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comparison toolfactory/README.md @ 56:68fbdbe35f08 draft

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author fubar
date Tue, 20 Oct 2020 03:20:32 +0000
parents 35a912ce0c83
children 8ea1133b9d9a
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55:dcf59d4e4515 56:68fbdbe35f08
135 135
136 *Installation* 136 *Installation*
137 137
138 The Docker container is the best way to use the TF because it is preconfigured 138 The Docker container is the best way to use the TF because it is preconfigured
139 to automate new tool testing and has a built in local toolshed where each new tool 139 to automate new tool testing and has a built in local toolshed where each new tool
140 is uploaded. It is easy to install without Docker, but you will need to make some 140 is uploaded. If you grab the docker container, it should just work.
141
142 If you build the container, there are some things to watch out for. Let it run for 10 minutes
143 or so once you build it - check with top until conda has finished fussing. Once everything quietens
144 down, find the container with
145 ```docker ps```
146 and use
147 ```docker exec [containername] supervisorctl restart galaxy:```
148 That colon is not a typographical mistake.
149 Not restarting after first boot seems to leave the job/worflow system confused and the workflow
150 just will not run properly until Galaxy has restarted.
151
152 Login as admin@galaxy.org with password "password". Feel free to change it once you are logged in.
153 There should be a companion toolshed at localhost:9090. The history should have some sample data for
154 the workflow.
155
156 Run the workflow and make sure the right dataset is selected for each of the input files. Most of the
157 examples use text files so should run, but the bwa example needs the right ones to work properly.
158
159 When the workflow is finished, you will have half a dozen examples to rerun and play with. They have also
160 all been tested and installed so you should find them in your tool menu under "Generated Tools"
161
162 It is easy to install without Docker, but you will need to make some
141 configuration changes (TODO write a configuration). You can install it most conveniently using the 163 configuration changes (TODO write a configuration). You can install it most conveniently using the
142 administrative "Search and browse tool sheds" link. Find the Galaxy Main 164 administrative "Search and browse tool sheds" link. Find the Galaxy Main
143 toolshed at https://toolshed.g2.bx.psu.edu/ and search for the toolfactory 165 toolshed at https://toolshed.g2.bx.psu.edu/ and search for the toolfactory
144 repository in the Tool Maker section. Open it and review the code and select the option to install it. 166 repository in the Tool Maker section. Open it and review the code and select the option to install it.
145 167