Tutorial:Howto use NCBI programs behind a HTTP proxy
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8.4 years ago
piet ★ 1.8k

Within most governmental and enterprise networks it is not possible to connect to the internet directly. HTTP connections are only permitted through HTTP proxy servers. Any application program doing HTTP requests must be aware of the proxy. On Unix operation systems the standard way to advertise the proxy to application programs is by passing environment variables 'http_proxy', 'https_proxy', 'ftp_proxy', 'no_proxy'. Unfortunately, NCBI programs do not adhere to this standard. NCBI programmers have invented their own ways to configure proxy settings, and this is not well documented in available manuals.

Blast+ suite of programs

Proxy setting are read from a hidden config file named '.ncbirc'. This file is expected to reside either in the user's home directory ('~/.ncbirc') or in the current working directory ('./.ncbirc'). The '.ncbirc' file is formated in INI style and proxy setting are placed into a [CONN] section:

HTTP_PROXY_HOST = proxy.example.org

Note: if your proxy does not has a DNS name, you may assign its IP address to HTTP_PROXY_HOST.

See also: http://www.dtd.nlm.nih.gov/projects/gbench/faq.html

SRA toolkit

Proxy setting are read from a config file located at '~/.ncbi/user-settings.mkfg'. This is a simple text file which can be easily modified with a standard text editor. Nevertheless, SRA toolkit provides a dedicated program for this task. The following command will add proxy support:

vdb-config --proxy proxy.example.org:8080

Running this command will just append two additional lines to '~/.ncbi/user-settings.mkfg':

/http/proxy/enabled = "true"
/http/proxy/path = "proxy.example.org:8080"

See also:

blast-plus HTTP-proxy SRA-toolkit • 12k views

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