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The Madeline 2.0 Pedigree Drawing Engine (PDE) is a pedigree drawing program for use in linkage and family-based association studies. The program is designed to handle large and complex pedigrees with an emphasis on readability and aesthetics.

References:

• Edward H. Trager, Ritu Khanna, Adrian Marrs, Lawrence Siden, Kari E.H. Branham, Anand Swaroop and Julia E. Richards,
  Madeline 2.0 PDE: a new program for local and web-based pedigree drawing.
  Bioinformatics, 2007, 23(14), pp. 1854–1856.
  

• Madeline 2.0_PDE Github page
• Madeline 2.0_PDE Home page

• Module Name: Madeline (see the modules page for more information)
• Unusual environment variables set
  • MADELINE_HOME  MADELINE installation directory
  • MADELINE_BIN       MADELINE executable directory
  • MADELINE_SRC     MADELINEsource code directory
  • MADELINE_DATA     MADELINE sample data directory

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive 
[user@cn0849 ~]$ module load Madeline 
[+] Loading madeline  2.0  on cn0849
[+] Loading singularity  3.8.5-1  on cn0849
[+] Loading ImageMagick  7.0.7  on cn0849

Copy test data to your current filder:

[user@cn0849 ~]$ cp -r $MADELINE_DATA/* . 

Run the madeline executable on the test data:

[user@cn0849 ~]$ madeline -L "IndividualID DOB" ./input/si_001.data
┌─────────────────────────────┐
│ Welcome to Madeline 2.0 PDE │
└─────────────────────────────┘
--------------------------------------------
 LABELS                          TOTAL: 2
--------------------------------------------
 1. IndividualID
 2. DOB
--------------------------------------------
Parser::readFile(): Opening a(n) UTF-8 file ...
Reading file data in Madeline flat file format ...
----------------------------------------------------------------
 ICON COLUMNS                                        TOTAL: 1
----------------------------------------------------------------
   1. Affected                         has 2 non-missing levels.
----------------------------------------------------------------
Table 1 is a pedigree table.
  Start of    addPedigreesFromDataTable 
Warning: Adding virtual father “S00100” who is not present in the input data file.
Warning: Adding virtual mother “S00101” who is not present in the input data file.
Siblings are ordered by DOB.
  End of      addPedigreesFromDataTable 
  Start of    draw                       
Pedigree output file is “si_001_pedigree.svg”
  End of      draw                       

[user@cn0849 ~]$ madeline --color ./input/si_002.data
┌─────────────────────────────┐
│ Welcome to Madeline 2.0 PDE │
└─────────────────────────────┘
--------------------------------------------
 LABELS                          TOTAL: 0
--------------------------------------------
--------------------------------------------
Parser::readFile(): Opening a(n) UTF-8 file ...
Reading file data in Madeline flat file format ...
----------------------------------------------------------------
 ICON COLUMNS                                        TOTAL: 1
----------------------------------------------------------------
   1. Affected                         has 3 non-missing levels.
----------------------------------------------------------------
Table 1 is a pedigree table.
  Start of    addPedigreesFromDataTable  
Siblings are ordered by DOB.
  End of      addPedigreesFromDataTable  
  Start of    draw                       
Pedigree output file is “si_002_pedigree.svg”
  End of      draw                       

Visualize the results:

[user@cn0849 ~]$ display si_001_pedigree.svg

[user@cn0849 ~]$ display si_002_pedigree.svg

[user@cn0849 ~]$ exit exit salloc.exe: Relinquishing job allocation 28896415 salloc.exe: Job allocation 28896415 has been revoked. [user@biowulf ~]$