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

Uploaded

--- 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 [e-mail] 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