InterProScan

https://interproscan-docs.readthedocs.io/en/v5
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InterProScan is a bioinformatics tool that scans protein and nucleic acid sequences against multiple...
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### Example InterProScan Lookup Service Startup Output

Source: https://interproscan-docs.readthedocs.io/en/v5/LocalLookupService

This is an example of the console output when the InterProScan lookup service starts successfully. It shows the initialization progress, including web application loading, port binding, and database indexing. Successful startup indicates the service is ready to receive requests.

```bash
$ java -Xmx8000m -jar server-5.76-107.0-jetty-console.war
10242 [Thread-2] INFO org.simplericity.jettyconsole.DefaultJettyManager - Added web application on path / from war /example/path/to/server-5.76-107.0-jetty-console.war
10243 [Thread-2] INFO org.simplericity.jettyconsole.DefaultJettyManager - Starting web application on port 8080
10245 [Thread-2] INFO org.eclipse.jetty.server.Server - jetty-8.1.12.v20130726
10818 [Thread-2] INFO org.eclipse.jetty.plus.webapp.PlusConfiguration - No Transaction manager found - if your webapp requires one, please configure one.
12226 [Thread-2] INFO org.eclipse.jetty.webapp.StandardDescriptorProcessor - NO JSP Support for /, did not find org.apache.jasper.servlet.JspServlet
12243 [Thread-2] INFO / - No Spring WebApplicationInitializer types detected on classpath
12344 [Thread-2] INFO / - Initializing Spring root WebApplicationContext
Initializing BerkeleyDB Match Database (creating indexes): Please wait...
Initializing BerkeleyDB MD5 Database (creating indexes): Please wait...
1049793 [Thread-2] INFO / - Initializing Spring FrameworkServlet 'mvc'
Initializing BerkeleyDB Match Database (creating indexes): Please wait...
Initializing BerkeleyDB MD5 Database (creating indexes): Please wait...
1050000 [Thread-2] INFO org.eclipse.jetty.server.AbstractConnector - Started @0.0.0.0:8080
```

--------------------------------

### Testing InterProScan Lookup Service

Source: https://interproscan-docs.readthedocs.io/en/v5/LocalLookupService

These commands demonstrate how to test the InterProScan lookup service after it has started. It includes examples using a web browser and `curl` to access the `/version` and `/matches` endpoints, verifying the service is operational.

```bash
# Assuming the lookup service has been started on the same machine and you are using
# the default port of 8080 then...

# in a web browser:
http://localhost:8080/version
http://localhost:8080/matches?md5=2E38C8D754C63117A4FA5F5E44F2194E

# or using curl on the command line:
curl http://localhost:8080/version
curl http://localhost:8080/matches?md5=2E38C8D754C63117A4FA5F5E44F2194E

# To access your lookup service from another machine replace "localhost" with
```

--------------------------------

### Starting the Lookup Service

Source: https://interproscan-docs.readthedocs.io/en/v5/_sources/LocalLookupService.rst

Instructions for starting the InterProScan 5 lookup service, including GUI and headless modes, memory allocation, and port configuration.

```APIDOC
## Running the Lookup Service

### GUI Mode
To start the service with a graphical user interface, navigate to the `lookup_service_5.76-107.0` directory and run the following command:

```bash
java -Xmx8000m -jar server-5.76-107.0-jetty-console.war
```
A new window will open where you can set the port number and start the web service.

### Headless Mode (Command Line)
For command-line execution, use the following command, specifying options as needed:

```bash
cd lookup_service_5.76-107.0
java -Xmx8000m -jar server-5.76-107.0-jetty-console.war  [--option=value] [--option=value]
```

**Example command:**

```bash
java -Xmx8000m -jar server-5.76-107.0-jetty-console.war --headless --port 8080
```

**Available Options:**

- `--sslProxied`: Running behind an SSL proxy.
- `--port n`: Create an HTTP listener on port `n` (default 8080).
- `--bindAddress addr`: Accept connections only on address `addr` (default: accept on any address).
- `--forwarded`: Set reverse proxy handling using X-Forwarded-For headers.
- `--contextPath /path`: Set context path (default: `/`).
- `--headless`: Don't open graphical console, even if available.
- `--help`: Print this help message.
- `--tmpDir /path`: Temporary directory, default is `/tmp`.

**Memory Allocation:**
The `-Xmx8000m` switch sets the available memory for Java to 8000MB. This is a recommended starting value and can be increased if the service is used heavily (tested up to -Xmx36000m).
```

