layout: true class: inverse, middle, large --- class: special # Advanced tool definiton slides by @martenson .footnote[\#usegalaxy / @galaxyproject] --- class: larger ## Please Interrupt! We answer to you. --- # Planemo [Command-line utilities](http://planemo.readthedocs.io/) to ease the development of tools. ```shell $ planemo lint $ planemo test $ planemo serve ``` [Full list of commands](http://planemo.readthedocs.io/en/latest/commands.html) --- # Port forwarding Planemo runs disposable Galaxy on port 9090 by default. Please make sure you ssh to VM with port forwarding. ```shell $ ssh -L 9090:localhost:9090 galaxyguest@YOUR_VM ``` --- # Bringing up to speed - Is seqtk present? If not run: ```shell $ sudo apt-get install seqtk ``` - Obtain the necessary files. ```shell $ 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](http://planemo.readthedocs.io/en/latest/writing_standalone.html#simple-parameters) - let's continue with the planemo-based tool wrapping!