bioGUI documentation¶
Bioinformatics is a highly interdisciplinary field providing tools for researchers from many disciplines. Nonetheless, most methods are implemented with a command line Interface only.
Using bioGUI, former command line-only tools can be started from a GUI, making them available to a broader scientific community.
If you are a user, it is recommended to start reading directly from bioGUI: a universal GUI for command line tools. Please also read through the User Guide. We also provide a video tutorial to demonstrate how to install a module with an install module and use this module/tool afterwards in Use an Install Module (video tutorial).
If you are a (bioinformatics) tools developer and want to learn how to build (install) templates, start reading here: How does bioGUI work?.
If the offered windows and execution nodes are not enough and you want to extend bioGUI, the bioGUI Developer Guide may be of help for you.
bioGUI: a universal GUI for command line tools¶
Bioinformatics is a highly interdisciplinary field providing tools for researchers from many disciplines. Nonetheless, most methods are implemented with a command line Interface only. Non-computer affine colleagues may well interpret results from such tools, but installing and starting tools on the command-Line often is a problem. Providing a Graphical User-Interface (GUI) for bioinformatics tools is a step towards routinely applying these command line-only tools, and, thus a more effective interdisciplinary work.
bioGUI is a universal GUI for command line tools making use of Window’s newest feature: WSL (Windows Subsystem for Linux), which provides a native Ubuntu bash on Windows. bioGUI templates are easily scriptable and render a GUI for user input from defined visual components elements. Install modules can install a tool and its template with few clicks from our emph{bioGUI} repository.
Using bioGUI, former command line-only tools can be started from a GUI, making them available to a broader scientific community.
Who is bioGUI for?¶
With bioGUI, domain experts, who don’t want to be bothered with the command Line, are enabled to use high standard bioinformatics tools. bioGUI specifically aims at Windows users, as Microsoft just introduced the Windows Subsystem for Linux (WSL) with its Bash on Ubuntu on Windows. This system allows the usage of said sophisticated tools on a regular Windows computer as most people have. With bioGUI one also does not need any knowledge about the command line, because the task of executing a given tools becomes a point & click solution.
What is bioGUI currently not?¶
It is not about generating a GUI by its own. Currently generating template files is a manual business, which is best performed by a tool’s developer. For the future, integration of automatic command line Interface to bioGUI converters are thought of. However, this could only be realised for a limited number of argument parsers, such as argparse for python.
User Guide¶
How to get bioGUI?¶
Download bioGUI releases from the github releases. Please note additional information provided in our User Guide.
Install bioGUI¶
Binary packages/releases for the following operating system are provided on github.
Windows¶
Extract the zip-File and place the contained bioGUI folder somewhere on your hard drives.
Follow the instructions to setup WSL: How to setup WSL (Bash on Ubuntu).
Please do not put bioGUI in your Program Files directory, as this is specially protected by Windows and may cause problems.
Place bioGUI into a location which does not contain spaces in its name, e.g not C:\Program Files\bioGUI !
You can put bioGUI for instance into the locations C:\bioGUI\ or D:\bioGUI\ !
If you want to access external drives (USB stick, network drive), you first need to mount this drive into WSL. The WSL Mount Drive install module will install a script which can do this for you. Make sure to save the template and use the Mount Drive (WSL) template to make the drive available to WSL. You need to enter the drive-letter you want to mount (e.g. F), and your sudo password.
Linux¶
Extract the tar.gz file and place the contained bioGUI folder somewhere on your hard drives.
On Ubuntu you can then execute the bioGUI.desktop file, e.g. from your Explorer equivalent, or being in the bioGUI folder, the command-line: dex bioGUI.desktop (you may need to install dex first: sudo apt-get install dex).
Alternatively you can also simply execute sh ./bioGUI.sh.
Mac OS¶
Download and open the provided dmg package. You can simply drag and drop the bioGUI.app into your Applications folder.
bioGUI has been built for Mac OS X 10.14 Mojave. Mac OS may bother your about running an app from a non-signed/verified developer.
In the Preferences->Security menu you can tell Mac OS to still run bioGUI.
In order to use bioGUI, it may be required to install the OSX command line tools as well as brew.
For the command line tools, open a Terminal and enter xcode-select --install.
You can get brew from here
To test brew, simply run the following code:
brew install wget netcat
Make sure to have brew in your path.
From the terminal, run:
echo "export PATH=/usr/local/bin/:\$PATH" >> ~/.bash_profile
This will tell Mac OS to look for (unix) applications also under /usr/local/bin/. This is where brew installs itself.
Installing new software with Install Modules¶
After downloading an Install Module, the Install Template Module will list the downloaded install template (you might need to reload once).
The screenshot below shows the Install Template Module.
In the dropdown menu, the hisat2 install template has been chosen.
Since this module is executed on Windows, WSL is selected.
hisat2 is supposed to be installed into the User Data Dir, which is on WSL and linux usually ~/.local/share/bioGUI.
This is the directory where bioGUI installs new programs.
Advanced users may want to change this settings, but in general, it should be left.
In order to automatically install dependencies, the sudo-password must be supplied. This is the password you set up during the installation of the WSL feature. This gives bioGUI administrative rights within WSL such that it can install dependencies automatically.
Finally the path for the specific GUI template has to be set. bioGUI by default only searches the template directory besides the executable.
GUI templates must have the file extension .gui. If your entered template name does not end with this extension, the extension is appended to your filename.
As a short-cut, if you just enter a name (e.g. mygui), bioGUI will save the new template in the template directoy with the filename mygui.gui.
Use-case: Windows setup¶
The binary distribution (zip-files) are targeted for end-users: [prebuilt binaries](https://github.com/mjoppich/bioGUI/releases). Download the Windows version.
Make sure that the Windows Subsystem for Linux (WSL) is installed. Please follow the steps on [how to setup WSL](http://biogui.readthedocs.io/en/latest/build_wsl.html).
After downloading the zip-archive, please unzip the archive to a location of your preference. Then simply start the executable (bioGUI.exe on Windows). Place bioGUI into a location which does not contain spaces in its name, e.g not C:Program FilesbioGUI ! C:bioGUI is fine though!
On any aptitude supported platform (e.g. Windows with WSL, Ubuntu), please download the “First Time Ubuntu/WSL/apt-get Setup” from the list of available templates and install it via Install Template Module (install program: First Time Ubuntu/WSL/apt-get setup).
Below this process is shown by an animation.
Setup First Time Use¶
For the First Time Use setups, please make sure to insert your sudo/user password and deselect to save a template.
Please make sure that bioGUI closes the setup with the following message:
If you do not see this message, (raise an issue on GitHub) with attaching the log.txt file in the bioGUI folder, or /tmp/log_biogui.txt on Mac OS, as well as an screenshot of the attempt.
Install an install module¶
After the install module has been installed, you will see a message stating that bioGUI installed the software:
If you do not see the message, but only blue text, like below, you need to scroll up:
If you do not see this message, (raise an issue on GitHub) with attaching the log.txt file in the bioGUI folder, or /tmp/log_biogui.txt on Mac OS, as well as an screenshot of the attempt.
Use an Install Module¶
After installing a software, e.g. graphmap, you can reload the list of available templates by pressing the reload button.
Download the install module for graphmap as shown in the previous section. Next select the graphmap install module in the Install Templates template and fill out your Linux User Password/sudo Password. If you are on Windows, make sure that the Use WSL? checkbox is selected.
Enter the name of the template you would like to use in the input field within the Store Template group box (which you should have selected). In order for bioGUI to find a template it must reside in the template folder next to the bioGUI executable. Finally press Install Program and wait until the installation finishes. Besides the template being sent to bioGUI (in blue text), you should see the green message that your program has been installed correctly:
You can now Reload the templates again and will see a graphmap template on the left:
In this template you have to possibility to select the alignment mode (align or overlap/owler), specify the reference sequence, reads, gene annotation file (for splice-aware alignment) as well as the output file. To select files via a file dialog, click the corresponding button on the right. Using the Additional Options field, you can also enter command-line parameters directly. This may be necessary because the template is not complete, or new options have been added (or because you know shortcuts).