--------------------------------

### Compile Hmmer 2 Binary

Source: https://interproscan-docs.readthedocs.io/en/v5/_sources/CompilingBinaries.rst

Instructions for downloading, compiling, and installing Hmmer 2. This process involves fetching the source code, configuring the build, and installing the binaries. The compiled binaries are then used by InterProScan for SMART analysis.

```shell
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
```

--------------------------------

### Testing InterProScan 5 Lookup Service

Source: https://interproscan-docs.readthedocs.io/en/v5/UserDocs

These examples show how to test if the InterProScan 5 lookup service is running correctly. Both web browser and curl commands are provided to query the '/version' and '/matches' endpoints. Replace 'localhost' with the actual machine name for remote access.

```bash
# in a web browser:
http://localhost:8080/version
http://localhost:8080/matches?md5=2E38C8D754C63117A4FA5F5E44F2194E
```

```bash
# or using curl on the command line:
curl http://localhost:8080/version
curl http://localhost:8080/matches?md5=2E38C8D754C63117A4FA5F5E44F2194E
```

--------------------------------

### Install libpcre2-dev library on Ubuntu

Source: https://interproscan-docs.readthedocs.io/en/v5/KnownIssues

This command installs the libpcre2-dev library on Ubuntu, which is required to resolve 'libpcre2.so: cannot open shared object file' errors when using Prosite/pfsearchV3.

```bash
sudo apt-get install -y libpcre2-dev
```

--------------------------------

### InterProScan Configuration for Licensed Databases

Source: https://interproscan-docs.readthedocs.io/en/v5/UserDocs

Example configuration for activating licensed member databases like Phobius, SignalP, and TMHMM in InterProScan. This involves setting signature library releases and specifying the path to the binary executable.

```properties
phobius.signature.library.release=1.01
binary.phobius.pl.path=bin/phobius/1.01/phobius.pl
```

--------------------------------

### Compile and install Coils binary

Source: https://interproscan-docs.readthedocs.io/en/v5/KnownIssues

Instructions for compiling and installing the Coils binary if the provided version is not compatible with the system. This involves navigating to the source directory, running make, and copying the compiled binary to the appropriate location.

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

--------------------------------

### Compile fingerPRINTScan Binary

Source: https://interproscan-docs.readthedocs.io/en/v5/_sources/CompilingBinaries.rst

Instructions for compiling the 'fingerPRINTScan' binary for PRINTS analysis within InterProScan. This process involves configuring the source code, building the binary, and potentially moving it to the correct location within the InterProScan directory structure. Detailed instructions are available in the INSTALL file.

```shell
cd src/prints/fingerprintscan/3597/
./configure
make
cd _interproscan_dir
```

--------------------------------

### Compile Hmmer 2 Binaries (Shell Script)

Source: https://interproscan-docs.readthedocs.io/en/v5/CompilingBinaries

This sequence of shell commands downloads, extracts, configures, and installs Hmmer version 2.3.2. This is useful if the pre-compiled Hmmer 2 binary causes issues with SMART analysis. It enables threading support during configuration.

```shell
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

```

--------------------------------

### Start InterProScan 5 Lookup Service (Java)

Source: https://interproscan-docs.readthedocs.io/en/v5/_sources/LocalLookupService.rst

Starts the InterProScan 5 lookup service using a Java executable. This command requires navigating to the service's directory and executing the specified JAR file. The `-Xmx` flag allocates memory, which can be adjusted based on usage. The service can be configured with various options.

```shell
cd lookup_service_5.76-107.0
java -Xmx8000m -jar server-5.76-107.0-jetty-console.war  [--option=value] [--option=value]
```

```shell
# Example command:
# java -Xmx8000m -jar server-5.76-107.0-jetty-console.war --headless --port 8080
```

--------------------------------

### InterProScan Convert Mode Example: XML to TSV Format

Source: https://interproscan-docs.readthedocs.io/en/v5/UserDocs

Shows a specific example of using InterProScan in 'convert' mode to convert an XML file to a single TSV format. This command uses '-i' for the input XML file and '-o' to explicitly define the output TSV file name.

```bash
./interproscan.sh -i /path/to/existing_output_file.xml -mode convert -f tsv -o /path/to/new_output_file.tsv

```

--------------------------------

### InterProScan 5 Convert Mode Examples (Bash)

Source: https://interproscan-docs.readthedocs.io/en/v5/ConvertMode

Demonstrates how to use the InterProScan 5 command-line tool in 'convert' mode. These examples show how to convert XML files to various other formats (TSV, GFF3, raw) using either a base output file name or an explicit output file name. Ensure the input XML file and output paths are correctly specified.

```bash
# Convert from XML format to all other available formats
./interproscan.sh -mode convert -f tsv,gff3,raw -i /path/to/existing_output_file.xml -b /path/to/output_file_basename

