Plink hangs if not started with --noweb option

[davidonlaptop]

Steps to reproduce

Start plink with any parameters, and here's all the output you'll get:

@----------------------------------------------------------@
|        PLINK!       |     v1.07      |   10/Aug/2009     |
|----------------------------------------------------------|
|  (C) 2009 Shaun Purcell, GNU General Public License, v2  |
|----------------------------------------------------------|
|  For documentation, citation & bug-report instructions:  |
|        http://pngu.mgh.harvard.edu/purcell/plink/        |
@----------------------------------------------------------@

Web-based version check ( --noweb to skip )
Connecting to web...

Cause of the issue

While investigating the issue with strace, the problem appears to be related to a DNS issue:

write(3, "Web-based version check ( --nowe"..., 44) = 44
write(1, "Web-based version check ( --nowe"..., 44Web-based version check ( --noweb to skip )
) = 44
write(3, "Connecting to web... ", 21)   = 21
write(1, "Connecting to web... ", 21Connecting to web... )   = 21
socket(PF_INET, SOCK_STREAM, IPPROTO_IP) = 4
connect(4, {sa_family=AF_INET, sin_port=htons(80), sin_addr=inet_addr("132.183.161.22")}, 16) = 0
sendto(4, "GET /~purcell/plink/version2.txt"..., 89, 0, NULL, 0) = 89
recvfrom(4,

So plink tries to connect to 132.183.161.22 (abilene.mgh.harvard.edu) but apparently the file
has moved to 155.52.206.11 (pngu.mgh.harvard.edu)

The following works:

wget http://pngu.mgh.harvard.edu/~purcell/plink/version2.txt)

Potential solution

We could setup a redirect IP route, but this isn't trival from Docker as iptable does not work
by default from within a container.

root@c5c368a98c93:/# iptables -t nat -A OUTPUT -d 132.183.161.22 -j DNAT --to-destination 155.52.206.11
iptables v1.4.21: can't initialize iptables table `nat': Permission denied (you must be root)

References:

• http://superuser.com/questions/681705/using-iptables-to-redirect-ip-address
• http://stackoverflow.com/questions/24889346/sed-how-to-uncomment-a-line-that-contains-a-specific-string-inline-editing
• http://superuser.com/questions/684652/iptables-gives-me-the-error-cant-initialize-iptables-nat

This thread recommands using PLINK/SEQ instead for annotation functions
http://seqanswers.com/forums/showthread.php?t=36214

[davidonlaptop]

FYI. A workaround has been made for the Dockerimage. See Dockerfile.