Mercurial > repos > fubar > toolfactory_gtn
changeset 1:f33aaec1f2c9 draft
Deleted selected files
| author | fubar |
|---|---|
| date | Sun, 18 Apr 2021 04:49:42 +0000 |
| parents | 06d2d758e5da |
| children | 2da2565f2e50 |
| files | toolfactory/LICENSE toolfactory/README.md |
| diffstat | 2 files changed, 0 insertions(+), 884 deletions(-) [+] |
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--- a/toolfactory/LICENSE Sun Apr 18 04:44:57 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,504 +0,0 @@ -GNU LESSER GENERAL PUBLIC LICENSE - Version 2.1, February 1999 - - Copyright (C) 1991, 1999 Free Software Foundation, Inc. - 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA - Everyone is permitted to copy and distribute verbatim copies - of this license document, but changing it is not allowed. - -(This is the first released version of the Lesser GPL. It also counts - as the successor of the GNU Library Public License, version 2, hence - the version number 2.1.) - - Preamble - - The licenses for most software are designed to take away your -freedom to share and change it. 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--- a/toolfactory/README.md Sun Apr 18 04:44:57 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,380 +0,0 @@ -## Breaking news! Docker container at https://github.com/fubar2/toolfactory-galaxy-docker recommended as at December 2020 - -### New demonstration of planemo tool_factory command  - -## This is the original ToolFactory suitable for non-docker situations. Please use the docker container if you can because it's integrated with a Toolshed... - -# WARNING - -Install this tool to a throw-away private Galaxy or Docker container ONLY! - -Please NEVER on a public or production instance where a hostile user may -be able to gain access if they can acquire an administrative account login. - -It only runs for server administrators - the ToolFactory tool will refuse to execute for an ordinary user since -it can install new tools to the Galaxy server it executes on! This is not something you should allow other than -on a throw away instance that is protected from potentially hostile users. - -## 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 an XML document describing how the application interacts with Galaxy. -This is sometimes termed "wrapping" the package because the instructions tell Galaxy how to run the package -as a new Galaxy tool. Any tool that has been wrapped is readily available to all the users through a consistent -and easy to use interface once installed in the local Galaxy server. - -Most Galaxy tool wrappers have been manually prepared by skilled programmers, many using Planemo because it -automates much of the boilerplate and makes the process much easier. -The ToolFactory (TF) now uses Planemo under the hood for testing, but hides the command -line complexities. The user will still need appropriate skills in terms of describing the interface between -Galaxy and the new application, but will be helped by a Galaxy tool form to collect all the needed -settings, together with automated testing and uploading to a toolshed with optional local installation. - - -## ToolFactory generated tools are ordinary Galaxy tools - -A TF generated tool that passes the Planemo test is ready to publish in any Galaxy Toolshed and ready to install in any running Galaxy instance. -They are fully workflow compatible and work exactly like any hand-written tool. The user can select input files of the specified type(s) from their -history and edit each of the specified parameters. The tool form will show all the labels and help text supplied when the tool was built. When the tool -is executed, the dependent binary or script will be passed all the i/o files and parameters as specified, and will write outputs to the specified new -history datasets - just like any other Galaxy tool. - -## Models for tool command line construction - -The key to turning any software package into a Galaxy tool is the automated construction of a suitable command line. - -The TF can build a new tool that will allow the tool user to select input files from their history, set any parameters and when run will send the -new output files to the history as specified when the tool builder completed the form and built the new tool. - -That tool can contain instructions to run any Conda dependency or a system executable like bash. Whether a bash script you have written or -a Conda package like bwa, the executable will expect to find settings for input, output and parameters on a command line. - -These are often passed as "--name value" (argparse style) or in a fixed order (positional style). - -The ToolFactory allows either, or for "filter" applications that process input from STDIN and write processed output to STDOUT. - -The simplest tool model wraps a simple script or Conda dependency package requiring only input and output files, with no user supplied settings illustrated by -the Tacrev demonstration tool found in the Galaxy running in the ToolFactory docker container. It passes a user selected input file from the current history on STDIN -to a bash script. The bash script runs the unix tac utility (reverse cat) piped to the unix rev (reverse lines in a text file) utility. It's a one liner: - -`tac | rev` - -The tool building form allows zero or more Conda package name(s) and version(s) and an optional script to be executed by either a system -executable like ``bash`` or the first of any named Conda dependency package/version. Tacrev uses a tiny