Difference between revisions of "Osiris Development"
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==Tool assignments== | ==Tool assignments== | ||
| − | THO: Phylogenetics | + | THO: Phylogenetics<br /> |
MAA: Alignment, Orthologs<br /> | MAA: Alignment, Orthologs<br /> | ||
CKCC: Phylovisualization, Phyloconversion, Tree manipulation<br /> | CKCC: Phylovisualization, Phyloconversion, Tree manipulation<br /> | ||
| − | |||
PJC: Get Data, Text manipulation<br /> | PJC: Get Data, Text manipulation<br /> | ||
| + | ===Completed Repos=== | ||
| + | THO: Phylostatistics<br /> | ||
| + | ::<code> PDpairs SHtest tree_species tree_support_phyutility tree_support_raxml</code> | ||
| + | MSP: Assembly: | ||
| + | ::<code> iAssembler, Newbler, Trinity, Assembly Stats</code> | ||
| + | MSP: NextGenQC: | ||
| + | ::<code> Tagdust (fixed version)</code> | ||
| + | MSP: BLAST tools and *.loc files: | ||
| + | ::<code> blastn, blastx, blastp, tblastn, tblastx, checkempty, Reciprocal Best Blast, Get Sequences</code> | ||
| + | GetData | ||
| + | ::<code> upload, get_seqs, get_1_gb, get_gb, phylota_with_taxID, generate_from_phylota, genbankstrip, gbgenesummary, get_gb_sp</code> | ||
Latest revision as of 17:07, 12 December 2012
Notes from the Galaxy Meeting on 10/12/2012 (CKCC)
Access[edit]
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[edit]
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[edit]
THO: Phylogenetics
MAA: Alignment, Orthologs
CKCC: Phylovisualization, Phyloconversion, Tree manipulation
PJC: Get Data, Text manipulation
Completed Repos[edit]
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