Exemplarily we filled our some parameters:
Clicking on Run Graphmap will now execute graphmap via bioGUI. In this case, the called command-line tool is graphmap -r <reference> -d <reads> -o <output>.
Upon completion, the bioGUI options button (lower left) will become enabled again, as well as the Run Graphmap button. If you need to cancel the current process, click the Cancel Run Graphmap button. You will see all the intermediate output from graphmap and have the option to save the command-line output using the Save log button. If you want to save the inputs you made, using the Save template button of the bioGUI options, you can save the inputs you made. Save the template in the template directory in the same folder as bioGUI to see the template.
Use an Install Module (video tutorial)¶
If you prefer to understand these steps as part of a video, please have a look attaching
Installing graphmap (from install module) and using it:
Using the circlator docker template:
Adding Own Templates¶
Part of bioGUI is a simple accessibility of templates for various programs. Therefore, application developers and sophisticated users can upload their templates to our website in order to make their template available to other users. The user has to submit his name, eMail address, a template name and the template itself. He can select whether he wants to be an anonymous user (user name is always hidden) and whether this is an installation script (which downloads and creates the ac{GUI} template specifically for this installed application) or a regular template. Additionally, categories for the template can be supplied, e.g. whether this is a template for a sequencing tool, or proteomics. A screenshot of the template submission is shown below.
Additionally the (bioGUI website) also contains a searchable list of already available templates. Available templates are only shown and can be downloaded via the bioGUI application.
Within bioGUI, clicking the Download Templates button, a new dialog window opens showing a list of available templates. Columns can be sorted by double clicking the header, and using the search only templates which contain the searched words are shown. Upon selecting one or multiple (keep ctrl-key down while clicking) rows and clicking the Download button, those templates are downloaded and available for the user. Since it is possible to copy or alter templates, bioGUI never overwrites existing templates, but will create a new copy.
How to setup WSL (Bash on Ubuntu)¶
Depending on your Windows version you need to activate Developer Mode first. How this is done is explained at the end of this page.
For all recent versions of Windows 10 you can start with step 1.
Warning
Some antivirus software (e.g. Kaspersky) disable internet access for unknown/new programs. Make sure bioGUI can access the internet!
Step 1: Activate WSL feature¶
First WSL has to be enabled from Windows features. Therefore, simply search for the Turn Windows features on or off option in the control panel.
Once found, look for the Windows Subsystem for Linux (Beta) row and make sure to check the corresponding box.
This will download and install the desired WSL feature. Finally apply the change and make sure to reboot your computer
Step 2: Install Linux¶
After having enabled the WSL feature, we can visit the Microsoft Windows Store to download Linux.
In order to do so, we open the Windows Store app, and search for Linux. We select the Run Linux on Windows menu entry.
There are many different flavors (comparable to strains in biology) of linux and some are already offered on the Windows store. Best compatibility for bioGUI has Ubuntu.
Important: You should consider using the latest Ubuntu version available. This is Ubuntu 18.04 at the time of writing. You specifically have to search for Ubuntu 18.04 in the store !
Now let the Windows store install your Linux app and once that is done, open your newly installed Linux:
The black screen will guide you through the install process. It will first unpack itself and then ask you to create a linux user account.
It is recommended to choose a username and password you can easily remember. Remembering the password is essential here, as it will be needed for any installation to be performed on WSL and by bioGUI.
Step 3: Prepare WSL¶
Before you can use bioGUI on WSL/Ubuntu please make sure to run the First time Ubuntu/WSL/apt-get Setup from bioGUI. For the sudo/user password please enter the password for your linux user account from the step above.
In case there are problems please contact the author of the software.
If you are running an old Windows 10 version, you first need to activate developer mode before you are able to enable the Windows Subsystem for Linux feature.
Step 0: Activate Developer Mode
Since WSL/Bash on Ubuntu on Windows is a developer feature, first the developer mode has to be actived. Therefore we go into the Settings app and select Update & Security.
We further navigate into the For developers tab on the left.
In the For developers options we switch from Windows Store apps to Developer mode.
How does bioGUI work?¶
bioGUI relies on the philosophy that the visual appearance as well as the assembly of the command line arguments can be represented as a network. Especially templates are seen as network, both in their visual description but most importantly also in the execution model.
Install modules¶
bioGUI install modules are designed to make the regular user’s life as easy as possible. Originally created for WSL, so pure Windows users can also easily install their needed software without the need to care about dependencies, the idea of the bioGUI repository evolved. Install modules are more than just templates, because they install the actual software onto the user’s system, while customizing the bioGUI template for this application. All install modules are regular shell scripts, that are called with fixed parameters.
In general, install modules can be divided into two parts:
- installing the software and its dependencies
- submitting the bioGUI template
For the first part, first the command line arguments are collected and saved. The order of the command line arguments is specified as
- installation directory (PROGDIR)
- sudo password (if not supplied, installing dependencies is allowed to fail)
- [0, 1] for adding software binary to $PATH.
- IP to send template to
- PORT to send template to
A typical template is then structured as follows:
#! Install hisat2-2.0.5
The text after the shebang is shown as title in the Install template Module.
if [ ! "$2" = "" ]; then
if [ "$(uname)" == "Darwin" ]; then
echo "Installing brew gcc"
brew install gcc
else
echo "No dependencies"
echo $2 | sudo -S apt-get update
echo $2 | sudo -S apt-get install build-essential
fi
else
echo "No sudo password, not installing dependencies"
fi
If a sudo password is supplied, dependencies are installed. This must be compatible with Ubuntu’s aptitude, as this is what WSL runs on. Using the uname switch, bioGUI also supports Mac OS and brew, for instance.
Since a lot of harm can be done using the super-user account, install modules are manually curated after submission.
## set all variables
PROG=hisat2-2.0.5
PROGDIR=$1
if [ -z "${PROGDIR}" ]; then
PROGDIR=~/bioGUI/progs/
fi
PROGDIRESC=$(echo $PROGDIR | sed 's/ /\\ /g')
## create progdir
mkdir -p "$PROGDIR"
Next some variables need to be set up. It showed of great benefit to create a $PROG variable containing the application and version. The $PROGDIR variable contains the installation path, which is also checked to exist. For several reasons it is also a good idea to have an escaped version of the install path by hand.
#download and unzip
if [ ! -f "$PROGDIR/$PROG.zip" ]; then
wget ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/downloads/hisat2-2.0.5-source.zip -O "$PROGDIR/$PROG.zip"
fi
if [ ! -d "$PROGDIR/$PROG" ]; then
cd "$PROGDIR"
unzip $PROG.zip -d "$PROGDIR/"
fi
Before actually installing the program, make sure to download and unzip/untar the application source code. For reasons of parsimony, this is only done when the expected file or folder does not exist.
#install prog
cd "$PROGDIR/$PROG"
make
if [ $# -gt 2 ]; then
if [ "$3" = "1" ]; then
if ! grep -q "$PROGDIRESC/$PROG" ~/.bashrc; then
echo "export PATH=\"$PROGDIRESC/$PROG:\$PATH\" " >> ~/.bashrc;
fi
fi
fi
After downloading and unzipping, the application can be built in the target directory. Finally, if wanted, the path to the application’s executable is added to the $PATH variable.
Certain programs may need some fixes to work properly on Mac OS, Linux or WSL. This is the place where such fixes could go.
Finally we can send the template to bioGUI, if an IP address and port have been specified:
if [ $# -eq 5 ]; then
IP=$4
PORT=$5
NCCMD=""
if [ "$(uname)" == "Darwin" ]; then
NCCMD="nc -c $IP $PORT"
else
NCCMD="nc -q 0 $IP $PORT"
fi
$NCCMD <<EOF
<template description="hisat2 2.0.5 aligner" title="hisat2 2.0.5">
...
