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INSTALLING SEQTOOLS ON LINUX
============================
Although these instructions are for Linux systems they will apply to most unix
systems that have the standard system libraries in the standard places and in
particular come with X Windows and GTK installed.
Install the following pre-requisites. This is most easily done using your system
package manager (e.g. synaptic on Ubuntu, available from the
System/Administration menu). Depending on your system, packages may be named
differently or additional packages may be required. In this case the ./configure
step below will fail and you will need to install the required package before
running it again. If you cannot find a package it can be useful to search for
just the main part of the name excluding numbers/dashes, e.g. "gtk" or "libgtk"
rather than "libgtk2.0-dev".
libcurl4-gnutls-dev (optional)
libgtk2.0-dev
libglib2.0-dev
libreadline6-dev
libsqlite3-dev (optional)
gcc-4.7 (or greater; see note below)
Note that you need a compiler that supports C++11, e.g. gcc version 4.7 or
greater. C++11 is required as of seqtools 4.41.0. If you have an older compiler,
you can still install seqtools version 4.40.0 and earlier.
In the terminal, unpack the downloaded seqtools tar file using the following
command, where XXX is the version you downloaded:
tar -xf seqtools-XXX.tar.gz
To install in the default location (usually /usr/bin):
cd seqtools-XXX
./configure
make
make install
To install in a different location, or for help with dependencies or for more
detailed instructions on configure see the tips below and also the INSTALL file
in this directory.
Environment
-----------
Before running the programs, you need to set the DISPLAY environment variable to
tell GTK which screen to use. Typically you would set this to ":0" (without the
quotes) to mean the first display on the local machine.
To do this automatically every time you open a new terminal, you can add it to
your profile using the following command (this only needs to be done once and
will then affect all new terminals):
In bash:
echo "export DISPLAY=:0" >> ~/.bash_profile
or in csh:
echo "setenv DISPLAY :0" >> ~/.cshrc
Tips
----
You may need to run make install using sudo if you do not have root privileges,
i.e.:
sudo make install
Alternatively, to install to a different location (e.g. one not requiring root
privileges), use the --prefix argument when you run ./configure. For example,
the following command would set the install location to foo/bar in your home
directory:
./configure --prefix=~/foo/bar
If GTK+ is not in the default location then you may need to pass its location to
the configure script. GTK+ is usually installed in /usr/lib, /usr/local/lib,
/opt/lib or /opt/local/lib. If GTK+ is in e.g. /opt/local/lib then you would
call configure with the following arguments:
./configure PKG_CONFIG_PATH=/opt/local/lib/pkgconfig LDFLAGS="-Xlinker -rpath -Xlinker /opt/local/lib"
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