Difference between revisions of "Installing BioConductor"
From Organic Design wiki
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=Configuring R to work behind a firewall= | =Configuring R to work behind a firewall= | ||
Within a company network you need to set the proxy server. The following command does this by setting an R environment variable to the proxy:port; | Within a company network you need to set the proxy server. The following command does this by setting an R environment variable to the proxy:port; | ||
| − | + | <table class=document-code><tr><td> | |
Sys.putenv("HTTP_PROXY"="[URL]:[PORT]") | Sys.putenv("HTTP_PROXY"="[URL]:[PORT]") | ||
| + | </table> | ||
Once this is set you can check if the variable is set with; | Once this is set you can check if the variable is set with; | ||
| − | + | <table class=document-code><tr><td> | |
Sys.getenv("HTTP_PROXY") | Sys.getenv("HTTP_PROXY") | ||
| − | + | </table> | |
Now you can fetch the following scripts over the internet; | Now you can fetch the following scripts over the internet; | ||
| − | + | <table class=document-code><tr><td> | |
<nowiki>source("http://www.bioconductor.org/getBioC.R") | <nowiki>source("http://www.bioconductor.org/getBioC.R") | ||
source("http://www.bioconductor.org/biocLite.R")</nowiki> | source("http://www.bioconductor.org/biocLite.R")</nowiki> | ||
| − | + | </table> | |
Typing the following commands will display the source code of the functions for installing BioConductor automatically. 'getBioC' installs a fairly comprehensive installation, | Typing the following commands will display the source code of the functions for installing BioConductor automatically. 'getBioC' installs a fairly comprehensive installation, | ||
'biocLite' installs a minimal installation. | 'biocLite' installs a minimal installation. | ||
| + | <table class=document-code><tr><td> | ||
getBioC | getBioC | ||
biocLite | biocLite | ||
| − | + | </table> | |
Type the following command to install Bioconductor ''getBioC()'' or ''biocLite()'' depending on type of installation. | Type the following command to install Bioconductor ''getBioC()'' or ''biocLite()'' depending on type of installation. | ||
=See also= | =See also= | ||
*[http://www.bioconductor.org/docs/install-howto.html BioConductor install guide] | *[http://www.bioconductor.org/docs/install-howto.html BioConductor install guide] | ||
Revision as of 04:49, 30 June 2006
Configuring R to work behind a firewall
Within a company network you need to set the proxy server. The following command does this by setting an R environment variable to the proxy:port;
Sys.putenv("HTTP_PROXY"="[URL]:[PORT]")
|
Once this is set you can check if the variable is set with;
Sys.getenv("HTTP_PROXY")
|
Now you can fetch the following scripts over the internet;
source("http://www.bioconductor.org/getBioC.R")
source("http://www.bioconductor.org/biocLite.R")
|
Typing the following commands will display the source code of the functions for installing BioConductor automatically. 'getBioC' installs a fairly comprehensive installation, 'biocLite' installs a minimal installation.
getBioC biocLite |
Type the following command to install Bioconductor getBioC() or biocLite() depending on type of installation.
