diff toolfactory/README.md @ 0:fc50a3f507ab draft

Need a new repo - old tool_factory_2 is broken

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+**Breaking news! Docker container is recommended as at August 2020**
+
+A Docker container can be built - see the docker directory.
+It is highly recommended for isolation. It also has an integrated toolshed to allow installation of new tools back 
+into the Galaxy being used to generate them. 
+
+Built from quay.io/bgruening/galaxy:20.05 but updates the
+Galaxy code to the dev branch - it seems to work fine with updated bioblend>=0.14
+with planemo and the right version of gxformat2 needed by the ToolFactory (TF).
+
+The runclean.sh script run from the docker subdirectory of your local clone of this repository
+should create a container (eventually) and serve it at localhost:8080 with a toolshed at
+localhost:9009.
+
+Once it's up, please restart Galaxy in the container with 
+```docker exec [container name] supervisorctl restart galaxy: ```
+Jobs just do not seem to run properly otherwise and the next steps won't work!
+
+The generated container includes a workflow and 2 sample data sets for the workflow
+
+Load the workflow. Adjust the inputs for each as labelled. The perl example counts GC in phiX.fasta. 
+The python scripts use the rgToolFactory.py as their input - any text file will work but I like the
+recursion. The BWA example has some mitochondrial reads and reference. Run the workflow and watch.
+This should fill the history with some sample tools you can rerun and play with.
+Note that each new tool will have been tested using Planemo. In the workflow, in Galaxy.
+Extremely cool to watch.
+
+*WARNING* 
+
+ Install this tool on a throw-away private Galaxy or Docker container ONLY
+ Please NEVER on a public or production instance
+
+*Short Story*
+
+Galaxy is easily extended to new applications by adding a new tool. Each new scientific computational package added as
+a tool to Galaxy requires some special instructions to be written. This is sometimes termed "wrapping" the package
+because the instructions tell Galaxy how to run the package as a new Galaxy tool. Any tool in a Galaxy is 
+readily available to all the users through a consistent and easy to use interface.
+
+Most Galaxy tool wrappers have been manually prepared by skilled programmers, many using Planemo because it 
+automates much of the basic boilerplate and makes the process much easier. The ToolFactory (TF) 
+uses Planemo under the hood for many functions, but hides the command
+line complexities from the TF user. 
+
+*More Explanation*
+
+The TF is an unusual Galaxy tool, designed to allow a skilled user to make new Galaxy tools. 
+It appears in Galaxy just like any other tool but outputs include new Galaxy tools generated
+using instructions provided by the user and the results of Planemo lint and tool testing using
+small sample inputs provided by the TF user. The small samples become tests built in to the new tool.
+
+It offers a familiar Galaxy form driven way to define how the user of the new tool will 
+choose input data from their history, and what parameters the new tool user will be able to adjust.
+The TF user must know, or be able to read, enough about the tool to be able to define the details of
+the new Galaxy interface and the ToolFactory offers little guidance on that other than some examples.
+
+Tools always depend on other things. Most tools in Galaxy depend on third party
+scientific packages, so TF tools usually have one or more dependencies. These can be
+scientific packages such as BWA or scripting languages such as Python and are
+usually managed by Conda. If the new tool relies on a system utility such as bash or awk 
+where the importance of version control on reproducibility is low, these can be used without 
+Conda management - but remember the potential risks of unmanaged dependencies on computational
+reproducibility.
+
+The TF user can optionally supply a working script where scripting is
+required and the chosen dependency is a scripting language such as Python or a system
+scripting executable such as bash. Whatever the language, the script must correctly parse the command line
+arguments it receives at tool execution, as they are defined by the TF user. The
+text of that script is "baked in" to the new tool and will be executed each time
+the new tool is run. It is highly recommended that scripts and their command lines be developed
+and tested until proven to work before the TF is invoked. Galaxy as a software development
+environment is actually possible, but not recommended being somewhat clumsy and inefficient.
+
+Tools nearly always take one or more data sets from the user's history as input. TF tools
+allow the TF user to define what Galaxy datatypes the tool end user will be able to choose and what 
+names or positions will be used to pass them on a command line to the package or script.
