Installing and compiling binaries used in Interproscan

The binaries that we distribute with InterProScan should work on most linux systems. However, in some cases they may not work on a particular system. If you are trying to run InterProScan and you get an error then you may need to compile the binary causing the error on your own system in order for it to work.

Once a binary has been compiled you can either: - Replace the binary in the relevant bin subdirectory in your InterProScan installation with your newly compiled version - Or update the location of the binary in your interproscan.properties configuration to point to your newly compiled version

InterProScan is designed to work with the same binary versions as used by the supported member database analyses. Therefore it is important to use the binary version numbers listed below, see the FAQ for more information.

cath-resolve-hits (used by CATH-Gene3D)

cath-resolve-hits is a tool written c/c++ and is used as part of the postprocessing for CATH-Gene3D. The binary bundled in InterProScan should work on most systems. If you get errors, download cath-resolve-hits v0.15.2 that corresponds to your system from the following page https://github.com/UCLOrengoGroup/cath-tools/releases/tag/v0.16.10 into bin/gene3d/4.3.0/ and rename it to bin/gene3d/4.3.0/cath-resolve-hits.

If the precompiled binary doesnt’ solve your problems, compile the binary for your system by following instructions on http://cath-tools.readthedocs.io/en/latest/build/

Then either replace the relevant binary with your new one or update the relevant interproscan.properties values to point at the new file location. The default property values are:

cath.resolve.hits.path=bin/gene3d/4.3.0/cath-resolve-hits

PfscanV3/PfsearchV3 (used by ProSite Profiles, ProSite Patterns and HAMAP)

PfscanV3 and PFsearchV3 binary packages for your platform can be downloaded from https://ftp.expasy.org/databases/prosite/ps_scan/.

Alternatively, you may download the source code from https://github.com/sib-swiss/pftools3 and compile the binaries yourself.

Then either replace the relevant files with your new ones or update the relevant interproscan.properties values to point at the new file locations:

binary.prosite.pfscanv3.path=bin/prosite/pfscan
binary.prosite.pfsearchv3.path=bin/prosite/pfsearch

Hmmer 2 (used by SMART)

wget ftp://selab.janelia.org/pub/software/hmmer/2.3.2/hmmer-2.3.2.tar.gz
tar -xzvf hmmer-2.3.2.tar.gz
cd hmmer-2.3.2
./configure --enable-threads
make
make check
make install

Then either replace the relevant binary with your new one or update the relevant interproscan.properties values to point at the new file location. The default property values are:

binary.hmmer2.hmmsearch.path=bin/hmmer/hmmer2/2.3.2/hmmsearch
binary.hmmer2.hmmpfam.path=bin/hmmer/hmmer2/2.3.2/hmmpfam

Hmmer 3 (used by CATH-Gene3D, HAMAP, PANTHER, Pfam, PIRSF, SFLD, SUPERFAMILY and NCBIFAM)

Instructions for downloading and compiling Hmmer 3.1b1 can be found at: http://hmmer.org/download.html

Then either replace the relevant binary with your new one or update the relevant interproscan.properties values to point at the new file location. The default property values are:

binary.hmmer3.path=bin/hmmer/hmmer3/3.1b1
binary.hmmer3.hmmscan.path=bin/hmmer/hmmer3/3.1b1/hmmscan
binary.hmmer3.hmmsearch.path=bin/hmmer/hmmer3/3.1b1/hmmsearch

ncoils (used by Coils)

If you get Coils (ncoils) errors, you may need to compile the Coils binary and it is straight forward as follows.

cd src/coils/ncoils/2.2.1
make
cd ../../../..
cp src/coils/ncoils/2.2.1/ncoils bin/ncoils/2.2.1/ncoils

The steps above normally solve the problem.

Instructions for compiling the “ncoils” binary can also be found in the src/coils/ncoils/2.2.1/README file in your extracted InterProScan 5 distribution (release 5.17-56.0 onwards).

