Difference between revisions of "Galaxy"
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[[Category:Galaxy]] [[Category:Biology]] | [[Category:Galaxy]] [[Category:Biology]] | ||
| − | + | UF researchers now have access to an instance of Galaxy at Research Computing - a web-based framework for accessible, reproducible, and transparent biological computing. Galaxy has arisen as the most popular framework for providing biological researchers access to the tools they need for the analysis of their data. It helps researchers survive and thrive in the face of ever growing computational and data management demands of contemporary biology. It also provides the convenience of a robust system of user account handling, data sharing, and security. Since most biological research projects now happen in a distributed collaborative environment, Galaxy's work history sharing and analytical pipeline building, as well as publishing and sharing the results in a convenient and secure manner, address the most important issues and allow UF researchers to be highly competitive. Other benefits of the UF instance of Galaxy are access to the high-speed campus Research Network, use of large HPC cluster resources for running jobs, transparent user account access and convenient data upload, as well as full system and user support by the RC staff. | |
| + | __TOC__ | ||
==UF Galaxy URI== | ==UF Galaxy URI== | ||
| − | '''[http://galaxy. | + | '''[http://galaxy.rc.ufl.edu Access the UF RC instance of Galaxy]'''. |
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==Getting Help== | ==Getting Help== | ||
| − | * Use the [http://support.rc.ufl.edu UFRC Support Ticket System] to request adding new tools or reference data to the Galaxy and to file problem reports. '''Note: If you are submitting a problem report the first step should be to share the history that contains a failed step with '' | + | * Use the [http://support.rc.ufl.edu UFRC Support Ticket System] to request adding new tools or reference data to the Galaxy and to file problem reports. '''Note: If you are submitting a problem report the first step should be to share the history that contains a failed step with by using the 'bug' icon in galaxy. |
* When submitting a problem report use the [[Galaxy_Report_a_Problem|Galaxy bug reporting tool]] to provide us with the information necessary for solving the problem. Click on the green "bug" icon in the problematic step in the history and submit the resulting form. This tool automatically shares your history with us, so you don't have to share it separately. Alternatively, you can just [[share your Galaxy history]] if necessary. | * When submitting a problem report use the [[Galaxy_Report_a_Problem|Galaxy bug reporting tool]] to provide us with the information necessary for solving the problem. Click on the green "bug" icon in the problematic step in the history and submit the resulting form. This tool automatically shares your history with us, so you don't have to share it separately. Alternatively, you can just [[share your Galaxy history]] if necessary. | ||
| − | * UFGI Office hours for | + | * UFGI Office hours for UFRC biological computing support including Galaxy support are 9am to 2pm on Tue and Thr in CGRC 119. |
==Learn Galaxy== | ==Learn Galaxy== | ||
| − | * [[Category:Training|UFRC Training]] sessions on using Galaxy take place every semester. See the schedule. | + | * [[:Category:Training|UFRC Training]] sessions on using Galaxy take place every semester. See the schedule. |
* The main documentation site for galaxy users is the [http://wiki.g2.bx.psu.edu/Learn Galaxy Wiki/Learn]. | * The main documentation site for galaxy users is the [http://wiki.g2.bx.psu.edu/Learn Galaxy Wiki/Learn]. | ||
* The main mailing list for users of Galaxy is [http://gmod.827538.n3.nabble.com/Galaxy-Users-f815892.html "Galaxy Users"]]. | * The main mailing list for users of Galaxy is [http://gmod.827538.n3.nabble.com/Galaxy-Users-f815892.html "Galaxy Users"]]. | ||
| − | * There is also a UFRC [http:// | + | * There is also a UFRC [http://www.rc/cgi-bin/mailman/listinfo/biocomputing BioComputing Mailing List]. |
* [[Media:2012-09-19-Galaxy_Admins-UFL-Moskalenko.pdf|History and setup of the UF Galaxy]] as presented at the Galaxy Admins tele-conference. | * [[Media:2012-09-19-Galaxy_Admins-UFL-Moskalenko.pdf|History and setup of the UF Galaxy]] as presented at the Galaxy Admins tele-conference. | ||
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===Large Dataset Import=== | ===Large Dataset Import=== | ||
