VCRU Bioinformatics - Install notes

This page was last updated on Friday, 23-Dec-2016 10:48:39 CST

Installation notes for Newick Utilities version xxx

Prerequisites

I used the disabled-extra version because I could not figure out libguile problem

libXML
$ sudo apt-get install libxml2-dev

Lua
$ sudo apt-get install lua5.1
but during tests:
../src/nw_display: error while loading shared libraries: liblua-5.1.so: cannot open shared object file: No such file or directory
To correct this I had to
$ cd /usr/lib/x86_64-linux-gnu/
$ sudo ln -s liblua5.1.so liblua-5.1.so

Guile
$ sudo apt-get install guile-2.0
but during tests:
../src/nw_display: error while loading shared libraries: libguile.so.17: cannot open shared object file: No such file or directory

Installation

$ ver="1.6"
$ cd /programinstallers/
$ wget -N http://cegg.unige.ch/pub/newick-utils-$ver-Linux-x86_64-disabled-extra.tar.gz
$ tar -zxvf newick-utils-$ver-Linux-x86_64-disabled-extra.tar.gz

Manual installation
$ sudo cp -puv newick-utils-$ver/src/nw_* /usr/local/bin/

‘newick-utils-1.6/src/nw_clade’ -> ‘/usr/local/bin/nw_clade’
‘newick-utils-1.6/src/nw_condense’ -> ‘/usr/local/bin/nw_condense’
‘newick-utils-1.6/src/nw_display’ -> ‘/usr/local/bin/nw_display’
‘newick-utils-1.6/src/nw_distance’ -> ‘/usr/local/bin/nw_distance’
‘newick-utils-1.6/src/nw_duration’ -> ‘/usr/local/bin/nw_duration’
‘newick-utils-1.6/src/nw_ed’ -> ‘/usr/local/bin/nw_ed’
‘newick-utils-1.6/src/nw_gen’ -> ‘/usr/local/bin/nw_gen’
‘newick-utils-1.6/src/nw_indent’ -> ‘/usr/local/bin/nw_indent’
‘newick-utils-1.6/src/nw_info.py’ -> ‘/usr/local/bin/nw_info.py’
‘newick-utils-1.6/src/nw_labels’ -> ‘/usr/local/bin/nw_labels’
‘newick-utils-1.6/src/nw_luaed’ -> ‘/usr/local/bin/nw_luaed’
‘newick-utils-1.6/src/nw_match’ -> ‘/usr/local/bin/nw_match’
‘newick-utils-1.6/src/nw_order’ -> ‘/usr/local/bin/nw_order’
‘newick-utils-1.6/src/nw_prune’ -> ‘/usr/local/bin/nw_prune’
‘newick-utils-1.6/src/nw_rename’ -> ‘/usr/local/bin/nw_rename’
‘newick-utils-1.6/src/nw_reroot’ -> ‘/usr/local/bin/nw_reroot’
‘newick-utils-1.6/src/nw_reroot.py’ -> ‘/usr/local/bin/nw_reroot.py’
‘newick-utils-1.6/src/nw_sched’ -> ‘/usr/local/bin/nw_sched’
‘newick-utils-1.6/src/nw_stats’ -> ‘/usr/local/bin/nw_stats’
‘newick-utils-1.6/src/nw_support’ -> ‘/usr/local/bin/nw_support’
‘newick-utils-1.6/src/nw_topology’ -> ‘/usr/local/bin/nw_topology’
‘newick-utils-1.6/src/nw_trim’ -> ‘/usr/local/bin/nw_trim'

Test
$ cd newick-utils-1.6/tests
Cleanup
$ cd /programinstallers && rm newick-utils-$ver -rf