InterProScan logo README  FAQ
RELEASE v4.0 by Emmanuel Quevillon, Ville Silventoinen and Florence Servant


What is InterProScan?
I've just started using InterPro for domain searches. Is there a downloadable version of InterPro for high throughput tasks i.e. without the limit for on-line submission. And if so, would all the databases have to be downloaded as well.
How is the package relates to the WWW interface at http://ebi.ac.uk/InterProScan ?
What are the terms for commercial companies to use InterProScan?
Which computing platforms are supported in the InterProScan package?
How can I get InterProScan locally?
Can I submit a nucleic acid sequence to the analysis?
I've found that not all matches from .output files are parsed into .raw files. Are you using additional filtering? Which cut-offs are you using to scan against Pfam?
What does the status flag mean?
How can I plug in SignalP / TMHMM predictions?
I am having problem with FingerPRINTScan on my Linux.
I am getting messages like: Can't locate loadable object for module DB_File in @INC ... or Can't locate auto/DB_File/autosplit.ix in @INC ... or the error message "your libdb and db.h file are not compatible"
I know that I have to make the installation visible to all machines through NFS, but then I am asked the name of an execution host and not of several execution hosts (which is what I expected). Without having a queuing system is it possible to use several hosts to work on a batch of sequences submitted to iprscan?
Do i have to start the jobs from the 'execution host' or is it possible to start them from any host?
What to do to change the url of the InterProScan server to my domain ?
I would like to use binary file for all my hmmer applications. How can I do this and have I to change something in configuration files?
The index_data.pl gives some errors when it is running. What should I do to stop it doing this?
I get less results with BlastProDom using my local InterProScan installation than when I use EBI InterProScan. What's wrong?
The SGI is an O2 running IRIX 6.5.12 and I am getting: .../iprscan/bin/IRIX/hmmpfam: cannot execute
Can I use more up to date source databases like PFAM 14.0 and others?
How to replace EMBOSS tools to reformat and translate nucleic sequences?
I have EMBOSS package installed and also seqret and sixpack but I get errors from InterProScan about them. What is the problem?
I would like to avoid removing of some session directories InterProScan created. Can I do it quickly?
I would like to configure some limits for maximum of input sequences given by the user. Is this possible?
I don't really understand how the configuration files work. Is it possible to change something or edit them?
I am using a queueing system, I looked at the configuration file but I don't understand what are the special tag 'optqueue' and 'optresource'
InterProScan gives me a report file containing some errors from FingerPRINTScan that are weird like : ERROR: Calculation has exceeded maximum allowed complexity Fingerprint PRICHEXTENSN matches this sequence
I would like to apply a time limit to running jobs How can I do it?
I would like to have some different right on the session directory to avoid other people to look in my session directory.
I would like to use more than one cpu for my hmmer searches using InterProScan. Is it possible to configure it?
How to use taxonomy filtering? How does it work?



=======================
What is InterProScan?
=======================
Top
InterProScan is a tool that combines different protein
signature recognition methods native to the InterPro member
databases into one resource with look up of corresponding 
InterPro and GO annotation.

See & cite:
Zdobnov E.M. and Apweiler R. "InterProScan - an integration
platform for the signature-recognition methods in InterPro"
Bioinformatics, 2001, 17(9): p. 847-8.

InterPro documentation: http://www.ebi.ac.uk/interpro/

========================================================
I've just started using InterPro for domain searches.
Is there a downloadable version of InterPro for high
throughput tasks i.e. without the limit for on-line
submission.
And if so, would all the databases have to be downloaded as
well.
========================================================
Top
Yes, we provide a stand alone solution optimized to bulk jobs.
Have a look at ftp://ftp.ebi.ac.uk/databases/interpro/iprscan/
where you will find all required data and executables.

The installation does not require any additional databases or root
privileges.

=====================================================
How is the package relates to the WWW interface at
http://ebi.ac.uk/InterProScan ?
=====================================================
Top
The WWW interface at EBI is based on standalone version with
the checksum option (crc64) on by default and some limitations for
user input sequences number and length.
The Perl-based version does not have any internal limitations unless
you want to fix some using the configuration file (iprscan.conf).
The architecture benefits from network distributed computing with
support of several UNIX systems (LSF, OpenPBS, SGE).


=====================================================
What are the terms for commercial companies to use InterProScan?
=====================================================
Top
Here is an extract from InterPro documentation:

InterPro - Integrated Resource Of Protein Domains And 
Functional Sites
Copyright (C) 2001 The InterPro Consortium.

This manual and the accompanying database may be copied and
redistributed freely, without advance permission, provided that 
this Copyright statement is reproduced with each copy.

The InterProScan software is distributed under GNU license as the
included scanning tools.

Therefore you do not need a special license for commercial use
but please cite the resource and keep the Copyright statement.

=====================================================
Which computing platforms are supported in the InterProScan
package?
=====================================================
Top
The InterProScan package has been developed in Perl5 under UNIX.
We provide precompiled binaries for :

   -DEC Alpha
   -Linux PC
   -SGI
   -SunOS
   -AIX
   -Darwin (MacOSX) 

See: 'System requirements' section in README file.