| + | * '''Create''' your Galaxy upload directory as '/ufrc/apps/galaxy/incoming/<your email address in galaxy>' and copy your datasets there. Note, it may take up to 15 minutes for Galaxy to fix the permissions before uploaded files will become available in a list at the bottom of the Galaxy 'Get Data > Upload File' tool. | ||
* Use the 'Upload File' tool and either upload smaller files from your local machine or select files in your galaxy incoming directory by clicking on the checkboxes in front of the file names and click on the 'Execute' button to start the upload. | * Use the 'Upload File' tool and either upload smaller files from your local machine or select files in your galaxy incoming directory by clicking on the checkboxes in front of the file names and click on the 'Execute' button to start the upload. | ||
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===Writing Custom Wrappers=== | ===Writing Custom Wrappers=== | ||
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===Share a History=== | ===Share a History=== | ||
* [[Share your Galaxy history]] | * [[Share your Galaxy history]] | ||
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===Administration=== | ===Administration=== | ||
* Notes on [[Galaxy_Configuration]] for instance administrators. | * Notes on [[Galaxy_Configuration]] for instance administrators. | ||
Revision as of 00:02, 14 June 2019
UF researchers now have access to an instance of Galaxy at Research Computing - a web-based framework for accessible, reproducible, and transparent biological computing. Galaxy has arisen as the most popular framework for providing biological researchers access to the tools they need for the analysis of their data. It helps researchers survive and thrive in the face of ever growing computational and data management demands of contemporary biology. It also provides the convenience of a robust system of user account handling, data sharing, and security. Since most biological research projects now happen in a distributed collaborative environment, Galaxy's work history sharing and analytical pipeline building, as well as publishing and sharing the results in a convenient and secure manner, address the most important issues and allow UF researchers to be highly competitive. Other benefits of the UF instance of Galaxy are access to the high-speed campus Research Network, use of large HPC cluster resources for running jobs, transparent user account access and convenient data upload, as well as full system and user support by the RC staff.
UF Galaxy URI
Access the UF RC instance of Galaxy.
Getting Help
- Use the UFRC Support Ticket System to request adding new tools or reference data to the Galaxy and to file problem reports. Note: If you are submitting a problem report the first step should be to share the history that contains a failed step with by using the 'bug' icon in galaxy.
- When submitting a problem report use the Galaxy bug reporting tool to provide us with the information necessary for solving the problem. Click on the green "bug" icon in the problematic step in the history and submit the resulting form. This tool automatically shares your history with us, so you don't have to share it separately. Alternatively, you can just share your Galaxy history if necessary.
- UFGI Office hours for UFRC biological computing support including Galaxy support are 9am to 2pm on Tue and Thr in CGRC 119.
Learn Galaxy
- UFRC Training sessions on using Galaxy take place every semester. See the schedule.
- The main documentation site for galaxy users is the Galaxy Wiki/Learn.
- The main mailing list for users of Galaxy is "Galaxy Users"].
- There is also a UFRC BioComputing Mailing List.
- History and setup of the UF Galaxy as presented at the Galaxy Admins tele-conference.
UFRC Galaxy specific documentation
User Access
- All users with UFRC accounts can access and use the UFRC Galaxy instance.
Large Dataset Import
- Create your Galaxy upload directory as '/ufrc/apps/galaxy/incoming/<your email address in galaxy>' and copy your datasets there. Note, it may take up to 15 minutes for Galaxy to fix the permissions before uploaded files will become available in a list at the bottom of the Galaxy 'Get Data > Upload File' tool.
- Use the 'Upload File' tool and either upload smaller files from your local machine or select files in your galaxy incoming directory by clicking on the checkboxes in front of the file names and click on the 'Execute' button to start the upload.
Writing Custom Wrappers
Known Galaxy Problems
Report a Galaxy Problem
Administration
- Notes on Galaxy_Configuration for instance administrators.