Peter Menzel

The download of Mar metadata fails at ``` Downloading MarRef metadata from MMP (databasesapi.sfb.uit.no) ``` I think it's a problem with the line ``` MARREF_VERSION=$(curl -Ls -o /dev/null -w %{url_effective}...

add list of chapters to JSON data in books/read API endpoint

2

### API Endpoint or Feature For the sake of completeness, the JSON data returned by the books/read API endpoint `/api/books/{id}` ([docs](https://demo.bookstackapp.com/api/docs#books-read)) should contain a list of chapters in the particular...

container won't start when data dir is NFS mount

4

Hi, I mounted an NFS share in my RPi filesystem for usage of the backuppc data directory. When I start the container with: ``` docker run --name backuppc --publish 8005:8080...

Suggestion: show coordinates in reference sequence

1

Hi, I love this program! One suggestion: The coordinates on top show the position in the alignment, and it would be lovely if they could show the position in the...

Hi, It would be nice to have support for reading gzipped fasta files when doing `kraken2-build --add-to-library ...`.

add option `--use-http` to kraken-build for downloading taxonomy and genomes from ftp.ncbi.nlm.nih.gov

1

This would help those poor souls whose network firewall does not allow FTP or rsync connections to outside server. Basically it would change `download_genomic_library.sh` and `download_taxonomy.sh` to use the HTTP...

Lineage family missing in text report

7

Dear Jody, I noticed that in v4.2.0 the lineage family is missing in the text report: ``` Summary ------- ID: xxx Date: Sun Jul 3 14:15:29 2022 Strain: lineage2.2.1 Drug-resistance:...

issue with tb-profiler + conda (+snakemake)

2

This is a fringe issue that I ran into when running TB-profiler through a conda installation that is shared by multiple users. I just want to write it down for...

add older taxdumps?

2

Hi, I really like this project! Do you also archive all the historical taxdump *.dmp files? If you are interested, I could send you some older files from before 2014-08-01....

for checking possibly missing plasmids in the assembly https://github.com/andrewjpage/tiptoft needs the original fastq files also I would need one example test dataset in which tiptoft found a missing plasmid