Difference between revisions of "Osiris Development"
| Line 14: | Line 14: | ||
==Protocol for checking tools== | ==Protocol for checking tools== | ||
1. '''Clone''' (use Bitbucket to copy newest instance) | 1. '''Clone''' (use Bitbucket to copy newest instance) | ||
| − | : | + | :Create your assigned repository in Bitbucket. Then click Clone and copy the command. galaxy_dev contains the galaxy-dist |
::<code>hg [type Bitbucket command here]</code> | ::<code>hg [type Bitbucket command here]</code> | ||
2. '''Add''' (add new file to the repository you're working on so that they're being tracked) | 2. '''Add''' (add new file to the repository you're working on so that they're being tracked) | ||
| Line 20: | Line 20: | ||
3. '''Make necessary changes to XML''' | 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 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 | + | *'''Check 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 following text format: | *'''Update help section.''' Include appropriate citations (e.g. Osiris, PHYTAB, programs). Use the following text format: | ||
Revision as of 08:36, 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 (use Bitbucket to copy newest instance)
- Create your assigned repository in Bitbucket. Then click Clone and copy the command. galaxy_dev contains the galaxy-dist
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.
- 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
