Arthur Eschenlauer

GigaScience rticle support

23

Works with the skeleton, albeit with a few workarounds: - the file `tlmgr_pkg` adds a few Tex*Live packages needed to generate PDFs from this and other rticles. 1. The gigascience...

fgrep (grep -F) option

1

`fgrep` functionality (available with `grep -F`) allows searching for `m` multiple fixed strings among `n` sequences in O(n) time rather than O(n*m) [by leveraging the Aho-Corasick algorithm.](https://en.wikipedia.org/wiki/Grep#Implementations) For a concrete...

shed_update seems to ignore shed_username in .planemo.yml

2

I am able to run `planemo shed_create` fine without the `--owner` parameter when `shed_username` is specified in `.planemo.yml`, but when I run `planemo shed_update` I must supply the `--owner` parameter...

### Your operating system name and version, versions of other relevant software such as Galaxy or Docker. Windows Services for Linux 2 ``` $ uname -a Linux DESKTOP-00J5NN6 5.10.16.3-microsoft-standard-WSL2 #1...

I am using generic dumps with SQLite3 and created `sqlite3_create_tables.sql` for this purpose. I am attaching it (zipped) and suggest adding it to [https://ftp.ebi.ac.uk/pub/databases/chebi/generic_dumps/](https://ftp.ebi.ac.uk/pub/databases/chebi/generic_dumps/) [sqlite3_create_tables.zip](https://github.com/ebi-chebi/ChEBI/files/6630766/sqlite3_create_tables.zip)

Please wrap the XCMS refineChromPeaks tool

15

The XCMS `refineChromPeaks-merge` tool ([https://rdrr.io/bioc/xcms/man/refineChromPeaks-merge.html](https://rdrr.io/bioc/xcms/man/refineChromPeaks-merge.html)) was added to the XCMS suite to help with irregularly shaped peaks such as are encountered in HILIC data. I would l like to use...