sandbox.bio
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sandbox-bio
Interactive bioinformatics tutorials
I encountered an issue while attempting to mount local files in different folders using the “mount local folder” function. When I select a folder with subfolders, all the content gets...
The current prompt in the terminal is `root@localhost:~/tutorial#` Would it be possible to change this prompt to a more user-like prompt? - replace `#` by `$` - change user from...
Tools without tutorials yet: * kraken2 (WIP) * freebayes * mummer * kalign * fasttree Tools not in Dockerfile: * vcflib (`apt-get install -y libvcflib-tools`) * bioawk (`apt-get install -y...
There are lots of small .bin files to download when launching certain commands, which is slow - [ ] Build tools as static when possible to avoid downloading lots of...
- [x] Hide terminal until ready and show what it's doing - https://github.com/sandbox-bio/sandbox.bio/commit/2320328219f17e64858299715824ae3505e2bd39 - [x] Playground for terminal shouldn't have extraneous break lines - https://github.com/sandbox-bio/sandbox.bio/commit/d919452d41b5b90d31e15c1c08d11e75ee44d6d9 - [x] Preload `.bin` files...
Opening any tutorial in sandbox.bio appears to dramatically increase the page width to the right, to the point where I can scroll all the actual content off the screen. The...
* https://bioinf.shenwei.me/seqkit/usage/ * https://bioinf.shenwei.me/seqkit/tutorial/ * https://bioinf.shenwei.me/csvtk/tutorial/ * Uses `csvtk` a lot * Can ignore `memusg`
* https://github.com/soedinglab/MMseqs2/wiki/Tutorials#metagenomic-pathogen-detection * During tests, had to set RAM to 2GB to run a simple `mmseqs easy-search examples/QUERY.10.fasta examples/DB.1000.fasta alnRes.m8 tmp` and `foldseek easy-search example/d1asha_ example/ aln tmpFolder`, so might...
Test that: - [x] Expected bioinformatics tools are present, and are at the expected version - [x] Exercises work - [x] Quizzes work - [ ] File system sync works...