Then either replace the relevant binary with your new one or update the relevant interproscan.properties values to point at the new file location. The default property values are:

binary.coils.path=bin/ncoils/2.2.1/ncoils

fingerPRINTScan (used by PRINTS)

Instructions for compiling the “fingerPRINTScan” binary can be found in the src/prints/fingerprintscan/3597/INSTALL file in your extracted InterProScan 5 distribution (release 5.17-56.0 onwards) and are summarised as below:

cd src/prints/fingerprintscan/3597/
./configure
make
cd _interproscan_dir
cp src/prints/fingerprintscan/3597/fingerPRINTScan bin/prints/

where “_interproscan_dir” is the directory where you have installed InterProScan 5.

If you choose not to replace the relevant binary with your new one then instead you can update the relevant interproscan.properties values to point at the new file location. The default property values are:

binary.fingerprintscan.path=bin/prints/fingerPRINTScan

rpsblast/rpsbproc (used by CDD)

There are two seperate application from NCBI that CDD uses for analysis in InterProScan. If the applications rpsblast and rpsbproc provided in InterProScan are not working for you,

We are working on a summary of how to compile rpsblast/rpsbproc for the latest Blast release - ncbi-blast-2.11.0+.

For an older release ncbi-blast-2.6.0+, below are the instructions. They could be adapted to work for ncbi-blast-2.11.0+.

Instructions on how to compile rpsblast/rpsbproc for interproscan are summarised as follows:

First check the c++ compiler version

c++ --version

if the c++ version is less than 4.8 compilation will most likely fail and you should upgrade to a c++ compiler version 4.8 or above.

If you have a c++ version 4.8 or above then follow the instructions below.

mkdir cddblast
cd cddblast
wget ftp://ftp.ncbi.nih.gov/blast/executables/blast+/2.6.0/ncbi-blast-2.6.0+-src.tar.gz
wget ftp://ftp.ncbi.nih.gov/blast/executables/blast+/2.6.0/ncbi-blast-2.6.0+-src.tar.gz.md5
md5sum -c ncbi-blast-2.6.0+-src.tar.gz.md5
# Above command should return "ncbi-blast-2.6.0+-src.tar.gz: OK" if download successful
tar xvzf ncbi-blast-2.6.0+-src.tar.gz
cd ncbi-blast-2.6.0+-src/c++/src/app/
wget -r --no-parent -l 1 -np -nd -nH -P rpsbproc ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/rpsbproc/rpsbproc-src/
#edit Makefile.in and make sure SUB_PROJ is assigned two applications as follows: SUB_PROJ = blast rpsbproc
cd ../../
./configure
/usr/bin/make
#after compilation is complete
cp ReleaseMT/bin/rpsblast <interproscan_install_dir>/bin/blast/ncbi-blast-2.6.0+/
cp ReleaseMT/bin/rpsbproc <interproscan_install_dir>/bin/blast/ncbi-blast-2.6.0+/

The complete instruction set can be found here: ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/rpsbproc/README

If you choose not to replace the relevant binary with your new one then instead you can update the relevant interproscan.properties values to point at the new file location. The default property values are:

binary.rpsblast.path=bin/blast/ncbi-blast-2.6.0+/rpsblast
binary.rpsbproc.path=bin/blast/ncbi-blast-2.6.0+/rpsbproc

sfld_preprocess/sfld_postprocess (used by SFLD)

Instructions for compiling the “sfld_preprocess” and “sfld_postprocess” binaries can be found in the src/sfld/1/README file in your extracted InterProScan 5 distribution (release 5.22-61.0 onwards).

Then either replace the relevant binary with your new one or update the relevant interproscan.properties values to point at the new file location. The default property values are:

sfld.postprocess.command=bin/sfld/sfld_postprocess

Phobius, TMHMM or SignalP

By default the Phobius, SignalP and TMHMM member database analyses are deactivated because they contain licensed components. For instructions on how to activate these analyses, obtain the relevant licenses and compile the binaries please see “activating licensed analyses”.