If you are a developer using the latest source code (from CVS, the code version control system used by the EMBOSS developers), then to install and compile EMBOSS the following GNU configuration tools must be installed on your system:
autoconf
automake
libtool
Some operating system distributions provide them in-the-box (e.g. most Linux distributions). Should you require the source code for these tools (and it is important to keep up-to-date) it can be downloaded from:
| ftp://ftp.gnu.org/pub/gnu |
Most users of EMBOSS however do not need the latest source code from CVS, and will use an EMBOSS "stable" release instead (Section 2.4, “Software Releases”). In this case, the GNU configuration tools are not required.
Some EMBOSS applications are "wrappers" and call third party applications which must be installed on the same system as EMBOSS. The location of the third party executables must be defined in your PATH. The dependencies are summarised in the table (Table 2.1, “EMBOSS Software Requirements”).
| Application | Software requirements |
|---|---|
| clustalw | clustalw is called by emma |
| primer3_core | primer3_core from the role="thirdparty">PRIMER 3.0 package is called by eprimer3 |
Some EMBASSY applications are "wrappers" and call third party applications which must be installed on the same system as EMBOSS. The location of the third party executables must be defined in your PATH. The dependencies are summarised in the table (Table 2.2, “EMBASSY Software Requirements”).
| EMBASSY package | Description | Software requirements |
|---|---|---|
| CBSTOOLS | CBSTOOLS is a suite of application wrappers to the original CBS prediction server applications at CBS DTU in Denmark. | chlorop, lipop, netnglyc, netoglyc, netphos, prop, signalp, tmhmm and yinoyang are called by these wrappers. |
| HMMERNEW | HMMERNEW is a suite of application wrappers to the original hmmer v2.3.2applications written by Sean Eddy. | HMMER v2.3.2 must be installed. |
| IPRSCAN | IPRSCAN contains applications for detecting protein domains and motifs. | eiprscan requires InterproScan 4.4 to be installed. |
| MIRA | MIRA contains wrappers for the MIRA sequence assembly software. | emira and emiraest require MIRA 2.8.3 to be installed. |
| DOMALIGN | DOMALIGN contains applications for manipulating a protein domain classification file and generating alignments of domains. | domainalign and domainrep require stamp to be installed. |
| seqalign requires stamp to be installed. | ||
| DOMSEARCH | DOMSEARCH contains applications for searching for and manipulating relatives of protein domain families. | seqsearch requires PSIBLAST to be installed. |
| STRUCTURE | STRUCTURE contains applications for parsing PDB files and for protein structure. | pdbplus requires NACCESS and STRIDE to be installed. |
| MEMENEW | MEMENEW contains "wrapper" applications providing an EMBOSS-style interface to the applications in the original MEME package version 4.0.0 developed by Timothy L. Bailey. | MEME 4.0.0 or later must be installed. |
In a few cases (e.g. naccess and stride) it may be necessary to modify the original source code to overcome certain limitations with the original software. Any such modifications are clearly described in the wrapper application documentation.
The MSE and EMNU packages, should you wish to install them, will require Ncurses support (see the EMBOSS Administrators Guide.