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

Bitbucket for Osiris

bitbucket.org

Login: ucsb_phylogenetics@lifesci.ucsb.edu

Protocol for checking tools

1. Clone

If not already created, create your assigned repository on the Bitbucket website. 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 help template file

  /labdata/nfs/galaxy_dev/galaxy-dist/tools/osiris/files/help_template.xml

The help section uses "restructured text" to format. This is described here [2]

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[3] 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
MAA: Alignment, Orthologs
CKCC: Phylovisualization, Phyloconversion, Tree manipulation
PJC: Get Data, Text manipulation

Completed Repos

THO: Phylostatistics

PDpairs SHtest tree_species tree_support_phyutility tree_support_raxml

MSP: Assembly:

iAssembler, Newbler, Trinity, Assembly Stats

MSP: NextGenQC:

Tagdust (fixed version)

MSP: BLAST tools and *.loc files:

blastn, blastx, blastp, tblastn, tblastx, checkempty, Reciprocal Best Blast, Get Sequences

GetData

upload, get_seqs, get_1_gb, get_gb, phylota_with_taxID, generate_from_phylota, genbankstrip, gbgenesummary, get_gb_sp