Difference between revisions of "Osiris Development"
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*'''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 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 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. | + | *'''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 following text format: | *'''Update help section.''' Include appropriate citations (e.g. Osiris, PHYTAB, programs). Use the following text format: | ||
<pre> | <pre> | ||
Revision as of 16:51, 12 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 (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
