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

Create your assigned repository in Bitbucket. Then click Clone and copy the command.

hg [type Bitbucket command here]

2. Add

Copy tools from Knot and add them 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 (e.g. phytab_mafft"). For tool names, capitalize formats (e.g. PHYTAB_MAFFT). Follow naming conventions of any programs (e.g. RAxML). Name of XML must match Tool ID.
• Update version. Versions should be 1.0.
• Check dependencies. Use the requirements tag set.[1]
• Update help section. Include appropriate citations (e.g. Osiris, PHYTAB, programs). Use the following text format:

    <help>
**What it does**

[brief explanation of what it does]
------

**Inputs**

[file format input. with example, or perhaps link to phytab description]

------

**Outputs**

[Output example or format]

-------    

**Additional Information**

[OPTIONAL: Link to blog post or other documentation; or perhaps similar tools.]
   
-------    

**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 consider citing the following.

Current Osiris Citation is here

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

Additional Citations for this tool

[Additional references, for the binary called, or for a description of the method employed]

    </help>

4. Status

Check 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