Difference between revisions of "Galaxy"
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[[Category:Galaxy]] [[Category:Biology]] | [[Category:Galaxy]] [[Category:Biology]] | ||
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| + | 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. | + | * 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 | + | * When submitting a problem report use bug button in Galaxy to provide us with the information necessary for solving the problem. Click on the "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. |
| − | * | + | * See the [[Support|Support page]] for other support options. |
==Learn Galaxy== | ==Learn Galaxy== | ||
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* 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 | + | * 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. | ||
| − | == | + | ==UFRC Galaxy specific documentation== |
===User Access=== | ===User Access=== | ||
| − | * All users with | + | * All users with UFRC accounts can access and use the UFRC Galaxy instance. |
===Large Dataset Import=== | ===Large Dataset Import=== | ||
| − | * [[ | + | * '''Create''' your Galaxy upload directory as '/data/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. See [[Transfer Data]] for more details if transferring files from outside of HiPerGator. |
| − | + | * 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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===Known Galaxy Problems=== | ===Known Galaxy Problems=== | ||
* [[Galaxy Known Issues]] | * [[Galaxy Known Issues]] | ||
| − | === | + | ===Share a History=== |
| − | + | * [[Share your Galaxy history]] | |
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| − | * [[Galaxy | ||
| − | === | + | ===Administration=== |
| − | * [[ | + | * Notes on [[Galaxy_Configuration]] for instance administrators. |
Latest revision as of 18:05, 9 November 2022
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 bug button in Galaxy to provide us with the information necessary for solving the problem. Click on the "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.
- See the Support page for other support options.
Learn Galaxy
- 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 '/data/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. See Transfer Data for more details if transferring files from outside of HiPerGator.
- 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.
Known Galaxy Problems
Administration
- Notes on Galaxy_Configuration for instance administrators.