```

```bash
# Convert from XML format to TSV format (which automatically includes all available InterPro entry/GO term/pathways information)
./interproscan.sh -i /path/to/existing_output_file.xml -mode convert -f tsv -o /path/to/new_output_file.tsv

```

--------------------------------

### Scan Nucleic Acid Sequences with InterProScan 5

Source: https://interproscan-docs.readthedocs.io/en/v5/UserDocs

Use the '-t n' or '--seqtype n' flag to scan nucleic acid sequences (DNA/RNA) in InterProScan 5. The default sequence type is protein. This example shows the command-line usage.

```bash
# Command to scan nucleic acid sequences
./interproscan.sh -t n -i /path/to/nucleic_acid_sequences.fasta
```

```text
-t,--seqtype <SEQUENCE-TYPE>   Optional, the type of the input sequences (dna/rna (n) or protein (p)).  The default sequence type is protein.

```

--------------------------------

### Run InterProScan 5 with Graphical User Interface

Source: https://interproscan-docs.readthedocs.io/en/v5/LocalLookupService

Instructions for starting the InterProScan 5 lookup service with a graphical interface to set the port number.

```APIDOC
## Run with graphical user interface (to set port number)

If you are running it on a machine with a desktop interface and just want to test the lookup service, a simple user interface is included to allow you to set the port number to run the service.

Note that in the example below, the memory available to Java has been set to 8000MB (using the `-Xmx8000m` switch). This is recommended as a good starting value - you may choose to set this higher if the service will be used heavily. (We have tested it with -Xmx36000m without problems).

### Command
```bash
cd lookup_service_5.76-107.0
java -Xmx8000m -jar server-5.76-107.0-jetty-console.war
```

A new window will open. Set the port number as required and click the “Start” button to start the web service running.

The initialization of the web service usually takes a while, depending on the machine you are running it. After successful initialization you will be forwarded to the ‘InterProScan 5 Pre-calculated Match Lookup Service’ landing page within your browser and from now on the lookup service is ready to be used.
```

--------------------------------

### Check Perl Installation (Shell)

Source: https://interproscan-docs.readthedocs.io/en/v5/InstallationRequirements

Verifies the installation and version of Perl 5 on the system. A default installation is usually sufficient, but the command allows checking availability. This is a prerequisite for InterProScan.

```shell
perl -version
```

--------------------------------

### Run InterProScan Lookup Service with GUI

Source: https://interproscan-docs.readthedocs.io/en/v5/LocalLookupService

This command executes the InterProScan lookup service using a graphical user interface. It requires Java and the server JAR file. The command sets the maximum Java heap size to 8000MB, which can be adjusted based on usage. The GUI allows users to set the service port.

```bash
cd lookup_service_5.76-107.0
java -Xmx8000m -jar server-5.76-107.0-jetty-console.war
```

--------------------------------

### Check Python 3 Installation (Shell)

Source: https://interproscan-docs.readthedocs.io/en/v5/InstallationRequirements

Confirms that Python 3 is installed and reports its version. InterProScan version 5.70-102.0 onwards requires Python 3.8 or later. A default installation is typically adequate.

```shell
python3 --version
```

