Planemo

Command-line utilities to ease the development of tools.

$ planemo lint
$ planemo test
$ planemo serve

Full list of commands

Port forwarding

Planemo runs disposable Galaxy on port 9090 by default.

Please make sure you ssh to VM with port forwarding.

$ ssh -L 9090:localhost:9090 galaxyguest@YOUR_VM

Bringing up to speed

• Is seqtk present? If not run:

$ sudo apt-get install seqtk

• Obtain the necessary files.

$ mkdir -p ~/tools/seqtk/test-data
$ cd ~/tools/seqtk/test-data
$ wget https://raw.githubusercontent.com/galaxyproject/galaxy-test-data/master/2.fastq
$ seqtk seq -A 2.fastq > 2.fasta
$ cd ..
$ wget https://raw.githubusercontent.com/martenson/dagobah-training/master/advanced/003-tools-advanced/seqtk_seq.xml

Make sure

$ planemo l
$ planemo t
$ planemo s

Check at http://localhost:9090 (with port forwarding)

Advanced tool building

Planemo advanced tool wrapping

• let's continue with the planemo-based tool wrapping!