bash script shown above and uses the system -bash. Conda bash can be specified if it is important to use the same version consistently for the tool. - -On the tool form, the repeat section allowing zero or more input files was set to be a text file to be selected by the tool user and -in the repeat section allowing one or more outputs, a new output file with special value `STDOUT` as the positional parameter, causes the TF to -generate a command to capture STDOUT and send it to the new history file containing the reversed input text. - -By reversed, we mean really, truly reversed. - -That simple model can be made much more complicated, and can pass inputs and outputs as named or positional parameters, -to allow more complicated scripts or dependent binaries that require: - -1. Any number of input data files selected by the user from existing history data -2. Any number of output data files written to the user's history -3. Any number of user supplied parameters. These can be passed as command line arguments to the script or the dependency package. Either -positional or named (argparse) style command line parameter passing can be used. - -More complex models can be seen in the Sedtest, Pyrevpos and Pyrevargparse tools illustrating positional and argparse parameter passing. - -The most complex demonstration is the Planemo advanced tool tutorial BWA tool. There is one version using a command-override to implement -exactly the same command structure in the Planemo tutorial. A second version uses a bash script and positional parameters to achieve the same -result. Some tool builders may find the bash version more familiar and cleaner but the choice is yours. - -## Overview - - - - -Steps in building a new Galaxy tool are all conducted through Galaxy running in the docker container: - -1. Login to the Galaxy running in the container at http://localhost:8080 using an admin account. They are specified in config/galaxy.yml and - in the documentation at - and the ToolFactory will error out and refuse to run for non-administrative tool builders as a minimal protection from opportunistic hostile use. - -2. Start the TF and fill in the form, providing sample inputs and parameter values to suit the Conda package being wrapped. - -3. Execute the tool to create a new XML tool wrapper using the sample inputs and parameter settings for the inbuilt tool test. Planemo runs twice. - firstly to generate the test outputs and then to perform a proper test. The completed toolshed archive is written to the history - together with the planemo test report. Optionally the new tool archive can be uploaded - to the toolshed running in the same container (http://localhost:9009) and then installed inside the Galaxy in the container for further testing. - -4. If the test fails, rerun the failed history job and correct errors on the tool form before rerunning until everything works correctly. - - - -## Planning and building new Galaxy tool wrappers. - -It is best to have all the required planning done to wrap any new script or binary before firing up the TF. -Conda is the only current dependency manager supported. Before starting, at the very least, the tool builder will need -to know the required software package name in Conda and the version to use, how the command line for -the package must be constructed, and there must be sample inputs in the working history for each of the required data inputs -for the package, together with values for every parameter to suit these sample inputs. These are required on the TF form -for preparing the inbuilt tool test. That test is run using Planemo, as part of the tool generation process. - -A new tool is specified by filling in the usual Galaxy tool form. - -The form starts with a new tool name. Most tools will need dependency packages and versions -for the executable. Only Conda is currently supported. - -If a script is needed, it can be pasted into a text box and the interpreter named. Available system executables -can be used such as bash, or an interpreter such as python, perl or R can be nominated as conda dependencies -to ensure reproducible analyses. - -The tool form will be generated from the input data and the tool builder supplied parameters. The command line for the -executable is built using positional or argparse (named e.g. --input_file /foo/baz) style -parameters and is completely dependent on the executable. These can include: - -1. Any number of input data sets needed by the executable. Each appears to the tool user on the run form and is included -on the command line for the executable. The tool builder must supply a small representative sample for each one as -an input for the automated tool test. - -2. Any number of output data sets generated by the package can be added to the command line and will appear in -the user's history at the end of the job - -3. Any number of text or numeric parameters. Each will appear to the tool user on the run form and are included -on the command line to the executable. The tool builder must supply a suitable representative value for each one as -the value to be used for the automated tool test. - -Once the form is completed, executing the TF will build a new XML tool wrapper -including a functional test based on the sample settings and data. - -If the Planemo test passes, the tool can be optionally uploaded to the local Galaxy used in the image for more testing. - -A local toolshed runs inside the container to allow an automated installation, although any toolshed and any accessible -Galaxy can be specified for this process by editing the default URL and API keys to provide appropriate credentials. - -## Generated Tool Dependency management - -Conda is used for all dependency management although tools that use system utilities like sed, bash or awk -may be available on job execution nodes. Sed and friends are available as Conda (conda-forge) dependencies if necessary. -Versioned Conda dependencies are always baked-in to the tool and will be used for reproducible calculation. - -## Requirements - -These are all managed automagically. The TF relies on galaxyxml to generate tool xml and uses ephemeris and -bioblend to load tools to the toolshed and to Galaxy. Planemo is used for testing and runs in a biocontainer currently at -https://quay.io/fubar2/planemo-biocontainer - -## Caveats - -This docker image requires privileged mode so exposes potential security risks if hostile tool builders gain access. -Please, do not run it in any situation where that is a problem - never, ever on a public facing Galaxy server. -On a laptop or workstation should be fine in a non-hostile environment. - - -## Example generated XML - -For the bwa-mem example, a supplied bash script is included as a configfile and so has escaped characters. -``` -<tool name="bwatest" id="bwatest" version="0.01"> - <!--Cite: Creating re-usable tools from scripts doi:10.1093/bioinformatics/bts573--> - <!--Source in git at: https://github.com/fubar2/toolfactory--> - <!--Created by admin@galaxy.org at 30/11/2020 07:12:10 using the Galaxy Tool Factory.--> - <description>Planemo advanced tool building sample bwa mem mapper as a ToolFactory demo</description> - <requirements> - <requirement version="0.7.15" type="package">bwa</requirement> - <requirement version="1.3" type="package">samtools</requirement> - </requirements> - <configfiles> - <configfile name="runme"><![CDATA[ -REFFILE=\$1 -FASTQ=\$2 -BAMOUT=\$3 -rm -f "refalias" -ln -s "\$REFFILE" "refalias" -bwa index -a is "refalias" -bwa mem -t "2" -v 1 "refalias" "\$FASTQ" > tempsam -samtools view -Sb tempsam > temporary_bam_file.bam -samtools sort -o "\$BAMOUT" temporary_bam_file.bam - -]]></configfile> - </configfiles> - <version_command/> - <command><![CDATA[bash -$runme -$input1 -$input2 -$bam_output]]></command> - <inputs> - <param optional="false" label="Reference sequence for bwa to map the fastq reads against" help="" format="fasta" multiple="false" type="data" name="input1" argument="input1"/> - <param optional="false" label="Reads as fastqsanger to align to the reference sequence" help="" format="fastqsanger" multiple="false" type="data" name="input2" argument="input2"/> - </inputs> - <outputs> - <data name="bam_output" format="bam" label="bam_output" hidden="false"/> - </outputs> - <tests> - <test> - <output name="bam_output" value="bam_output_sample" compare="sim_size" format="bam" delta_frac="0.1"/> - <param name="input1" value="input1_sample"/> - <param name="input2" value="input2_sample"/> - </test> - </tests> - <help><![CDATA[ - -**What it Does** - -Planemo advanced tool building sample bwa mem mapper - -Reimagined as a bash script for a ToolFactory demonstration - - ------- - -Script:: - - REFFILE=$1 - FASTQ=$2 - BAMOUT=$3 - rm -f "refalias" - ln -s "$REFFILE" "refalias" - bwa index -a is "refalias" - bwa mem -t "2" -v 1 "refalias" "$FASTQ" > tempsam - samtools view -Sb tempsam > temporary_bam_file.bam - samtools sort -o "$BAMOUT" temporary_bam_file.bam - -]]></help> -</tool> - -``` - - - -## 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 -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 - -The TF will generate the new tool described on the TF form, and test it -using planemo. Optionally if a local toolshed is running, it can be used to -install the new tool back into the generating Galaxy. - -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 using the default toolshed and Galaxy URL and API keys. - -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 -TF 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. It does not deal with -repeated elements or conditional parameters such as allowing a user to choose to see "simple" -or "advanced" parameters (yet) and there will be plenty of packages it just -won't cover - but it's a quick and efficient tool for the other 90% of cases. Perfect for -that bash one liner you need to get that workflow functioning correctly for this -afternoon's demonstration! - -## Installation - -The Docker container https://github.com/fubar2/toolfactory-galaxy-docker/blob/main/README.md -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 after a restart and you -can run a workflow to generate all the sample tools. Running the samples and rerunning the ToolFactory -jobs that generated them allows you to add fields and experiment to see how things work. - -It can be installed like any other tool from the Toolshed, 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. - -If not already there please add: - -``` -<datatype extension="tgz" type="galaxy.datatypes.binary:Binary" mimetype="multipart/x-gzip" subclass="True" /> -``` - -to your local config/data_types_conf.xml. - - -## Restricted execution - -The tool factory tool itself will ONLY run for admin users - -people with IDs in config/galaxy.yml "admin_users". - -*ONLY admin_users can run this tool* - -That doesn't mean it's safe to install on a shared or exposed instance - please don't. - -## 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. - -## 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 -