--------------------------------

### InterProScan 5 JSON Output Example

Source: https://interproscan-docs.readthedocs.io/en/v5/UserDocs

This JSON output represents the results of an InterProScan 5 analysis for a given sequence. It includes the InterProScan version, sequence details like MD5 hash, and a list of 'matches' detailing detected protein domains, their signatures, and locations. Dependencies include the InterProScan 5 software. Input is a protein or nucleotide sequence. Output is a structured JSON object.

```json
{
 "interproscan-version": "5.26-65.0",
"results": [{
 "sequence" : "MSKIGKSIRLERIIDRKTRKTVIVPMDHGLTVGPIPGLIDLAAAVDKVAEGGANAVLGHMGLPLYGHRGYGKDVGLIIHLSASTSLGPDANHKVLVTRVEDAIRVGADGVSIHVNVGAEDEAEMLRDLGMVARRCDLWGMPLLAMMYPRGAKVRSEHSVEYVKHAARVGAELGVDIVKTNYTGSPETFREVVRGCPAPVVIAGGPKMDTEADLLQMVYDAMQAGAAGISIGRNIFQAENPTLLTRKLSKIVHEGYTPEEAARLKL",
 "md5" : "88d47cc807fe8e977130b0cc93e0bd61",
 "matches" : [ { 
 "signature" : { 
 "accession" : "PIRSF038992",
 "name" : "Aldolase_Ia",
 "description" : null,
 "type" : null,
 "signatureLibraryRelease" : { 
 "library" : "PIRSF",
 "version" : "3.01"
 },
 "models" : { 
 "PIRSF038992" : { 
 "accession" : "PIRSF038992",
 "name" : "Aldolase_Ia",
 "description" : null,
 "key" : "PIRSF038992"
 }
 },
 "entry" : { 
 "accession" : "IPR002915",
 "name" : "DeoC/FbaB/lacD_aldolase",
 "description" : "DeoC/FbaB/ lacD aldolase",
 "type" : "FAMILY",
 "goXRefs" : [ { 
 "identifier" : "GO:0016829",
 "name" : "lyase activity",
 "databaseName" : "GO",
 "category" : "MOLECULAR_FUNCTION"
 } ],
 "pathwayXRefs" : [ { 
 "identifier" : "R-HSA-71336",
 "name" : "Pentose phosphate pathway (hexose monophosphate shunt)",
 "databaseName" : "Reactome"
 }, { 
 "identifier" : "R-HSA-6798695",
 "name" : "Neutrophil degranulation",
 "databaseName" : "Reactome"
 } ]
 }
 },
 "locations" : [ { 
 "start" : 1,
 "end" : 265,
 "hmmStart" : 2,
 "hmmEnd" : 262,
 "hmmBounds" : "INCOMPLETE",
 "evalue" : 3.3E-94,
 "score" : 302.6,
 "envelopeStart" : 1,
 "envelopeEnd" : 265
 } ],
 "evalue" : 3.0E-94,
 "score" : 302.7
 }, { 
 "..."
 }]
}
]
}
```

--------------------------------

### Test InterProScan 5 Lookup Service (HTTP/curl)

Source: https://interproscan-docs.readthedocs.io/en/v5/_sources/LocalLookupService.rst

Demonstrates how to test the InterProScan 5 lookup service once it has started. This includes accessing the service's version and performing a match lookup using an MD5 hash via a web browser or the curl command-line tool. It also explains how to access the service from other machines.

```shell
# in a web browser:
http://localhost:8080/version
http://localhost:8080/matches?md5=2E38C8D754C63117A4FA5F5E44F2194E

# or using curl on the command line:
curl http://localhost:8080/version
curl http://localhost:8080/matches?md5=2E38C8D754C63117A4FA5F5E44F2194E

# To access your lookup service from another machine replace "localhost" with
# the fully qualified name of the machine where the lookup service is running.
# The Linux command "uname -n" can be used to find the machine name.
# Alternatively you could use the machines IP address instead of the hostname.
```

--------------------------------

### Check C++ Compiler Version

Source: https://interproscan-docs.readthedocs.io/en/v5/_sources/CompilingBinaries.rst

Command to check the version of the C++ compiler installed on the system. A version of 4.8 or above is recommended for successful compilation of certain InterProScan binaries.

```bash
c++ --version
```

--------------------------------

### Run InterProScan 5 Headless (Command Line)

Source: https://interproscan-docs.readthedocs.io/en/v5/LocalLookupService

Instructions for running the InterProScan 5 lookup service as a command-line tool without a graphical interface.

```APIDOC
## Run “Headless” (no graphical user interface)

It is most likely that you will want to run the lookup service “headless”, i.e. purely as a command line tool. In this case, the port number and other options can be passed in on the command line as follows:

Note that in the example below, the memory available to Java has been set to 8000MB (using the `-Xmx8000m` switch). This is recommended as a good starting value - you may choose to set this higher if the service will be used heavily. (We have tested it with -Xmx36000m).

### Command
```bash
cd lookup_service_5.76-107.0
java -Xmx8000m -jar server-5.76-107.0-jetty-console.war  [--option=value] [--option=value]

# Example command:
# java -Xmx8000m -jar server-5.76-107.0-jetty-console.war --headless --port 8080
```

Where options include:

### Options
```
Options:
 --sslProxied        - Running behind an SSL proxy
 --port n            - Create an HTTP listener on port n (default 8080)
 --bindAddress addr  - Accept connections only on address addr (default: accept on any address)
 --forwarded         - Set reverse proxy handling using X-Forwarded-For headers
 --contextPath /path - Set context path (default: /)
 --headless          - Don't open graphical console, even if available
 --help              - Print this help message
 --tmpDir /path      - Temporary directory, default is /tmp
```
```

