Mercurial > repos > fubar > tool_factory_2
diff toolfactory/README.md @ 56:68fbdbe35f08 draft
Uploaded
author | fubar |
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date | Tue, 20 Oct 2020 03:20:32 +0000 |
parents | 35a912ce0c83 |
children | 8ea1133b9d9a |
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--- a/toolfactory/README.md Mon Aug 31 00:20:27 2020 -0400 +++ b/toolfactory/README.md Tue Oct 20 03:20:32 2020 +0000 @@ -137,7 +137,29 @@ The Docker container is the best way to use the TF because it is preconfigured to automate new tool testing and has a built in local toolshed where each new tool -is uploaded. It is easy to install without Docker, but you will need to make some +is uploaded. If you grab the docker container, it should just work. + +If you build the container, there are some things to watch out for. Let it run for 10 minutes +or so once you build it - check with top until conda has finished fussing. Once everything quietens +down, find the container with +```docker ps``` +and use +```docker exec [containername] supervisorctl restart galaxy:``` +That colon is not a typographical mistake. +Not restarting after first boot seems to leave the job/worflow system confused and the workflow +just will not run properly until Galaxy has restarted. + +Login as admin@galaxy.org with password "password". Feel free to change it once you are logged in. +There should be a companion toolshed at localhost:9090. The history should have some sample data for +the workflow. + +Run the workflow and make sure the right dataset is selected for each of the input files. Most of the +examples use text files so should run, but the bwa example needs the right ones to work properly. + +When the workflow is finished, you will have half a dozen examples to rerun and play with. They have also +all been tested and installed so you should find them in your tool menu under "Generated Tools" + +It is easy to install without Docker, but you will need to make some configuration changes (TODO write a configuration). You can install it most conveniently using the administrative "Search and browse tool sheds" link. Find the Galaxy Main toolshed at https://toolshed.g2.bx.psu.edu/ and search for the toolfactory