<const id="bindir">${PROGDIR}/${PROG}/</const>
...
<execute program="hisat2" param="\${cl}" location="\${bindir}" exec="hisat2" wsl="WSLsel">
<output type="COUT" color="green" to="outputstream1" />
<output type="CERR" color="red" to="outputstream2" />
</execute>
</template>
EOF
fi
Make sure to use nc to send the content back to bioGUI.
Unfortunately the nc-programs differ on Mac OS and Ubuntu, hence the command must be altered according to the underlying OS.
In order to customize the template inbetween the EOF, bash variables to be replaced must be written as ${var-name}.
This conflicts with how bioGUI expects variables. Therefore, make sure to escape the backslaash where you want to access variables in the bioGUI template!
bioGUI Templates¶
bioGUI templates consist of two parts: the <window>-part which defines the visual appearance and the <execute>-part which defines how the command line arguments of an application are assembled from the graphical input elements.
Visual Model of Templates¶
Layouts¶
There exist three different layouts in bioGUI:
- horizontal
- vertical
- grid
Layouts may have either visual components as child, or further layouts. However a visual component may only have one layout child and this must be the first child.
For instance, the cols attribute for the grid layout tells how many columns are needed. If only one attribute is specified, the other attribute is calculated from the number of children and the given attribute.
Layout Components¶
| node name | allowed attributes |
| <GRID> | [cols, rows] |
| <HGROUP> | [] |
| <VGROUP> | [] |
Visual Elements¶
In contrast to layout components, visual elements are direct input elements.
Graphical Components¶
| node name | allowed attributes |
| <ACTION> | [program] |
| <CHECKBOX> | [selected, selectonwindows, value] |
| <COMBOBOX> | [selected] |
| <COMBOITEM> | [value] |
| <FILEDIALOG> | [filter, folder, location, multiples, multiples_delim, output] |
| <FILELIST> | [height, title, width] |
| <FILESELECTBOX> | [delim, filter, location] |
| <GROUP> | [height, title, width] |
| <GROUPBOX> | [multi] |
| <IMAGE> | [height, src, width] |
| <INPUT> | [multi, type {string, int, float, password}] |
| <LABEL> | [link] |
| <RADIOBUTTON> | [value] |
| <SLIDER> | [max, min, step] |
| <SLIDERITEM> | [display, value] |
| <STREAM> | [height, title, width] |
| <STREAMBOX> | |
| <WINDOW> | [height, title, width] |
Execution Model of Templates¶
Execution Network¶
Within a bioGUI template, the <execution>...</execution> part defines how the command line argument to be executed is assembled.
The idea is again based on a network of predefined nodes.
The nodes can either be visual components, accessed by their respective id, or Execution Nodes .
Upon starting an application with bioGUI, the execution network is responsible to construct the command line arguments with which the target application is called.
Therefore, all executable nodes in the <execution> part are searched and evaluated one after the other (if there exist several).
Since execution must be started via an action visual element, which can have a program attribute, this allows to specify which executable nodes are executed: if the program attribute is set, this must match with the program attribute of the executable node.
Finally an executable node is executed. Upon this the command line arguments are assembled. This is shown exemplarily in the below figure:
Illustration of an Execution Network for a simple example application.
The command line arguments for the executable sh are collected from the nodes with id s input and output.
While input refers to a visual component node, the output id refers to an if node, which collects data from another visual component node (3) or a node which constructs a netcat command, depending on whether the visual node with id os (2) equals TRUE or not.
List of available execution nodes:
Execution Nodes¶
| node name | allowed attributes |
| <add> | [ID, TYPE, sep] |
| <const> | [ID, TYPE] |
| <else> | [] |
| <env> | [GET, ID, TYPE] |
| <execute> | [EXEC, ID, PROGRAM, TYPE, location, param, program, wsl] |
| <update> | [deferred, target, attrib, value] |
| <messagebox> | [deferred] |
| <file> | [FROM, ID, SEP, TO, TYPE] |
| <httpexecute> | [CL_TO_POST, DELIM, ID, PORT, PROGRAM, TYPE] |
| <if> | [COMP, ID, SEP, TYPE, VALUE1, VALUE2] |
| <math> | [ID, OP, TYPE] |
| <orderedadd> | [FROM, ID, SELECTED, TYPE] |
| <output> | [COLOR, DEFERRED, FROM, HOST, ID, LOCATION, PORT, TO, TYPE, TYPE] |
| <relocate> | [FROM, ID, PREPEND, TO, TYPE, UNIX, WSL] |
| <replace> | [ID, REPLACE, REPLACE_WITH, TYPE] |
| <script> | [ARGV, ID, SCRIPT, TYPE] |
| <value> | [FOR, FROM, ID, TYPE] |
Developer Guide¶
It is highly recommend to read the mechanism section How does bioGUI work? first. For more information about visual/execution node behaviour, check section bioGUI Nodes Description.
Extending bioGUI¶
The creation of nodes for both the visual model as well as the execution model is organised by factories.
Window component factory¶
In order to add new visual components, one must register the constructor for a new visual elements in the WindowComponentFactory.
Each constructor for new components must extend the WindowWidgetNode class to return CreatedElement objects.
This class contains the retriever function for the created element (which fetches values from nodes in bioGUI) as well as a WidgetFunctionNode.
The WidgetFunctionNode contains a pointer to the widget, as well as attribute setters.
These attribute setters can update specific attributes/properties of the widget, for instance the image to be displayed (<UPDATE> node).
Execution node factory¶
The execution model has no special node factory, but the XMLParserExecution serves as such (this may change soon).
Here, nodes must be registered.
Execution nodes must extend the ExecutionNode class.
The most important function to implement is the std::string evaluate(...) function.
This function has three parameters, namely std::map< std::string, ExecutionNode*>* pID2Node, std::map<std::string, std::string>* pInputID2Value and std::map<std::string, WidgetFunctionNode*>* pInputID2FunctionWidget.
pID2Node is a map which contains a pointer to the ExecutionNode for a given id.
pInputID2Value is a map which maps any visual element (by id) to its value (determined by the retriever function).
Finally pInputID2FunctionWidget is a map from any visual element (by id) to its WidgetFunctionNode. This map is essential for updating visual elements (e.g. changing the image being displayed).
bioGUI Nodes Description¶
Visual Model Nodes¶
<GROUP> node¶
<group ordered="true" id="orderedgroup" title="Step options">
<grid rows="1" cols="2">
<group id="slidingwindow_opt" selected="false" title="Sliding Window" checkable="true">
<label>Size</label>
<input id="slidingwindow_size" type="int"/>
<label>Quality</label>
<input id="slidingwindow_quality" type="int"/>
</group>
<group id="leadingwindow_opt" selected="false" title="Leading Window" checkable="true">
<hgroup>
<label>Quality</label>
<input id="leadingwindow_quality" type="int"/>
</hgroup>
</group>
</grid>
</group>
<orderedadd id="steps" from="orderedgroup" selected="true">
<value from="slidingwindow" for="slidingwindow_opt"/>
<value from="leading" for="leadingwindow_opt"/>
</orderedadd>
Each group node can have its own layout, which must be the first and only child of a group node.
An ordered group node will give its children (visual model nodes) an order, so the user can select in which order something is taken.
For this to function, the values must be retrieved using the orderedadd node in the exeuction model.
The for attribute must be the id of an element within the ordered group. And the from attribute must be the attribute of an exeuction node which contains the value to be written at this position.
A group may also be checkable, which means that it has a checkbox. It will return “true” if checked, “false” otherwise.
Setting checked_value or unchecked_value, respectively, allows custom values.
Setting selected="true" will make it checked right from the beginning.
If exclusive="true" is set as attribute, only one child may be selected at a time.
<COMBOBOX> node¶
A combobox is checkable, which means that it has a checkbox. It will return “true” if checked, “false” otherwise.
