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annotate README.md @ 2:856bd14e6e96 draft

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author pablocarb
date Thu, 02 May 2019 07:16:40 -0400
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1 # Galaxy wrappers for SynBio Design Tools
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3 ## galaxy_selenzyme
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5 Creating a tool within Galaxy to run Selenzyme.
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7 See:
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9 * Tutorial to create a Galaxy tool: https://galaxyproject.org/admin/tools/add-tool-tutorial/
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10 * How to install it in the Galaxy container: https://github.com/bgruening/docker-galaxy-stable
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11 * Example for Uniprot: https://toolshed.g2.bx.psu.edu/repository?repository_id=c8774310981b07c5
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13 Plan:
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14 - [x] Create a basic command line tool using Python `requests` that submits a the reaction SMILES and gets the predicted sequences.
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15 - [x] Create a Galaxy Tool XML file.
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16 - [x] Check that the Galaxy container has `requests` installed, otherwise add to the `docker-compose` file.
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17 - [x] Mount the folder with the tool in the container.
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18 - [x] Install the tool locally in Galaxy.
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19 - [x] Use planemo in order to create a repository in the toolshed.
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20 - [x] Register in the toolshed.
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21 - [x] Install in the Galaxy container from the toolshed.
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22 - [ ] Create a tool using Galaxy XML that post JSON request and receives a JSON response (no local tool running in the Galaxy server).
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23 - [ ] Submit the purely XML tool to the [Galaxy Tool Shed](https://toolshed.g2.bx.psu.edu/).