Use released packagemanager to install packages

[walterxie]

From Remco:

./bin/packagemanager -add SSM
Packages user path : /home/.../.beast/2.8
Access URL : https://raw.githubusercontent.com/CompEvol/CBAN/master/packages2.8.xml
Getting list of packages ...Done!

Determine packages to install

beast.pkgmgmt.DependencyResolver$DependencyResolutionException: Package SSM depends on unknown package BEAST.app
	at beast.pkgmgmt@2.8.0/beast.pkgmgmt.DependencyResolver.resolve(DependencyResolver.java:57)
	at beast.pkgmgmt@2.8.0/beast.pkgmgmt.DependencyResolver.resolve(DependencyResolver.java:37)
	at beast.pkgmgmt@2.8.0/beast.pkgmgmt.PackageManager.populatePackagesToInstall(PackageManager.java:1226)
	at beast.pkgmgmt@2.8.0/beast.pkgmgmt.PackageManagerCLI.main(PackageManagerCLI.java:318)
	at beast.pkgmgmt@2.8.0/beast.pkgmgmt.PackageManager.main(PackageManager.java:1639)

./bin/packagemanager -list
Packages user path : /home/.../.beast/2.8
Access URL : https://raw.githubusercontent.com/CompEvol/CBAN/master/packages2.8.xml
Getting list of packages ...Done!

Name | Installed Version | Latest Version | Dependencies | Description

BEAST.base | 2.8.0 | NA | |
BDMM-Prime | NA | 3.0.0 | BEAST.app, SA, BEAST.base | Linear birth-death phylodynamics
ORC | 1.3.1 | 1.3.1 | BEAST.base | Optimised Relaxed Clock model
ReMASTER | NA | 3.0.1 | BEAST.base | Phylodynamic simulation system
SA | NA | 2.3.0 | BEAST.base | Sampled ancestor trees for BEAST
SSM | NA | 1.3.0 | BEAST.base, BEAST.app | Standard Nucleotide Substitution Models

[walterxie]

BEAST.app was not there after -list

[walterxie]

#95