Setting checked_value or unchecked_value, respectively, allows custom values.
Setting selected="true" will make it checked right from the beginning.
<STREAMBOX>/<STREAM> node¶
The STREAMBOX is the default output box, where standard out could be written to.
In order to function, a streambox must have at least one STREAM child with an ID.
This stream is then connected with one or multiple <EXECUTE>/<ACTION> node .
<streambox id="output1">
<stream id="outputstream1">std out</stream>
<stream id="outputstream2">err out</stream>
</streambox>
Layout Nodes¶
<HGROUP>/<VGROUP> node¶
<vgroup>
<label>First:</label>
<label>Second: under first</label>
</vgroup>
<GRID> node¶
The GRID node layouts its children visual model nodes in a grid. If only rows or columns are specified, the other value is calculated from the number of children.
<grid rows="2" cols="2">
<label>Top Left</label>
<label>Top Right</label>
<label>Bottom Left</label>
<label>Bottom Right</label>
</grid>
Execution Model Nodes¶
<RELOCATE> node¶
The relocate node probably is the most useful node of all, at least for templates aiming at Windows Subsystem for Linux/Bash on Ubuntu on Windows enabled templates.
If the relocate node is used as below, the windows_location is transformed from a Windows path, to a UNIX path if the value of the node with ID WSLsel is true.
For example, C:\files\sample.dat is transformed into /mnt/c/files/sample.dat.
<checkbox id="WSLsel" value="true" selectonwindows="true">run in WSL?</checkbox>
<relocate id="wsl_location" wsl="${WSLsel}" from="${windows_location}"/>
Apart from the WSL use-case, the reloacte node can also be used manually, e.g. to change pathes on a remote server.
<relocate from="" to=""/>
<IF>/<ELSE> node¶
Using if nodes, condition specific evaluation of nodes can be performed.
For instance, depending on the state of a checkbox, either one or the other file can be taken as input.
An if node accepts three comp*arison modes: ``is_set``, ``equals`` or ``EQUALS``.
The first mode evaluates true, if the node reference in attribute *value1 evaluates to any value which is not empty.
The other two modes compare the node referance output of value1 and value2 and evaluate the if part if value1 and value2 are equal (equals, case sensitive) or are non-case-sensitive equal (EQUALS).
If the comparison does not return, the else part
<if value1="id_elem1" comp="is_set">
<value from="inputfile_1"/>
<else>
<value from="inputfile_2"/>
</else>
</if>
<VALUE> node¶
The value node collects the value from the node with the id given in the from attribute. If no such node exists, the value is interpreted as text. However, the const node may be more suitable here.
<value from="inputfile_1"/>
<ORDEREDADD> node¶
See <GROUP> node .
<ENV> node¶
The env (environment) node returns several system properties, such as IP addresses, the current OS, etc. .
If asked for a specific OS, the node may return true or false.
The DATADIR returns the path to where applications are stored, such as applications installed via WSL.
<env id="envip" get="IP"/>
<env id="..." get="IP|IPv4|IPv6|LINUX|UNIX|MAC|WIN|DATADIR"/>
<SCRIPT> node¶
For highest flexibility, <script> nodes can refer to or contain LUA code. For instance
<const id="node1">some_file.tex</const>
<script argv="${node1},pdf">
<![CDATA[
function evaluate(arg1, arg2)
return(string.sub(arg1, 0, -3) .. arg2)
end
]]>
</script>
would first split all supplied arguments from the script argv attribute and resolve those, which refer to another node (indicated by ${nodeid}).
In this case, the node with id node1 is a constant value of somefile.tex. The second argument is also constant text (_pdf_).
Therefore the inline script would be called as evaluate(some_file.tex, pdf).
The return value is thus somefile.pdf.
<EXECUTE>/<ACTION> node¶
<image id="statimg" src="" width="100" height="100"/>
...
<action id="with_program" program="python-prog"/>
<action id="no_program"/>
</window>
<execution>
<execute program="python-prog" exec="python" param="some.py" wsl="${WSLsel}">
<output type="COUT" color="green" to="outputstream1"/>
<output type="CERR" color="red" to="outputstream1"/>
<update deferred="true" target="statimg" attrib="src" value="..."/>
<messagebox deferred="false">This is shown before program starts.</messagebox>
<messagebox deferred="true">This is shown when program ended.</messagebox>
</execute>
<execute exec="cowsay" param="hello" wsl="${WSLsel}">
<output type="COUT" color="green" to="outputstream1"/>
<output type="CERR" color="red" to="outputstream2"/>
</execute>
</execution>
Execution and action node form a unit: the action button uses the exeuction network to execute a program. For instance, the action node with id with_program has the program attribute set. Thus, only executable nodes with a program attribute set to this value will be executed. Here, only the python program will be executed.
In contrast, the action node with id no_program has no program attribute set. Therefore, all available executable nodes will be executed. Thus, both the python program and the cowsay program will be executed.
Executable nodes may have several children. In general, these children may have a deferred attribute which means that these nodes are either activated before (deferred="false") the executable is started, or after (deferred="true").
The WSL attribute signals bioGUI whether a program should be executed in WSL/Bash on Ubuntu on Windows, or not. If this is set to true, the application is executed in WSL on Windows.
<OUTPUT> node¶
Output nodes transfer information while a program is running.
If they are of type STD, they transfer both standard console output (COUT) as well as standard console error (CERR).
The output is transported to the specified stream (<STREAMBOX>/<STREAM> node) in the given color.
There also exist output nodes of type TCP. These must have host (from where is information received) and port attributes set.
Additionally nodes of type FILE directly save output to a file.
<UPDATE> node¶
Using update nodes, attributes of visual elements can be updated. This could, for instance, be the location of an image to be displayed (as in the example above).
<MESSAGEBOX> node¶
Using messagebox nodes, message boxes can be created. The text of a message box may also contain node ids (given in brackets ${id}).
bioGUI Install Modules Example¶
Example: hisat2¶
Dependency/Install Part¶
This is already covered in section Install modules.
Template Part¶
The template description and title is shown in the left, template selection window of bioGUI.
The title attribute of the window tag is shown as application window title.
<template description="hisat2 2.0.5 aligner" title="hisat2 2.0.5">
<window title="hisat2 2.0.5 aligner">
All following elements are placed in a vertical layout (therefore from top to bottom). The following group collects the hisat2 index as well as the output file via a file dialog window. Remember to specify whether a file to be selected is input our output, a directory or whether multiple files can be selected (and how they are delimited).
If you know your application can run in WSL/Bash on Ubuntu on Windows, include a checkbox with the selectonwindows="true" attribute.
<vgroup>
<group title="Alignment Information">
<checkbox id="WSLsel" value="true" selectonwindows="true">run in WSL?</checkbox>
<label>hisat2 Index</label> <filedialog id="hisat_index" output="false" folder="false">Select hisat2 index</filedialog>
<label>output file</label> <filedialog id="hisat_output" output="true" folder="false">Select output file</filedialog>
</group>
Further input is collected. Not here, that you can either activate paried end or single end read data. The exclusive="true" signals bioGUI to only allow one group child to be checked.
<group title="Input Data" exclusive="true">
<hgroup>
<group id="pairedend" selected="false" title="Paired End" checkable="true">
<filedialog id="hisat_paired_m1" location="1" multiple="true">Mate 1 files</filedialog>
<filedialog id="hisat_paired_m2" location="2" multiple="true">Mate 2 files</filedialog>
</group>
<group id="singleend" selected="true" title="Unpaired reads" checkable="true">
<filedialog id="hisat_unpaired_reads" location="">Input File 1</filedialog>
</group>
</hgroup>
</group>
The following group contains several input options where a checkbox is sufficient. For more program control the phred-/report-checkboxes could also be placed inside an exclusive group.
