Osiris Development

Notes from the Galaxy Meeting on 10/12/2012 (CKCC)

Access

Galaxy development instance on Macroevolution

macroevolution.eemb.ucsb.edu/galaxy_dev

Login: galaxy_dev

Password: 1manawa

Bitbucket for Osiris

bitbucket.org

Login: ucsb_phylogenetics@lifesci.ucsb.edu

Password: 1manawa

Protocol for checking tools

1. Clone (use Bitbucket to copy newest instance)

In Bitbucket click Clone and copy the command. Make a directory and clone it

hg [type Bitbucket command here]

2. Add (add new file to the repository you're working on so that they're being tracked)

hg add phytab_mafft.*

3. Make necessary changes to XML

• Check tool ID and name. Tool ID is lowercase. For tool names, capitalize formats (e.g. PHYTAB). Follow naming conventions of any programs (e.g. RAxML). Name of XML must match Tool ID.
• Check version. Versions should be 1.0 unless named for the binary they call (e.g. RaxML 7.0.4)
• Check dependencies. Use the requirements tag set.[1]
• Update help section. Include appropriate citations (e.g. Osiris, PHYTAB, programs). Use the following text format:

 -------

 **Citations**

 This tool is part of the Osiris Phylogenetics Tool Package for Galaxy. If you make extensive use of this tool in a publication, please cite the following

 Current Osiris Citation is here

 http://osiris-phylogenetics.blogspot.com/2012/10/citation.html

 Additional Citations for this tool

 --

4. Status (see how many files have been changed)

hg status

5. Commit (makes collection of things that will change in the repository) Include a message with your initials and a brief description of the update.

hg commit -m "THO adding PHYTAB-MAFFT"

6. Push (pushes changes to Bitbucket)

hg push

7. Create Issues on Bitbucket Login to Bitbucket and create issues for tools that need tests (or anything else that needs to be fixed).
8. Post to Osiris blog[2] Include information from the help section, and suggest uses and improvements for the tool. You can also link to the blog post in the help section.

Tool assignments

THO: Phylogenetics, Phylostatistics
MAA: Alignment, Orthologs
CKCC: Phylovisualization, Phyloconversion, Tree manipulation
MSP: BLAST, QC
PJC: Get Data, Text manipulation