Network proxy error during "myRast" commands

Question

[surendra]

Hi,

I am trying to run the command "svr_assign_to_dna_using_figfams" from myRast package.

But I am getting the following error, which might be due the script not able to connect the server due to proxy restrictions.

svr_assign_to_dna_using_figfams <contigs.fasta> functions.tab

500 Can't connect to pubseed.theseed.org:80 (connect: Connection timed out) at /home/user/Softwares/sas/lib/ClientThing.pm line 724.
    ClientThing::_send_request(ANNOserver=HASH(0x183b8a0), "function", "methods", "args", "--- []\x{a}", "source", "ClientThing", "dbName", undef, ...) called at /home/user/Softwares/sas/lib/ClientThing.pm line 476
    ClientThing::_call_method(ANNOserver=HASH(0x183b8a0), "methods", ARRAY(0x184c858)) called at /home/user/Softwares/sas/lib/ClientThing.pm line 186
    ClientThing::new("ANNOserver", "ANNO", "url", "http://pubseed.theseed.org/anno/server.cgi") called at /home/user/Softwares/sas/lib/ANNOserver.pm line 56
    ANNOserver::new("ANNOserver", "url", undef) called at /home/user/Softwares/sas/plbin/svr_assign_to_dna_using_figfams.pl line 131

Can anyone suggest how to use MyRast script behind the proxy server on Linux using terminal.

Thanks in advance

Surendra

[Cytosine]

Maybe try setting your proxy environment variable in the terminal session? <export http_proxy="http://host:port/">

Or try the LWP::UserAgent module inside the script for setting the proxy. Suggested from: http://stackoverflow.com/questions/1746614/use-proxy-with-perl-script

[surendra]

Thanks for the reply Cytosine

The proxy server is already in the environment setting. Also the script from myRast package "ClientThing.pm" includes the LWP::UserAgent module.

but still the script is not woirking.

[Cytosine]

Hard to guess then...

First thing I would do is check whether the server is accessible at all.

Can you manually ping/telnet the server from your terminal? If no, then you need to configure the system, if yes then you need to modify the script.

I'm not familiar with MyRast so I can't give you any more specific suggestions, sorry.

[surendra]

Yes, I have checked and found that server is accessible. It starts gethering the results in output file but then fails with the error. I will check the scripts to modify.

[eugeniolcv]

I'm trying to use myrast as well on debian but I get the same errors. Did you solve the issue in the end?