<group title="Input Options">
<checkbox id="hisat_input_f">Reads are FASTA files</checkbox>
<checkbox id="hisat_input_r">Reads are files with one input sequence per line</checkbox>
<checkbox id="hisat_input_trim5">Trim bases from 5p</checkbox><input id="hisat_input_trim5_bases" type="int"></input>
<checkbox id="hisat_input_trim3">Trim bases from 3p</checkbox><input id="hisat_input_trim3_bases" type="int"></input>
<checkbox id="hisat_input_phred33">Qualities are phred+33</checkbox>
<checkbox id="hisat_input_phred64">Qualities are phred+64</checkbox>
<checkbox id="hisat_input_max_reports">Search at most x distinct, primary alignments for each read</checkbox><input id="hisat_input_max_reports_num" type="int"></input>
</group>
<group title="Alignment Options">
<checkbox id="hisat_align_nofw">Do not attempt to align unpaired reads to the forward reference strand</checkbox>
<checkbox id="hisat_align_norc">Do not attempt to align unpaired reads to the reverse reference strand</checkbox>
<checkbox id="hisat_align_no-softclip">Disable soft-clipping</checkbox>
<checkbox id="hisat_align_no-spliced">Disable spliced alignment</checkbox>
<checkbox id="hisat_align_no-mixed">Disable mixed alignments (if no conc/disc)</checkbox>
<checkbox id="hisat_align_no-discordant">Do not look for discordant alignments if no concordant are available</checkbox>
<combobox id="hisat_align_mate_orientations">
<comboitem value="--fr">forward/reverse</comboitem>
<comboitem value="--rf">reverse/forward</comboitem>
<comboitem value="--ff">forward/forward</comboitem>
</combobox>
</group>
<group title="Output Options">
<checkbox id="hisat_align_no-unaligned">Disable output of unaligned reads</checkbox>
<checkbox id="hisat_align_reorder">Guarantees output to be in order of input</checkbox>
<checkbox id="hisat_transcriptome_assembly_stringtie">Report alignments tailored for transcript assemblers including StringTie</checkbox>
<checkbox id="hisat_transcriptome_assembly_cufflinks">Report alignments tailored specifically for Cufflinks</checkbox>
</group>
<group title="Performance Options">
<label>Number of threads</label><input id="hisat_perf_threads" type="int">1</input>
<checkbox id="hisat_perf_reorder">Maintain order of reads</checkbox>
</group>
HISAT allows many option. Sometimes not all are documented or some are used so seldom, that it is not worth to include them as visual checkboxes.
A simple input element can serve as container for user-defined command line arguments.
Note that this action button has the program attribute set!
<group title="Advanced">
<label>Additional command-line flags</label><input id="hisat_adv_specific_options"></input>
</group>
<action program="hisat2">Align!</action>
A very important preprocessing step for HISAT is to build the index. Here (the minimal) needed input for building the index is collected.
Also the action button will only launch the program to build an index.
<group title="build index">
<label>Input Reference</label> <filedialog id="hisat_build_inref" output="false" folder="false">Select hisat2 index</filedialog>
<label>hisat2 Index</label> <filedialog id="hisat_build_idx_out" output="true" folder="false">Select hisat2 index</filedialog>
<action program="hisat2index">Build Index</action>
</group>
Finally we need a streambox to collect any (command line) output.
<streambox id="output1">
<stream id="outputstream1">std out</stream>
<stream id="outputstream2">err out</stream>
</streambox>
</vgroup>
</window>
As the visual part has been closed, we need to start the execution part.
First a const-node containing the location of the binary is created. This is filled from the install template (note the unescaped $).
Then nodes needed for launching the hisat2index program are defined.
Since this program is WSL-enabled, any folder/file must be relocated from the windows path to the WSL path.
This is done using relocate nodes.
Then the command line arguments are assembled using the add node. With the sep attribute, the delimiter can be set.
Finally the program is executed and output is redirected to the outputstream nodes.
<execution>
<const id="bindir">${PROGDIR}/${PROG}/</const>
<relocate id="hisat_build_inref_rel" from="\${hisat_build_inref}" wsl="\${WSLsel}"/>
<relocate id="hisat_build_idx_out_rel" from="\${hisat_build_idx_out}" wsl="\${WSLsel}"/>
<add id="cl_idx" sep=" ">
<value from="hisat_build_inref_rel"/>
<value from="hisat_build_idx_out_rel"/>
</add>
<execute program="hisat2index" param="\${cl_idx}" location="\${bindir}" exec="hisat2-build" wsl="WSLsel">
<output type="COUT" color="green" to="outputstream1" />
<output type="CERR" color="red" to="outputstream2" />
</execute>
The actual HISAT exeuction more input files are needed, thus more relocations are needed. Note that we also use a LUA script here to crop the file extensions from the HISAT index. For a detailled description of the script node, see <SCRIPT> node.
<relocate id="hisat_paired_m1_rel" wsl="\${WSLsel}" from="\${hisat_paired_m1}"/>
<relocate id="hisat_paired_m2_rel" wsl="\${WSLsel}" from="\${hisat_paired_m2}"/>
<relocate id="hisat_unpaired_reads_rel" wsl="\${WSLsel}" from="\${hisat_unpaired_reads}"/>
<relocate id="hisat_output_rel" wsl="\${WSLsel}" from="\${hisat_output}"/>
<relocate id="hisat_index_rel_raw" from="\${hisat_index}" wsl="\${WSLsel}"/>
<script id="hisat_index_rel" argv="\${hisat_index_rel_raw}">
<![CDATA[
function evaluate(arg1)
if (string.match(arg1, ".%d.ht2$")) then
return(string.sub(arg1, 0, arg1:find(".%d.ht2$")-1))
end
return(arg1)
end
]]>
</script>
Depending on whether pairedend or singleend data is being used, the input file arguments are assembled:
<if id="input_files" sep=" " comp="EQUALS" value1="pairedend" value2="true">
<const>-1</const>
<value from="hisat_paired_m1_rel"/>
<const>-2</const>
<value from="hisat_paired_m2_rel"/>
<else>
<const>-U</const>
<value from="hisat_unpaired_reads_rel"/>
</else>
</if>
Then all command line arguments are combined in the cl add node.
Here checkboxes are masked using if nodes. However, setting the attribute unchecked_value="" in the checkbox would have the same effect.
Finally the execute node with the program attribute for HISAT is placed.
It is important to remember that only when the action button is pressed, this node is activated.
Only then the cl node is evaluated and all the referenced input nodes are collected and evaluated!
<add id="cl" sep=" ">
<value from="hisat_adv_specific_options"/>
<const>-x</const>
<value from="hisat_index_rel"/>
<value from="input_files"/>
<const>-S</const>
<value from="hisat_output_rel"/>
<if comp="IS_SET" value1="hisat_input_f" >-f</if>
<if comp="IS_SET" value1="hisat_input_r" >-r</if>
<if comp="IS_SET" value1="hisat_input_trim5" ><value from="hisat_input_trim5_bases"/></if>
<if comp="IS_SET" value1="hisat_input_trim3" ><value from="hisat_input_trim3_bases"/></if>
<if comp="IS_SET" value1="hisat_input_phred33" >--phred33</if>
<if comp="IS_SET" value1="hisat_input_phred64" >--phred64</if>
<if comp="IS_SET" value1="hisat_align_nofw" >--nofw</if>
<if comp="IS_SET" value1="hisat_align_norc" >--norc</if>
<if comp="IS_SET" value1="hisat_transcriptome_assembly_stringtie">--downstream-transcriptome-assembly</if>
<if comp="IS_SET" value1="hisat_transcriptome_assembly_cufflinks" >--dta-cufflinks</if>
<if comp="IS_SET" value1="hisat_input_max_reports" ><value from="hisat_input_max_reports_num"/></if>
<if comp="IS_SET" value1="hisat_align_no-softclip" >--no-softclip</if>
<if comp="IS_SET" value1="hisat_align_no-spliced" >--no-spliced</if>
<if comp="IS_SET" value1="hisat_align_no-mixed" >--no-mixed</if>
<if comp="IS_SET" value1="hisat_align_no-discordant" >--no-discordant</if>
<value from="hisat_align_mate_orientations"/>
</add>
<execute program="hisat2" param="\${cl}" location="\${bindir}" exec="hisat2" wsl="WSLsel">
<output type="COUT" color="green" to="outputstream1" />
<output type="CERR" color="red" to="outputstream2" />
</execute>
</execution>
</template>
Example: Trimmomatic¶
Dependency/Install Part¶
For the install module, we start with the shebang which gives the module its name:
#! Install Trimmomatic 0.36
The text after the shebang is shown as title in the Install Trimmomatic 0.36. For the install part we remember that this is essentially a bash script. Thus any bash commands will work here.