+
+Tools often have various parameter settings. The TF allows the TF user to define how each
+parameter will appear on the tool form to the end user, and what names or positions will be
+used to pass them on the command line to the package. At present, parameters are limited to
+simple text and number fields. Pull requests for other kinds of parameters that galaxyxml
+can handle are welcomed.
+
+Best practice Galaxy tools have one or more automated tests. These should use small sample data sets and
+specific parameter settings so when the tool is tested, the outputs can be compared with their expected
+values. The TF will automatically create a test for the new tool. It will use the sample data sets 
+chosen by the TF user when they built the new tool.
+
+The TF works by exposing *unrestricted* and therefore extremely dangerous scripting
+to all designated administrators of the host Galaxy server, allowing them to
+run scripts in R, python, sh and perl. For this reason, a Docker container is
+available to help manage the associated risks.
+
+*Scripting uses*
+
+To use a scripting language to create a new tool, you must first prepared and properly test a script. Use small sample
+data sets for testing. When the script is working correctly, upload the small sample datasets
+into a new history, start configuring a new ToolFactory tool, and paste the script into the script text box on the TF form.
+
+*Outputs*
+
+Once the script runs sucessfully, a new Galaxy tool that runs your script
+can be generated. Select the "generate" option and supply some help text and
+names. The new tool will be generated in the form of a new Galaxy datatype
+*tgz* - as the name suggests, it's an archive ready to upload to a
+Galaxy ToolShed as a new tool repository.
+
+It is also possible to run a tool to generate test outputs, then test it
+using planemo. A toolshed is built in to the Docker container and configured
+so a tool can be tested, sent to that toolshed, then installed in the Galaxy
+where the TF is running.
+
+If the tool requires a command or test XML override, then planemo is 
+needed to generate test outputs to make a complete tool, rerun to test 
+and if required upload to the local toolshed and install in the Galaxy 
+where the TF is running.
+
+Once it's in a ToolShed, it can be installed into any local Galaxy server
+from the server administrative interface.
+
+Once the new tool is installed, local users can run it - each time, the 
+package and/or script that was supplied when it was built will be executed with the input chosen
+from the user's history, together with user supplied parameters. In other words, the tools you generate with the
+ToolFactory run just like any other Galaxy tool.
+
+TF generated tools work as normal workflow components.
+
+
+*Limitations*
+
+The TF is flexible enough to generate wrappers for many common scientific packages
+but the inbuilt automation will not cope with all possible situations. Users can
+supply overrides for two tool XML segments - tests and command and the BWA
+example in the supplied samples workflow illustrates their use.  
+
+*Installation*
+
+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. 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
+repository in the Tool Maker section. Open it and review the code and select the option to install it.
+
+Otherwise, if not already there pending an accepted PR,
+please add:
+<datatype extension="tgz" type="galaxy.datatypes.binary:Binary"
+mimetype="multipart/x-gzip" subclass="True" />
+to your local data_types_conf.xml.
+
+
+*Restricted execution*
+
+The tool factory tool itself will then be usable ONLY by admin users -
+people with IDs in admin_users. **Yes, that's right. ONLY
+admin_users can run this tool** Think about it for a moment. If allowed to
+run any arbitrary script on your Galaxy server, the only thing that would
+impede a miscreant bent on destroying all your Galaxy data would probably
+be lack of appropriate technical skills.
+
+**Generated tool Security**
+
+Once you install a generated tool, it's just
+another tool - assuming the script is safe. They just run normally and their
+user cannot do anything unusually insecure but please, practice safe toolshed.
+Read the code before you install any tool. Especially this one - it is really scary.
+
+**Send Code**
+
+Pull requests and suggestions welcome as git issues please?
+
+**Attribution**
+
+Creating re-usable tools from scripts: The Galaxy Tool Factory
+Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team
+Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573
+
+http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&keytype=ref
+
+**Licensing**
+
+Copyright Ross Lazarus 2010
+ross lazarus at g mail period com
+
+All rights reserved.
+
+Licensed under the LGPL
+