Difference between revisions of "Osiris Development"
From Ucsbgalaxy
| Line 13: | Line 13: | ||
==Protocol for checking tools== | ==Protocol for checking tools== | ||
| − | 1. '''Clone''' | + | 1. '''Clone''' |
| − | :Create your assigned repository in Bitbucket. Then click Clone and copy the command. | + | :Create your assigned repository in Bitbucket. Then click Clone and copy the command. |
::<code>hg [type Bitbucket command here]</code> | ::<code>hg [type Bitbucket command here]</code> | ||
| − | 2. '''Add''' | + | 2. '''Add''' |
| + | :Copy tools from Knot and add them to the repository you're working on so that they're being tracked. | ||
::<code>hg add phytab_mafft.*</code> | ::<code>hg add phytab_mafft.*</code> | ||
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. | + | *'''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.[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: | ||
<pre> | <pre> | ||
| − | + | <help> | |
| + | **What it does** | ||
| − | + | [brief explanation of what it does] | |
| + | ------ | ||
| − | + | **Inputs** | |
| − | + | [file format input. with example, or perhaps link to phytab description] | |
| − | + | ------ | |
| − | + | **Outputs** | |
| + | |||
| + | [Output example or format] | ||
| + | |||
| + | ------- | ||
| + | |||
| + | **Additional Information** | ||
| + | |||
| + | [OPTIONAL: Link to blog post or other documentation; or perhaps similar tools.] | ||
| + | |||
| + | ------- | ||
| + | |||
| + | **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 consider citing the following. | ||
| + | |||
| + | Current Osiris Citation is here | ||
| + | |||
| + | http://osiris-phylogenetics.blogspot.com/2012/10/citation.html | ||
| + | |||
| + | Additional Citations for this tool | ||
| + | |||
| + | [Additional references, for the binary called, or for a description of the method employed] | ||
| + | |||
| + | </help> | ||
| − | |||
</pre> | </pre> | ||
| − | 4. '''Status''' | + | 4. '''Status''' |
| − | :<code>hg status</code> | + | :Check files have been changed. |
| − | 5. '''Commit''' | + | ::<code>hg status</code> |
| − | :<code>hg commit -m "THO adding PHYTAB-MAFFT"</code> | + | 5. '''Commit''' |
| − | 6. '''Push''' | + | :Makes collection of things that will change in the repository. Include a message with your initials and a brief description of the update. |
| − | :<code>hg push</code> | + | ::<code>hg commit -m "THO adding PHYTAB-MAFFT"</code> |
| + | 6. '''Push''' | ||
| + | :Pushes changes to Bitbucket. | ||
| + | ::<code>hg push</code> | ||
7. '''Create Issues on Bitbucket''' Login to Bitbucket and create issues for tools that need tests (or anything else that needs to be fixed).<br /> | 7. '''Create Issues on Bitbucket''' Login to Bitbucket and create issues for tools that need tests (or anything else that needs to be fixed).<br /> | ||
8. '''Post to Osiris blog'''[http://osiris-phylogenetics.blogspot.com/] 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. | 8. '''Post to Osiris blog'''[http://osiris-phylogenetics.blogspot.com/] 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. | ||
Revision as of 08:59, 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 following text format:
<help>
**What it does**
[brief explanation of what it does]
------
**Inputs**
[file format input. with example, or perhaps link to phytab description]
------
**Outputs**
[Output example or format]
-------
**Additional Information**
[OPTIONAL: Link to blog post or other documentation; or perhaps similar tools.]
-------
**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 consider citing the following.
Current Osiris Citation is here
http://osiris-phylogenetics.blogspot.com/2012/10/citation.html
Additional Citations for this tool
[Additional references, for the binary called, or for a description of the method employed]
</help>
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
