BEAUTI: Could not get an internet connection.

[Lahn Serio]

Hi,

I installed beauti on Redhat Linux 7.3 but I'm having issue with the internet connection when installing packages. I'm using proxy to connect to the internet. I'm sure I have internet connection as I have no problem downloading the package using wget.

I also tried to use addonmanager, but still having same internet connection issue. Please see screenshot of error below.

# addonmanager -list
Error reading the following package repository URLs: https://raw.githubusercontent.com/CompEvol/CBAN/master/packages.xml
Could not get an internet connection. The BEAST Package Manager needs internet access in order to list available packages and download them for installation. Possibly, some software (like security software, or a firewall) blocks the BEAST Package Manager.  If so, you need to reconfigure such software to allow access.

Wget works (This means I have internet connection):
#wget https://raw.githubusercontent.com/CompEvol/CBAN/master/packages.xml
--2017-10-04 16:35:34--  https://raw.githubusercontent.com/CompEvol/CBAN/master/packages.xml
Resolving proxy.....
Connecting to proxy ....... connected.
Proxy request sent, awaiting response... 200 OK
Length: 23028 (22K) [text/plain]
Saving to: ‘packages.xml.1’

100%[=============================================================================================>] 23,028      --.-K/s   in 0.01s

2017-10-04 16:35:35 (1.92 MB/s) - ‘packages.xml.1’ saved [23028/23028]

I also tried to install it manual (download the packages from the internet and manually install/unzip it on the Linux PC), but beauti could not find it.

Can someone please help how I am able to resolve this internet connection?

Any help will be much appreciated. Thank you.

Regards,

Lahn

[Tim Vaughan]

Dear Lahn,

You need to tell java about your proxy configuration. According to the documentation (http://docs.oracle.com/javase/8/docs/technotes/guides/net/proxies.html) this is done by setting the https.proxyHost and https.proxyPort system properties.  You can set these for addonmanager by opening up the launch script (use "which addonmanager" to find it) in a text editor and modifying the last line by replacing

$JAVA -Xms256m -Xmx1024m

with

$JAVA -Xms256m -Xmx1024m -Dhttps.proxyHost=HOSTNAME -Dhttps.proxyPort=PORT

where HOSTNAME and PORT are the host name and port of your HTTP proxy.  If you don't know what these are, they're probably specified in your environment variables, which you can list using the "env" command. There'll probably be a variable named "http_proxy" or "https_proxy" that contains your proxy configuration.   (Your proxy could also be configured specifically for wget in ~/.wgetrc, /usr/local/etc/wgetrc, or somewhere like that.)

After this configuration, you should be able to use addonmanager to download packages without problem.

As for manual installation, this should work just fine as long as you download the zip file corresponding to the package (see the packages.xml file you downloaded for locations of these files) and extract it to a directory with the same name as the package and located in ~/.beast/2.4/.

All the best,

Tim

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[ac.a...@gmail.com]

Had same issue. Downloading the package and extracting in a folder with same name in ~/.beast/2.7/ worked!