Network proxy error during "myRast" commands

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

network error proxy myrast

• 3,111 views • link

written 10.4 years ago by surendra •

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

• 1 views • link

written 10.4 years ago by Cytosine

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.

• 1 views • link

written 10.4 years ago by surendra •

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.

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written 10.4 years ago by Cytosine

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.

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written 10.4 years ago by surendra •

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

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written 9.2 years ago by eugeniolcv •

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