Difference between revisions of "Osiris Development"
From Ucsbgalaxy
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*'''Update version.''' Versions should be 1.0. | *'''Update version.''' Versions should be 1.0. | ||
*'''Check dependencies.''' Use the requirements tag set.[http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Crequirement.3E_tag_set] | *'''Check dependencies.''' Use the requirements tag set.[http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Crequirement.3E_tag_set] | ||
| − | *'''Update help section.''' Include appropriate citations (e.g. Osiris, PHYTAB, programs). Use the | + | *'''Update help section.''' Include appropriate citations (e.g. Osiris, PHYTAB, programs). Use the help template file <pre>/labdata/nfs/galaxy_dev/galaxy-dist/tools/osiris/files/help_template.xml</pre> |
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4. '''Status''' | 4. '''Status''' | ||
:Check files have been changed. | :Check files have been changed. | ||
Revision as of 09:07, 13 October 2012
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 help template file
/labdata/nfs/galaxy_dev/galaxy-dist/tools/osiris/files/help_template.xml
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