We first have to ensure that all dependencies are installed. Trimmomatic has only java as dependency. We can install java (openJDK) on Ubuntu and in WSL, however, will ask the user to install JAVA on Mac OS:
if [ ! "$2" = "" ]; then
if [ "$(uname)" == "Darwin" ]; then
echo "PLEASE INSTALL JAVA PRIOR USING TRIMMOMATIC!"
else
echo "Installing dependencies: openjdk 9"
echo $2 | sudo -S apt-get update
echo $2 | sudo -S apt-get -y install openjdk-9-jre
fi
else
echo "No sudo password, not installing dependencies"
fi
Following the dependencies we should set multiple variables. It has shown useful to have the program name in a variable (once for processing, and once for displaying to the user):
## set all variables
PROG=trimmomatic_0_36
PROGNICE=Trimmomatic-0.36
Apart from the program name we also fetch the install dir as the first parameter given to the install module:
PROGDIR=$1
if [ -z "${PROGDIR}" ]; then
PROGDIR=~/bioGUI/progs/
fi
PROGDIRESC=$(echo $PROGDIR | sed 's/ /\\ /g')
APPBINARYDIR=${PROGDIRESC}/${PROG}/
If the PROGDIR (install dir) has not been given (is empty), we set it to a default value. We create an escaped version of the install dir (PROGDIRESC) and save the program directory where we expect the program to reside (APPBINARYDIR). In the following we create the progam’s install directory, download the application and move everything into place:
## create progdir
mkdir -p "$PROGDIR"
#download and unzip
echo "Downloading Trimmomatic"
wget http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/$PROGNICE.zip -O "$PROGDIR/$PROG.zip"
unzip -o "$PROGDIR/$PROG.zip" -d "$PROGDIR/$PROG"
mv "$PROGDIR/$PROG/"*/* "$PROGDIR/$PROG"
The user can select to add the program to the system’s PATH variable. If this should be done, the third parameter supplied to the install module is a 1. We add the escaped path to the PATH variable:
if [ $# -gt 2 ]; then
if [ "$3" = "1" ]; then
if ! grep -q "$PROGDIR/$PROG" ~/.bashrc; then
echo "export PATH=\"$PROGDIRESC/$PROG:\$PATH\" " >> ~/.bashrc;
fi
fi
fi
We are almost done. We now want to verify whether the installation has been successful. We determine this by checking whether the install directory is not empty and whether the executable is available at the thought place. If this is not the case we return the content of all affected paths for better debugging possibilities. Additionally we give the user an ERROR message with possible actions.
APPBINARYESC="${PROGDIRESC}/${PROG}/"
APPBINARY="${PROGDIRESC}/${PROG}/trimmomatic-0.36.jar"
if [ -z "$(ls -A ${APPBINARYESC})" ] || [ ! -f ${APPBINARY} ]; then
(>&2 echo ${APPBINARYESC})
(>&2 ls ${APPBINARYESC})
(>&2 echo " \n \n \n")
(>&2 echo ${PROGDIRESC})
(>&2 ls ${PROGDIRESC})
(>&2 echo " \n \n \n")
(>&2 echo ${APPBINARY})
(>&2 ls ${APPBINARY})
(>&2 echo " \n \n \n")
(>&2 echo "ERROR: The application directory is empty after installation.")
(>&2 echo "ERROR: If you experience problems please re-install the software and create an issue on https://github.com/mjoppich/bioGUI.")
(>&2 echo "ERROR: For creating the issue, please upload the log.txt file of your installation attempt.")
(>&2 echo " \n \n \n")
else
echo "${PROG} has been installed into ${APPBINARYESC}"
echo "Binary location ${APPBINARY}"
fi
Now we need to transfer the template to bioGUI. This is done via a TCP connection (because std-out and std-err are already used by the install module). The user’s IP address is given as fourth parameter to the install module, the corresponding port as the fifth parameter. Unfortunately netcat behaves differently on virtually every operating system, we must call netcat differently on Mac OS and Ubuntu, to ensure that the connection is closed upon sending the EOF.
IP=$4
PORT=$5
NCCMD=""
if [ "$(uname)" == "Darwin" ]; then
NCCMD="nc -c $IP $PORT"
else
NCCMD="nc -q 0 $IP $PORT"
fi
Finally the template is sent via netcat and the bash EOF feature:
$NCCMD <<EOF
<template ...>
...
</template>
EOF
The following section explains the template
Template Part¶
The template description and title is shown in the left, template selection window of bioGUI.
The title attribute of the window tag is shown as application window title.
We must remember that this template is sent via netcat and the EOF feature of bash. Thus any bash variable (indicated by a leading dollar sign) are replaced. If we need a bioGUI variable in the template (e.g. in the execution network), the dollar sign must be escaped!
<template description="Trimming short RNA-Seq Reads" title="$PROGNICE">
<window title="$PROGNICE">
All following elements are placed in a vertical layout (therefore from top to bottom). The following group collects the input files. If the user selected single-end mode, only one input and output file is needed. For paired-end sequencing data, 2 input files and 4 output files are needed.
If your application should be run in WSL/Bash on Ubuntu on Windows, include a checkbox with the selectonwindows="true" attribute.
The exclusive="true" signals bioGUI to only allow one group child to be checked.
<checkbox id="WSLsel" value="true" selectonwindows="true">Run in WSL?</checkbox>
<group title="Method" exclusive="true">
<hgroup>
<group id="pairedend" selected="false" title="Paired End" checkable="true">
<filedialog id="paired_if1" location="1">Input File 1</filedialog>
<filedialog id="paired_if2" location="2">Input File 2</filedialog>
<group title="Options">
<checkbox>Validate Pairs</checkbox>
</group>
<filedialog id="paired_of1p" location="" output="true">Output 1P</filedialog>
<filedialog id="paired_of1u" location="" output="true">Output 1U</filedialog>
<filedialog id="paired_of2p" location="" output="true">Output 2P</filedialog>
<filedialog id="paired_of2u" location="" output="true">Output 2U</filedialog>
</group>
<group id="singleend" selected="true" title="Single End" checkable="true">
<filedialog id="single_if1" location="">Input File 1</filedialog>
<filedialog id="single_of1" location="" output="true">Output</filedialog>
</group>
</hgroup>
</group>
Further options are now collected. Trimmomatic is a special case, because the order of the parameters can alter the result. We thus need an ordered group (ordered=true). The order can then later, in the execution network, be retrieved. For a better visual appearance, elements are arranged in a 3x3 grid.
