Install Haploview on Ubuntu

Question

[lubegaritah]

Hey!

I need to install Haploview so as to produce a Manhattan plot (summarise the output of my association analysis). I however can't seem to reach the broad Institute website.

Any one know how else I could progress?

[Sej Modha]

Are you sure that the local firewall or security settings are not blocking access to broad institute website? Have you tried accessing the webpage from a different computer and/or different internet browser?

[lubegaritah]

Thank you. It was a block from my computer.

[cpad0112]

1. Try pinging broad url
2. If you can ping, see if there are any local or network rules that prevent downloading either in full or certain types of files

[lubegaritah]

Thank you all. I have succeeded with R. For some reason the haploview.jar has failed for me

Answer 1

[zx8754]

Alternatively, you can use R to create Manhattan plots:

• qqman package (there are many others, too.)
• point & click shinyapp website: https://chikudaisei.shinyapps.io/shinyaim/

[lubegaritah]

Worked for me too. Thank you

Answer 2

[Joe]

Works for me, so Sej’s suggestion of your local firewall or similar is probably right on the money:

$ wget https://www.broadinstitute.org/ftp/pub/mpg/haploview/Haploview.jar
--2018-09-25 12:03:58--  https://www.broadinstitute.org/ftp/pub/mpg/haploview/Haploview.jar
Resolving www.broadinstitute.org www.broadinstitute.org)... 50.17.215.99, 107.20.224.46
Connecting to www.broadinstitute.org www.broadinstitute.org)|50.17.215.99|:443... connected.
HTTP request sent, awaiting response... 301 Moved Permanently
Location: ftp://ftp.broadinstitute.org/pub/mpg/haploview/Haploview.jar [following]
--2018-09-25 12:03:58--  ftp://ftp.broadinstitute.org/pub/mpg/haploview/Haploview.jar
           => `Haploview.jar'
Resolving ftp.broadinstitute.org ftp.broadinstitute.org)... 69.173.80.251
Connecting to ftp.broadinstitute.org ftp.broadinstitute.org)|69.173.80.251|:21... connected.
Logging in as anonymous ... Logged in!
==> SYST ... done.    ==> PWD ... done.
==> TYPE I ... done.  ==> CWD (1) /pub/mpg/haploview ... done.
==> SIZE Haploview.jar ... 5300252
==> PASV ... done.    ==> RETR Haploview.jar ... done.
Length: 5300252 (5.1M) (unauthoritative)

 0% [                                                                                                     ] 21,224      76.0K/s              
100%[====================================================================================================>] 5,300,252   1.97M/s   in 2.6s    

2018-09-25 12:04:02 (1.97 MB/s) - `Haploview.jar' saved [5300252]

$  ls
Haploview.jar