=====================================================
How can I get InterProScan locally?
=====================================================
Top
Go to ftp://ftp.ebi.ac.uk/databases/interpro/iprscan/
and download the following files:
iprscan_vX.tar.gz - the InterProScan itself
iprscan_data.tar.gz - databases used by the InterProScan
and one or more iprscan_bin_XXX.tar.gz - executables of signature 
scanning applications specific to the UNIX platform(s) you are 
going to use.

See: README file.

=====================================================
Can I submit a nucleic acid sequence to the analysis?
=====================================================
Top
Yes. It will be translated and scanned in all 6 frames without
any further assumptions except transcript length cut-off (orfminsize).
and/or codon translation table of EMBOSS sixpack tool:

      0 	(Standard)
      1 	(Standard (with alternative initiation codons))
      2 	(Vertebrate Mitochondrial)
      3 	(Yeast Mitochondrial)
      4 	(Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma)
      5 	(Invertebrate Mitochondrial)
      6 	(Ciliate Macronuclear and Dasycladacean)
      9 	(Echinoderm Mitochondrial)
      10 	(Euplotid Nuclear)
      11 	(Bacterial)
      12 	(Alternative Yeast Nuclear)
      13 	(Ascidian Mitochondrial)
      14 	(Flatworm Mitochondrial)
      15 	(Blepharisma Macronuclear)
      16 	(Chlorophycean Mitochondrial)
      21 	(Trematode Mitochondrial)
      22 	(Scenedesmus obliquus)
      23 	(Thraustochytrium Mitochondrial)

If you wish more sophisticated protein sequence predictions replace or
modify conf/sixpack.sh script and the command line for the translation
in conf/iprscan.conf file (See 'How to replace EMBOSS tools'). 


=====================================================
I've found that not all matches from .output files are parsed into
.raw files. Are you using additional filtering?
Which cut-offs are you using to scan against Pfam?
=====================================================
Top
Yes. InterProScan implements additional filtering for Pfam, PRINTS 
and Smart databases. 

Pfam:
each Pfam HMM model has its own cut-off scores for each domain match 
and the total model match. These bit score cut-offs are defined in 
the GA lines of the Pfam database. Initial results are obtained with 
quite a high common cut-off and then the matches (of the signature or 
some of its domains) with a lower score than the family specific 
cut-offs are dropped.

PRINTS:
there is a test version of PRINTS families specific p-value cut-offs.
All matches with p-value more than p_min for the signature are dropped.

Smart:
Smart filtering implements the same algorithm as the SMART web site.
NOTE: that the smart.thresholds and smart.desc data files are not publicly distributed 
so you are not getting the filtering by default.

See: README 'Results filtering / Match status' section.

=====================================================
What does the status flag mean?
=====================================================
Top
InterProScan supports two flags:
'T' means that we believe it is a true positive match and
'?' means that we are not so sure :)

As a result of manual curation InterPro supports more values for status.
See: InterPro documentation.

=====================================================
How can I plug in SignalP / TMHMM predictions?
=====================================================
Top
The InterProScan package provides all required scripts/parsers
for the methods but you have to contact the authors to get the
programs and data since they are not publicly available.

Intallation:
SignalP : 1) Save the signalpshell script (well configured)into iprscan/bin/binaries 
	     or made a soft link to your installation. 
	  2) You should not have to do anything with data as they are in your
	     signalp-vxx package by default and signalp shell script is pointing on.
	  3) Open iprscan/conf/signalp.conf file and check if all the path etc are ok.
	     You can use different versions of SignalP: v1.X, v2.X or newer.
	     To do so, open iprscan/conf/signalp.conf and search for signalp.version tag.
	     Then, change value (1-> v1.X, 2-> v2.X or newer).

	  NOTE: SignalP version 2.0 and newer have limitations in the number of submitted sequences
		to 4000.
		If you don't want any restrictions you can try to hack the code editing signalp
		shell script (suggestion). Search for:

		# Maximal number of sequences (command line and WWW):
		# Leave it empty of you don't want any limitations for the max number of input sequence (huge analysis).
		# Default (4000)
		#MAXSEQ=4000
		MAXSEQ=
		MAXWWWSEQ=4000

		#We check if the $MAXSEQ is set. If not it means we don't want any limitations in the number
		#of input sequences. 
		if [ "$MAXSEQ" != "" ] 
		then
			if [ $NSEQ -gt $MAXSEQ ]
			then
				echo signalp: too many sequences, the limit is $MAXSEQ
				exit 1
			elif [ "$WWW" -a \( "$NSEQ" -gt "$MAXWWWSEQ" \) ]
			then
				cat $SIGNALP/doc/wwwtoomany.html | sed 's/_NUM_/'$MAXWWWSEQ'/'
				exit
			fi	
		fi


TMHMM :   1) Save decodeanhmm binary in iprscan/bin/binaries or make a soft link to your
	     installation.
	  2) Save TMHMM2.X.X.model in your iprscan/data directory.
	  3) Uncomment the applications in the header of CONFIG.pl and run it.

