Question: Network proxy error during "myRast" commands
0
gravatar for surendra
3.4 years ago by
surendra30
South Africa
surendra30 wrote:

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

proxy network error myrast • 1.2k views
ADD COMMENTlink written 3.4 years ago by surendra30
1

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

ADD REPLYlink written 3.4 years ago by Cytosine440

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.

ADD REPLYlink written 3.4 years ago by surendra30

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.

ADD REPLYlink written 3.4 years ago by Cytosine440

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.

ADD REPLYlink written 3.4 years ago by surendra30

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

ADD REPLYlink written 2.3 years ago by eugeniolcv0
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