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Install code

You can install MDI tool suites, including svx-mdi-tools, in one of two ways:

  • as a multi-suite installation that carries one or more distinct tool suites (recommended),
  • as a dedicated single-suite installation.

Choose one of the methods to install the code, then continue on to build your runtime environments and obtain your required genome(s).

In the recommended multi-suite mode, you will:

  • clone and install the MDI framework
  • add svx-mdi-tools (and potentially other suites) to your MDI installation
  • call the mdi utility to use tools from any installed suite

Install the MDI framework

Please read the install.sh menu options and the MDI utility instructions to decide which installation option is best for you. Choose option 1 if you will only run Stage 1 HPC pipelines from your installation.

git clone https://github.com/MiDataInt/mdi.git
cd mdi
./install.sh

OPTIONAL: Add an mdi alias to .bashrc

These commands will create a permanent named alias to the mdi target script in your new installation.

./mdi alias --help
./mdi alias --alias mdi # change the alias name if you'd like 
`./mdi alias --alias mdi --get` # activate the alias in the current shell (or log out and back in)

Alternatively, you can add the MDI installation directory to your PATH variable, or change into the directory prior to calling ./mdi.

Add the svx-mdi-tools suite to your MDI installation 

./mdi add --help
./mdi add -s wilsontelab/svx-mdi-tools

Alternatively, you can perform the required suite addition steps one at a time:

nano config/suites.yml # or use any other text editor to edit suites.yml

# mdi/config/suites.yml
suites:
    - wilsontelab/svx-mdi-tools # add this tools suite to the config file

./install.sh # re-install to add the new tool suite

Execute a Stage 1 pipeline from the command line

For help, call the mdi utility with no arguments, which describes the format for pipeline calls.

./mdi  # call the mdi utility directly without an alias, OR
mdi    # if you created an alias as described above
mdi svCapture # or change to one of the other pipelines...
# etc.

Launch the Stage 2 web apps server

To launch the MDI web server, we recommend using the MDI Desktop app, which allows you to control both local and remote MDI web servers.

Installation Method 2: single-suite installation

In the alternative single-suite mode, you will install just the svx-mdi-tools suite by:

  • cloning this tool suite repository
  • running install.sh to create a suite-specific MDI installation
  • OPTIONAL: calling alias.pl to create an alias to the suite’s run utility
  • calling the run utility to use a tool from the suite

Install this tool suite 

git clone https://github.com/wilsontelab/svx-mdi-tools.git
cd svx-mdi-tools
./install.sh

OPTIONAL: Create an alias to the suite’s run utility 

perl alias.pl svx # you can use a different alias name if you'd like

Alternatively, you can add the installation directory to your PATH variable, or change into the directory prior to calling ./run.

Execute a Stage 1 pipeline from the command line

For help, call the run utility with no arguments, which describes the format for pipeline calls.

./run  # call the run utility directly without an alias, OR
svx    # use the alias, if you created it as described above

Launch the Stage 2 web apps server

To launch the MDI web server, we recommend using the MDI Desktop app, which allows you to control both local and remote MDI web servers.