An easy way to check that all is working is to use the EMBOSS application embossversion.

% embossversion
Writes the current EMBOSS version number
6.1.0

If the version number of EMBOSS is not printed similarly to the above then all is not well; if it is printed then celebrate appropriately.

If you wish to use the restriction mapping, domain recognition and amino acid index applications in EMBOSS then you will need to download the following databases from the Internet; all are relatively small. Download them all to a temporary directory.

If you followed our advice and gave a --prefix option to the configure command, thereby specifying a directory where EMBOSS alone would be installed, then there are two methods for deleting EMBOSS.

From time to time, bugfixes or new functionalities are provided, which can be applied to the version of EMBOSS you have installed. At such times new source code files will appear on our FTP server in the directory:

ftp://emboss.open-bio.org/pub/EMBOSS/fixes/

Usually these source code files are replacements for files that came with the EMBOSS distribution. You should read the README.fixes file in the above directory to see what the file fixes and whereabouts in the EMBOSS source directory it lives.

To apply the fixes, copy the source code file to its correct location, return to the top level of your EMBOSS source code tree and type:

This is, of course, another very good reason for not deleting your EMBOSS source code tree.

A more convenient way of applying all the fixes from the above directory is to use the patch file in the subdirectory:

ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/

The patch files are of the form patch-1-n.gz where n refers to the latest source code correction in the README.fixes file in the directory above. So, if there are ten corrections in the latter file then the patch file would be called patch-1-10.gz.

The patch files are applied using the UNIX patch command e.g.:

Or, if the file has been uncompressed in transit:

You should always start with freshly extracted EMBOSS source code, as above, before applying a patch. This allows you to see any errors more easily. On rare occasions the developers will provide a patch file that contains fixes to a binary file. Some operating systems (e.g. FreeBSD) cannot handle binary patches and will report that such a patch file is malformed. In those circumstances follow the instructions in the nonbinary directory.

A new version of EMBOSS is released at least once per year, typically on St Swithun's Day (15th July). Before installing the new version you should either delete the existing EMBOSS version (if installing to the same directory) or install EMBOSS in a new location. Do not install a new version of EMBOSS on top of an existing installation as files from previous versions may cause compatibility problems.

EMBOSS includes two files that are used to configure the package, particularly for defining databases and for making global settings that influence the behaviour of all EMBOSS programs.

The file emboss.default is used for site-wide configuration. Template files are included:

The file .embossrc, which you can create in your personal home directory, is used for user-specific customisation. Typically you might test, for example, database definitions in your own ~/.embossrc file before adding them to emboss.default.

# this is a comment

INCLUDE "project_databases.def"

SET dbdir /data/sequencedbs

file: $dbdir/data.dat

SET EMBOSS_HELP 1

EMBOSS defines various environment variables. They include global variables used to control the behaviour of all EMBOSS programs, and variables to set the location of system files or directories, specify default values etc. There is normally no need to set the environment variables, but you may do so to customise the behaviour of your instance of EMBOSS.

Environment variables are useful for simplifying maintenance of your .embossrc file. If, for example, you specify the location of your databases as an environment variable, then if you move the databases you only have to update one line in the configuration file. For example, for the data directory:

you might have something like this:

set EMBOSS_database_dir /data/databases/flatfiles

SET EMBOSS_embldir $EMBOSS_database_dir/embl

The second line sets another variable to the directory:

Global environment variables must have UPPERCASE names and usually have Boolean values; they can be turned on by setting them to "1", or "Y" (they are off by default.) The global variables can also be set in the UNIX session by defining an environment variable with the commands:

where NAME is the name of the variable and value is the value you wish to set it to.

set EMBOSS_VERBOSE Y

set EMBOSS_FORMAT gcg
set EMBOSS_OUTFORMAT gcg

set EMBOSS_ACDROOT /path/to/acd

set EMBOSS_DATA /path/to/data

set EMBOSS_LOGFILE /site/log/emboss.log

prettyplot      joeuser        Wed Aug 02 14:29:13 2000

set EMBOSS_LOGFILE /dev/null

acdcommandlinelog string  "" "Log file for full commandline, used to convert QA test definitions into memory leak test command lines"
acdlog boolean "N" "Log ACD processing to file program.acdlog"
acdprompts integer "1" "Number of times to prompt for a value when interactive"
acdroot string "(install directory)" "EMBOSS root directory for finding files"
acdutilroot string "(source directory)" "EMBOSS source directory for finding files"

EMBOSS data files are included in the distribution and stored in the standard EMBOSS data directory, which can be defined by the EMBOSS environment variable EMBOSS_DATA.

If you built EMBOSS using make install, EMBOSS will by default install the data files, including those installed with rebaseextract, prosextract, printsextract, aaindexextract or cutgextract, in the directory:

under the install directory, which is defined by the --prefix when you configured the package (see the EMBOSS Users Guide). Typically this is:

If EMBOSS was not installed using make install but just compiled using make, then by default the data files are in:

under the directory where emboss was built.

If you want to keep your data files somewhere else, or have a set of datafiles you want to keep separate from those distributed with the package, then you can set the EMBOSS_DATA environment variable in your emboss.default or .embossrc file.

To see the available EMBOSS data files, run:

To fetch one of the data files into your current directory for you to inspect or modify, run:

where EDatafileName.dat is the name of the data file.

Users can provide their own data files in their own directories. Project specific files can be put in the current directory or, for tidier directory listings, in a subdirectory called ".embossdata". Similarly, for files to be accessible to all EMBOSS applications, invoked from any location, they can be put in your home directory, or in a subdirectory under it called ".embossdata".

The directories are searched in the following order: