Thomas Roder

So far, OrthoFinder only recognized real files that end in `{"fa", "faa", "fasta", "fas", "pep"}`. With this patch, valid symlinks are also recognized. It seems to work, but I only...

What is the license of Blasterjs? [LICENSE](https://github.com/sing-group/biojs-vis-blasterjs/blob/master/LICENSE) says it's GPL-3. In [index.js](https://github.com/sing-group/biojs-vis-blasterjs/blob/master/lib/index.js) it says MIT. (I'd much prefer MIT, so I can bundle the library with my code more easily!)

Hi! Thanks for this great library. I have integrated it into [my software](https://opengenomebrowser.github.io/opengenomebrowser/tutorials/blast.html)! Some of my users would like additional columns in the output, such as `nident` (Number of identical...

Additional features inspired by Windows clipboard manager

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### Problem description Having had to spend a few weeks on Windows 🤮, I noticed a few niceties they built into their clipboard manager: - If opened using keyboard shortcut,...

I tried to filter the raw data SRR14458708 from this [paper](https://journals.asm.org/doi/full/10.1128/MRA.00530-21). Data download: [SRA](https://trace.ncbi.nlm.nih.gov/Traces/?view=run_browser&acc=SRR14458708&display=data-access) Extraction: ```bash $ docker run -v .:/data -it staphb/sratoolkit bash (docker)$ fastq-dump -I --split-files SRR14458708 ```...

More flexible remove_annots_from_page function

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I would like to dynamically remove certain annotations from a page but not others. I solved it like this: ```python from pypdf import PageObject, PdfWriter, PdfReader from pypdf.constants import PageAttributes...

## PR checklist Closes #5178 - [x] Added new module LJA. - [x] LJA works (tested Singularity and Docker) with container [`troder/lja`](https://hub.docker.com/repository/docker/troder/lja) - [x] Test works with in-house PacBio HiFi...

Docker

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Hi! I wanted to run gfaviz without GUI through Docker. I achieved it using this Dockerfile available on [Docker Hub](https://hub.docker.com/r/troder/gfaviz): ```Dockerfile FROM debian:bookworm as builder MAINTAINER Thomas Roder # install...

Dear Anton There is a contig (`6`) in `mdbg.gfa` that is missing in `assembly.fasta`: ```shell $ grep ">" assembly.fasta >20 >7 >10 >1 >3 >16 >15 ``` Preview of `mdbg.gfa`:...

Hey I created a Dockerfile and wanted to share it in case it's useful to anyone else: ```dockerfile FROM debian:bullseye MAINTAINER Thomas Roder RUN apt update RUN apt install -y...