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Install Haploview on Ubuntu

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?

snp manhattan haploview ubuntu
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written by lubegaritah • lubegaritah

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?

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written by Sej Modha Sej Modha

Thank you. It was a block from my computer.

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written by lubegaritah • lubegaritah
  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
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written by cpad0112 cpad0112

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

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written by lubegaritah • lubegaritah

2 answers

Alternatively, you can use R to create Manhattan plots:

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written by zx8754 zx8754

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
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written by Joe Joe

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