<group ordered="true" id="orderedgroup" title="Step options">
<grid rows="3" cols="3">
<group id="adapters_sel" title="Adapters" checkable="true">
<filelist id="illuminaclip_auto_file" allowempty="true" path="${APPBINARYDIR}/adapters/" ext="*.fa"/>
<filedialog id="illuminaclip_man_file" location="">Adapter Sequence</filedialog>
<label>Seed Mismatches</label>
<input type="int" id="illuminaclip_seed">2</input>
<label>Palindrome Clip Threshold</label>
<input type="int" id="illuminaclip_palin">30</input>
<label>Simple Clip Threshold</label>
<input type="int" id="illuminaclip_simple">10</input>
</group>
<group id="slidingwindow_opt" selected="false" title="Sliding Window" checkable="true">
<label>Size</label>
<input id="slidingwindow_size" type="int"/>
<label>Quality</label>
<input id="slidingwindow_quality" type="int"/>
</group>
<group id="leadingwindow_opt" selected="false" title="Leading Window" checkable="true">
<hgroup>
<label>Quality</label>
<input id="leadingwindow_quality" type="int"/>
</hgroup>
</group>
<group id="trailingwindow_opt" selected="false" title="Trailing Window" checkable="true">
<hgroup>
<label>Quality</label>
<input id="trailingwindow_quality" type="int"/>
</hgroup>
</group>
<group id="crop_opt" selected="false" title="Crop" checkable="true">
<hgroup>
<label>Length</label>
<input id="crop_length" type="int"/>
</hgroup>
</group>
<group id="headcrop_opt" selected="false" title="Headcrop" checkable="true">
<hgroup>
<label>Length</label>
<input id="headcrop_length" type="int"/>
</hgroup>
</group>
<group id="minlen_opt" selected="false" title="Min Len" checkable="true">
<hgroup>
<label>Length</label>
<input id="minlen_length" type="int"/>
</hgroup>
</group>
<group title="PHRED base">
<combobox id="phred" selected="phred64">
<comboitem>phred33</comboitem>
<comboitem>phred64</comboitem>
</combobox>
</group>
</grid>
</group>
<group title="Options">
<checkbox>Quiet Mode</checkbox>
</group>
<group title="System Settings">
<label title="example 2">Threads</label>
<input id="threads_opt" hint="Amount of Threads">2</input>
</group>
The remaining part of the GUI template are output options. The streambox captures stdout and stderr output from the launched processes and shows this to the user. The action element is a button which starts the execution of the execution network (or a specific program if specified).
<streambox id="output1">
<stream id="outputstream1">OS1</stream>
<stream id="outputstream2">OS2</stream>
</streambox>
<action id="runprog" hint="click here to run program">run program</action>
</window>
We have now finished the visual part (closed window element) and need to start the execution part. This part Unfortunately is relatively bulky, because of the many input/output files.
<execution>
<if id="illuminaclip_file_tmp" value1="illuminaclip_auto_file" comp="is_set">
<value from="illuminaclip_man_file"/>
<else>
<value from="illuminaclip_man_file"/>
</else>
</if>
<if id="illuminaclip_file" comp="EQUALS" value1="WSLsel" value2="true">
<relocate from="\${illuminaclip_file_tmp}" wsl="true"/>
<else>
<value from="illuminaclip_file_tmp"/>
</else>
</if>
<relocate id="paired_if1_rel" from="\${paired_if1}" sep=" " wsl="\${WSLsel}"/>
<relocate id="paired_if2_rel" from="\${paired_if2}" sep=" " wsl="\${WSLsel}"/>
<relocate id="paired_of1p_rel" from="\${paired_of1p}" sep=" " wsl="\${WSLsel}"/>
<relocate id="paired_of1u_rel" from="\${paired_of1u}" sep=" " wsl="\${WSLsel}"/>
<relocate id="paired_of2p_rel" from="\${paired_of2p}" sep=" " wsl="\${WSLsel}"/>
<relocate id="paired_of2u_rel" from="\${paired_of2u}" sep=" " wsl="\${WSLsel}"/>
<relocate id="single_if1_rel" from="\${single_if1}" sep=" " wsl="\${WSLsel}"/>
<relocate id="single_of1_rel" from="\${single_of1}" sep=" " wsl="\${WSLsel}"/>
The relocate nodes are only used within WSL, when the Windows file path must be translated into the Unix one. For all other Operating Systems the input path is maintained and no changes are made.
<add sep=":" id="illuminaclip">
<const>ILLUMINACLIP</const>
<value from="illuminaclip_file"/>
<value from="illuminaclip_seed"/>
<value from="illuminaclip_palin"/>
<value from="illuminaclip_simple"/>
</add>
<add sep=":" id="slidingwindow">
<const>SLIDINGWINDOW</const>
<value from="slidingwindow_size"/>
<value from="slidingwindow_quality"/>
</add>
<add sep=":" id="leading">
<const>LEADING</const>
<value from="leadingwindow_quality"/>
</add>
<add sep=":" id="trailing">
<const>TRAILING</const>
<value from="trailingwindow_quality"/>
</add>
<add sep=":" id="crop">
<const>CROP</const>
<value from="crop_length"/>
</add>
<add sep=":" id="headcrop">
<const>HEADCROP</const>
<value from="headcrop_length"/>
</add>
<add sep=":" id="minlen">
<const>MINLEN</const>
<value from="minlen_length"/>
</add>
Using the above add-nodes all options are assembled. For each possible option, one add-node fetches the user supplied parameters.
Using the orderedadd-node we can assemble these parameters in the order specified by the User in the GUI. Using the selected attribute, only selected options are added together. Note that the for-attribute in the value nodes is the ID within the ordered group of the GUI template.
<orderedadd id="steps" from="orderedgroup" selected="true">
<value from="illuminaclip" for="adapters_sel"/>
<value from="slidingwindow" for="slidingwindow_opt"/>
<value from="leading" for="leadingwindow_opt"/>
<value from="trailing" for="trailingwindow_opt"/>
<value from="crop" for="crop_opt"/>
<value from="headcrop" for="headcrop_opt"/>
<value from="minlen" for="minlen_opt"/>
</orderedadd>
Finally the input files are added together, as well as the remaining general settings.
<add sep=" " id="files_pe">
<const>PE</const>
<value from="paired_if1_rel"/>
<value from="paired_if2_rel"/>
<value from="paired_of1p_rel"/>
<value from="paired_of1u_rel"/>
<value from="paired_of2p_rel"/>
<value from="paired_of2u_rel"/>
</add>
<add sep=" " id="files_se">
<const>SE</const>
<value from="single_if1_rel"/>
<value from="single_of1_rel"/>
</add>
<if id="files" value1="pairedend" comp="EQUALS" value2="true">
<value from="files_pe"/>
<else>
<value from="files_se"/>
</else>
</if>
<if id="threads" value1="threads_opt" comp="is_set">
<value from="threads_opt"/>
<else>
<const>1</const>
</else>
</if>
The remaining work to be done is to assemble all input arguments: files, settings and the steps to be executed. This outcome can be accessed via the add node with id cl.
<add sep=" " id="cl">
<value from="files"/>
<add sep="">
<const>-threads </const>
<value from="threads"/>
</add>
<add sep="">
<const>-</const>
<value from="phred"/>
</add>
<value from="steps"/>
</add>
Finally the execute node defines what program is executed. The location contains the path to the exec-utable, to which the param-eters are passed, which are here referenced from the node with id cl. The output nodes within the execute environment define where the STDOUT and STDERR output from the process should be displayed (which is the outputstream1/2 here, as defined in the GUI template). Developers can also add deferred nodes here, which are executed as soon as the program has terminated. This might be useful to move files, open/show files, etc.
<const id="bindir">${PROGDIR}/${PROG}/</const>
<execute location="" exec="java" param="-jar "\${bindir}/trimmomatic-0.36.jar" \${cl}" wsl="WSLsel">
<output type="COUT" color="green" to="outputstream1" />
<output type="CERR" color="red" to="outputstream2" />
</execute>
</execution>
</template>
Licences¶
bioGUI & Qt¶
bioGUI is licenced under GPL v3 (also due to its Qt dependancy). Thus for bioGUI and Qt the following GNU General Public License version 3 is relevant.
GNU GENERAL PUBLIC LICENSE
Version 3, 29 June 2007
Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
Everyone is permitted to copy and distribute verbatim copies
of this license document, but changing it is not allowed.
Preamble
The GNU General Public License is a free, copyleft license for
software and other kinds of works.
