AffyMAPSDetector

From CLAB

AffyMAPSDetector is an Affymetrix MicroArray Probe SNP Detector. More information about the software can be found at: AffyMAPSDetector

[edit] Installation instructions

1. Install Xming on your machine and launch the Xming program.

  a.         Download the Xming setup file from online: 
             http://sourceforge.net/project/downloading.php?group_id=156984&filename=Xming-6-9-0-31-setup.exe

  b.         Run the downloaded .exe file (leave the default options) and Xming will be installed.

  c.         Run the Xming program. User may be requested to block or unblock the Xming program. 
             Please choose the option to unblock the Xming program.

2. ssh to sapling.gds.unomaha.edu or biobase.ist.unomaha.edu using your username and password (provided by the administrator) with X11 Forwarding enabled.

  a.         Download putty from: http://the.earth.li/~sgtatham/putty/latest/x86/putty.exe

  b.         Launch putty.exe

  c.         In the Host name section, type: sapling.gds.unomaha.edu or biobase.ist.unomaha.edu

  d.         Under the Category section on the left side of the putty window, go to Connection->SSH->X11 and 
             select the ‘Enable X11 Forwarding’ button.

  e.         Click the ‘Open’ button to connect to sapling.gds.unomaha.edu or biobase.ist.unomaha.edu under SSH.

3. After logging in, type wget http://www.binf.gmu.edu/weller/BMC_bioinformatics/AffyMapsDetector/data_archive/AffyMAPSDetector_v1.zip

4. mkdir affy; mv AffyMAPSDetector_v1.zip affy; cd affy; unzip AffyMAPSDetector_v1.zip 5. cd AffyMAPSDetector_v1

6. chmod +x run.sh

7. Open the run.sh file and make the -Xmx400m to -Xmx1024m.

8. type: wget http://www.binf.gmu.edu/weller/BMC_bioinformatics/AffyMapsDetector/data_archive/HG_U95Av2_gene_info

9. Type: ./run.sh

10. The following url has the instructions of how to select the input files and start the run in AffyMAPSDetector. http://www.binf.gmu.edu/weller/BMC_bioinformatics/AffyMapsDetector/index.html