--------------------------------

### Copy FingerprintScan Binary

Source: https://interproscan-docs.readthedocs.io/en/v5/_sources/CompilingBinaries.rst

Command to copy the FingerprintScan binary to the designated location within the InterProScan 5 installation directory. This is typically done after compiling a custom version.

```bash
cp src/prints/fingerprintscan/3597/fingerPRINTScan bin/prints/
```

--------------------------------

### Run InterProScan Lookup Service Headless (Command Line)

Source: https://interproscan-docs.readthedocs.io/en/v5/LocalLookupService

This command runs the InterProScan lookup service in headless mode, suitable for command-line operations. It allows specifying various options, including port number, SSL proxy settings, and bind address. The example demonstrates setting heap size and provides a template for passing options.

```bash
cd lookup_service_5.76-107.0
java -Xmx8000m -jar server-5.76-107.0-jetty-console.war  [--option=value] [--option=value]

# Example command:
# java -Xmx8000m -jar server-5.76-107.0-jetty-console.war --headless --port 8080
```

--------------------------------

### Install libgomp1 library on Ubuntu

Source: https://interproscan-docs.readthedocs.io/en/v5/KnownIssues

This snippet shows how to install the missing libgomp1 library on Ubuntu systems to resolve CDD/RPSBlast errors. This is a common dependency for some Linux environments.

```bash
sudo apt-get install -y libgomp1
```

--------------------------------

### InterProScan 5 Command Line Usage

Source: https://interproscan-docs.readthedocs.io/en/v5/ConvertMode

Displays the general usage instructions for the InterProScan 5 command-line tool. This includes information on Java memory settings, jar file execution, and a comprehensive list of available options for file input, output, and mode selection. It also provides copyright and licensing information.

```bash
./interproscan.sh -mode convert

```

```text
Welcome to InterProScan 5RC7
usage: java -XX:+UseParallelGC -XX:+AggressiveOpts
            -XX:+UseFastAccessorMethods -Xms512M -Xmx2048M -jar
            interproscan-5.jar

Please give us your feedback by sending an email to
interhelp@ebi.ac.uk
 -b,--output-file-base <OUTPUT-FILE-BASE>   Optional, base output filename
                                            (relative or absolute path).
                                            Note that this option and the
                                            --outfile (-o) option are
                                            mutually exclusive.  The
                                            appropriate file extension for
                                            the output format(s) will be
                                            appended automatically. By
                                            default the input file
                                            path/name will be used.
 -d,--output-dir <OUTPUT-DIR>               Optional, output directory.
                                            Note that this option and the
                                            --outfile (-o) option or the
                                            --output-file-base (-b) option
                                            are mutually exclusive. The
                                            appropriate file extension for
                                            the output format(s) will be
                                            appended automatically. By
                                            default the input file
                                            path/name will be used.
 -f,--formats <OUTPUT-FORMATS>              Optional, case-insensitive,
                                            comma separated list of output
                                            formats. Supported formats are
                                            TSV, XML, JSON, and GFF3.
                                            Default for protein sequences
                                            are TSV, XML and GFF3, or
                                            for nucleotide sequences
                                            GFF3 and XML.
 -i,--input <INPUT-FILE-PATH>               Optional, path to fasta file
                                            that should be loaded on
                                            Master startup. Alternatively, 
                                            in CONVERT mode, the
                                            InterProScan 5 XML file to
                                            convert.
 -o,--outfile <EXPLICIT_OUTPUT_FILENAME>    Optional explicit output file
                                            name (relative or absolute
                                            path).  Note that this option
                                            and the --output-file-base (-b)
                                            option are mutually exclusive. If this option is
                                            given, you MUST specify a
                                            single output format using the
                                            -f option.  The output file
                                            name will not be modified.
                                            Note that specifying an output
                                            file name using this option
                                            OVERWRITES ANY EXISTING FILE.
 -T,--tempdir <TEMP-DIR>                    Optional, specify temporary
                                            file directory (relative or
                                            absolute path). The default
                                            location is temp/.
Copyright (c) EMBL European Bioinformatics Institute, Hinxton, Cambridge,
UK. (http://www.ebi.ac.uk) The InterProScan software itself is provided
under the Apache License, Version 2.0
(http://www.apache.org/licenses/LICENSE-2.0.html). Third party components
(e.g. member database binaries and models) are subject to separate
licensing - please see the individual member database websites for
details.

```
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