBSD ports system. To install as a binary package, run:
pkg install py39-cutadapt
Did you intend to write more here? That's just the command that was already part of the text.
Yes, I suspected you would want to abbreviate the info. I deliberately provide more than enough details so upstream developers will understand the system and can better choose what to post.
I think it's important to mention 3 things:
- It can be installed via binary packages with the command shown.
- The mainstream python version will change from time to time.
- It can also be installed from source to change build options, install prefix, etc.. For this you could just provide a link for those interested in the details.
FreeBSD only builds binary packages for the mainstream python version, which is still stuck at 3.9 for some reason. Probably some important port is blocking an upgrade.
Pkgsrc tries to build packages for all supported python versions, so the user can choose.
NetBSD netbsd9.acadix bacon ~ 998: (pkgsrc): pkgin search cutadapt
py310-cutadapt-3.5 Find and remove adapter sequences, primers, poly-A tails, etc
py311-cutadapt-3.5 Find and remove adapter sequences, primers, poly-A tails, etc
py312-cutadapt-3.5 Find and remove adapter sequences, primers, poly-A tails, etc
py38-cutadapt-3.5 Find and remove adapter sequences, primers, poly-A tails, etc
py39-cutadapt-3.5 Find and remove adapter sequences, primers, poly-A tails, etc
from cutadapt.
This is taking more of my time than I would have liked it to, to be honest.
As a suggestion, it would be helpful to provide concise installation instructions suitable for copy&paste (or even a PR) so that the upstream author doesn’t have to do the work.
Please see 1cf43d8 for what I’ve written now. Feel free to comment on the commit or here if this is insufficient.
from cutadapt.
Related Issues (20)
- FYI: Macos-14 runners available for M1 macs. HOT 2
- Reads not trimmed for PE with poly-G HOT 5
- Cutadapt 4.7 hangs when using process substitution HOT 10
- Crash on sending interleaved output to stdout
- cutadapt cannot read from stdin with xopen 2.0.0 HOT 3
- Feature request: Support for multiple FastQ pairs
- Ensuring to find the correct file after Demultiplexing my 16S amplicon raw dataset with combinatorial dual indexes cutadapt command HOT 5
- Pipe multiple adatper trimming steps is unsupported when using the python API. HOT 5
- Error: BiocParallel errors HOT 5
- Remove the "Incomplete adapter sequence" warning
- Nanopore adapter detection HOT 1
- "OverflowError: FASTA/FASTQ record does not fit into buffer" when trimming ONT reads HOT 7
- Unexpected trimming behavior HOT 5
- cutadapt: error: cutadapt not able to trim the desired adapto HOT 3
- Error in FASTQ file at line 20136: Length of sequence and qualities differ HOT 2
- Adapter matches in the middle of a read masked with N HOT 2
- Feature request: shorten paired-end reads with separate values for --length HOT 1
- Help to get accurate counts of demultiplexed amplicons using cutadapt HOT 2
- Adapters in form of file and linked mode HOT 4
- Problems reading stdin on Windows 11 Python 3.12 HOT 5
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