Plink hangs if not started with --noweb option #1
Description
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