The licenses for most software and other practical works are designed
to take away your freedom to share and change the works. By contrast,
the GNU General Public License is intended to guarantee your freedom to
share and change all versions of a program--to make sure it remains free
software for all its users. We, the Free Software Foundation, use the
GNU General Public License for most of our software; it applies also to
any other work released this way by its authors. You can apply it to
your programs, too.
When we speak of free software, we are referring to freedom, not
price. Our General Public Licenses are designed to make sure that you
have the freedom to distribute copies of free software (and charge for
them if you wish), that you receive source code or can get it if you
want it, that you can change the software or use pieces of it in new
free programs, and that you know you can do these things.
To protect your rights, we need to prevent others from denying you
these rights or asking you to surrender the rights. Therefore, you have
certain responsibilities if you distribute copies of the software, or if
you modify it: responsibilities to respect the freedom of others.
For example, if you distribute copies of such a program, whether
gratis or for a fee, you must pass on to the recipients the same
freedoms that you received. You must make sure that they, too, receive
or can get the source code. And you must show them these terms so they
know their rights.
Developers that use the GNU GPL protect your rights with two steps:
(1) assert copyright on the software, and (2) offer you this License
giving you legal permission to copy, distribute and/or modify it.
For the developers' and authors' protection, the GPL clearly explains
that there is no warranty for this free software. For both users' and
authors' sake, the GPL requires that modified versions be marked as
changed, so that their problems will not be attributed erroneously to
authors of previous versions.
Some devices are designed to deny users access to install or run
modified versions of the software inside them, although the manufacturer
can do so. This is fundamentally incompatible with the aim of
protecting users' freedom to change the software. The systematic
pattern of such abuse occurs in the area of products for individuals to
use, which is precisely where it is most unacceptable. Therefore, we
have designed this version of the GPL to prohibit the practice for those
products. If such problems arise substantially in other domains, we
stand ready to extend this provision to those domains in future versions
of the GPL, as needed to protect the freedom of users.
Finally, every program is threatened constantly by software patents.
States should not allow patents to restrict development and use of
software on general-purpose computers, but in those that do, we wish to
avoid the special danger that patents applied to a free program could
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patents cannot be used to render the program non-free.
The precise terms and conditions for copying, distribution and
modification follow.
TERMS AND CONDITIONS
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public, and in some countries other activities as well.
To "convey" a work means any kind of propagation that enables other
parties to make or receive copies. Mere interaction with a user through
a computer network, with no transfer of a copy, is not conveying.
An interactive user interface displays "Appropriate Legal Notices"
to the extent that it includes a convenient and prominently visible
feature that (1) displays an appropriate copyright notice, and (2)
tells the user that there is no warranty for the work (except to the
extent that warranties are provided), that licensees may convey the
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1. Source Code.
The "source code" for a work means the preferred form of the work
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The Corresponding Source need not include anything that users
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The Corresponding Source for a work in source code form is that
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All rights granted under this License are granted for the term of
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or that patent license was granted, prior to 28 March 2007.
Nothing in this License shall be construed as excluding or limiting
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If conditions are imposed on you (whether by court order, agreement or
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the Program, the only way you could satisfy both those terms and this
License would be to refrain entirely from conveying the Program.
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Notwithstanding any other provision of this License, you have
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under version 3 of the GNU Affero General Public License into a single
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the GNU General Public License from time to time. Such new versions will
be similar in spirit to the present version, but may differ in detail to
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15. Disclaimer of Warranty.
THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
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PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
SUCH DAMAGES.
17. Interpretation of Sections 15 and 16.
If the disclaimer of warranty and limitation of liability provided
above cannot be given local legal effect according to their terms,
reviewing courts shall apply local law that most closely approximates
an absolute waiver of all civil liability in connection with the
Program, unless a warranty or assumption of liability accompanies a
copy of the Program in return for a fee.
END OF TERMS AND CONDITIONS
LUA¶
This project requires a static LUA library to build. For the release of this software, LuaBinaries static liblua53.a was used and requires the following copyright notice to be included:
Copyright © 2005-2016 Tecgraf/PUC-Rio and the Kepler Project.
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
OpenSSL¶
This project also requires a static OpenSSL library to build. For the release of this software, OpenSSL static libraries were used and require the following copyright notice to be included:
This product includes software developed by the OpenSSL Project for use in the OpenSSL Toolkit (http://www.openssl.org/) This product includes cryptographic software written by Eric Young (eay@cryptsoft.com). This product includes software written by Tim Hudson (tjh@cryptsoft.com).
LICENSE ISSUES
==============
The OpenSSL toolkit stays under a dual license, i.e. both the conditions of
the OpenSSL License and the original SSLeay license apply to the toolkit.
See below for the actual license texts.
OpenSSL License
---------------
====================================================================
Copyright (c) 1998-2016 The OpenSSL Project. All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions
are met:
1. Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
2. Redistributions in binary form must reproduce the above copyright
notice, this list of conditions and the following disclaimer in
the documentation and/or other materials provided with the
distribution.
3. All advertising materials mentioning features or use of this
software must display the following acknowledgment:
"This product includes software developed by the OpenSSL Project
for use in the OpenSSL Toolkit. (http://www.openssl.org/)"
4. The names "OpenSSL Toolkit" and "OpenSSL Project" must not be used to
endorse or promote products derived from this software without
prior written permission. For written permission, please contact
openssl-core@openssl.org.
5. Products derived from this software may not be called "OpenSSL"
nor may "OpenSSL" appear in their names without prior written
permission of the OpenSSL Project.
6. Redistributions of any form whatsoever must retain the following
acknowledgment:
"This product includes software developed by the OpenSSL Project
for use in the OpenSSL Toolkit (http://www.openssl.org/)"
THIS SOFTWARE IS PROVIDED BY THE OpenSSL PROJECT ``AS IS'' AND ANY
EXPRESSED OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE OpenSSL PROJECT OR
ITS CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED
OF THE POSSIBILITY OF SUCH DAMAGE.
====================================================================
This product includes cryptographic software written by Eric Young
(eay@cryptsoft.com). This product includes software written by Tim
Hudson (tjh@cryptsoft.com).
Original SSLeay License
-----------------------
Copyright (C) 1995-1998 Eric Young (eay@cryptsoft.com)
All rights reserved.
This package is an SSL implementation written
by Eric Young (eay@cryptsoft.com).
The implementation was written so as to conform with Netscapes SSL.
This library is free for commercial and non-commercial use as long as
the following conditions are aheared to. The following conditions
apply to all code found in this distribution, be it the RC4, RSA,
lhash, DES, etc., code; not just the SSL code. The SSL documentation
included with this distribution is covered by the same copyright terms
except that the holder is Tim Hudson (tjh@cryptsoft.com).
Copyright remains Eric Young's, and as such any Copyright notices in
the code are not to be removed.
If this package is used in a product, Eric Young should be given attribution
as the author of the parts of the library used.
This can be in the form of a textual message at program startup or
in documentation (online or textual) provided with the package.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions
are met:
1. Redistributions of source code must retain the copyright
notice, this list of conditions and the following disclaimer.
2. Redistributions in binary form must reproduce the above copyright
notice, this list of conditions and the following disclaimer in the
documentation and/or other materials provided with the distribution.
3. All advertising materials mentioning features or use of this software
must display the following acknowledgement:
"This product includes cryptographic software written by
Eric Young (eay@cryptsoft.com)"
The word 'cryptographic' can be left out if the rouines from the library
being used are not cryptographic related :-).
4. If you include any Windows specific code (or a derivative thereof) from
the apps directory (application code) you must include an acknowledgement:
"This product includes software written by Tim Hudson (tjh@cryptsoft.com)"
THIS SOFTWARE IS PROVIDED BY ERIC YOUNG ``AS IS'' AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHOR OR CONTRIBUTORS BE LIABLE
FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
SUCH DAMAGE.
The licence and distribution terms for any publically available version or
derivative of this code cannot be changed. i.e. this code cannot simply be
copied and put under another distribution licence
[including the GNU Public Licence.]