BOTH) Edit configuration file tags (signalp.conf) to reflect your system. (queue : local/lsf42/pbs54/sge)
      and host.exec for local implementation or queue.name and/or resource for queueing systems.
      Have a look at other applications configuration file already set.

See: README for the relevant URLs and references.


=====================================================
I am having problem with FingerPRINTScan on my Linux.
=====================================================
Top
Try change the binaries to the correct one from
ftp://proline.sbc.man.ac.uk/pub/fingerPRINTScan/ .


=====================================================
I am getting messages like:
Can't locate loadable object for module DB_File in @INC ... or
Can't locate auto/DB_File/autosplit.ix in @INC ... or
the error message "your libdb and db.h file are not compatible"
=====================================================
Top
Check your installation of DB_File.pm & BerkeleyDB (both are
required and not a part of the InterProScan distribution). 
This module is an interface to Berkeley DB and available as a part
of standard Perl distribution or from CPAN.

Check that dynaloader actually picks it up.

=====================================================
I know that I have to make the installation visible to all
machines through NFS, but then I am asked the name of an
execution host and not of several execution hosts (which is
what I expected).
Without having a queuing system is it possible to use several
hosts to work on a batch of sequences submitted to iprscan?
=====================================================
Top
Without queuing system you can configure InterProScan to perform
scanning of different methods on different hosts (a method per host) 
in parallel. In case of queuing system you are asked for a
submission host.


=====================================================
Do i have to start the jobs from the 'execution host' or is it
possible to start them from any host?
=====================================================
Top
You can start it from any host which can do rsh to the
'execution host'.
Check that you have access to each host you want to run applications on
using 'rsh THE_HOST hostname' for example.
You could be also asked to edit the file called .rhost on each host
to allow connection to other host.
(e.g. : to allow connection from foo.bar.com to blah.co.uk as john user
your .rhost on blah must contain something like : 'foo.bar.com john').


=====================================================
What to do to change the url of the InterProScan server to my domain ?
=====================================================
Top
Go to your iprscan/conf directory and edit iprscan.conf 'workserver' tag :
Old value (http://fido.ebi.ac.uk:4000) to your domain (http://foo.bar.com).

workserver=http://fido.ebi.ac.uk:4000 => workserver=http://foo.bar.com

You can precise a specific port to listen and also put a https url.


=====================================================
I would like to use binary file for all my hmmer
applications. How can I do this and have I to change
something in configuration files?
=====================================================
Top
You can convert easily all your hmmer datafile to a binary version which can
speed up to 40% the execution of hmmpfam.
To do this, you just need to run iprscan/bin/index_data.pl giving the file(s)
you want to convert (option -f) (type ./index_data.pl -h to see which file are supported 
and you can convert) and tell script to run binary conversion (option -bin).
This binary conversion uses hmmconvert, if not present into your bin archive, please download
the hmmer package from http://hmmer.wustl.edu/ for your platform and copy it into iprscan/bin/binaries.
When all the conversions are done, you will need to edit application configuration
file that use hmmpfam (hmmpfam.conf, hmmcath.conf, hmmsmart.conf, hmmtigr.conf, superfamily.conf)
by changing the name of the data(base/file) adding '.bin' at the end :

hmmfile=[%env IPRSCAN_HOME]/data/Pfam => hmmfile=[%env IPRSCAN_HOME]/data/Pfam.bin
NOTE: For superfamily the name of the file is superfamily.hmm => superfamily.hmm.bin


=====================================================
The index_data.pl gives some errors when it is
running. What should I do to stop it doing this?
=====================================================
Top
Error can be from multiple cases:

->ERROR: No action precised to do (indexing or binary conversion?)
	 You have to tell the script what you want it to do for you
	 This script can be used to index data file for InterProScan
	 (-inx option) or used to convert ascii hmm model files to
	 binary (-bin option) to speed up the analysis up to 40%.

->ERROR: No path set for configuration file
	 It means either your 'iprscan.home' tag is not set in your
	 iprscan.conf file or value '$ENV{IPRSCAN_HOME}' is not set.
	 Check the 'BEGIN' statement at the begining of the script to
	 know if it point to the right directory where InterProScan
	 is installed.

->ERROR: File [XX] not found : No such file or directory
	 Check if the file XX is in your data directory or
	 if you made a soft link check if the link is still
	 correct.

->ERROR: This file [YYY] is not supported by InterProScan
	 This file is not in the list of indexed file that
	 InterProScan uses. You can have a list of supported files
	 typing './index_data.pl -h'.
	 If you want to index this file see section 'How to index new file'.

->ERROR: No tag input record delimeter [recdel.interpro] configured in index.conf
	 Check in index.conf file that the tag is set. It should be set at ''

->ERROR: Index file and output file have different size, index out of date?
	 A previous indexed file already exists but does not fit with the original
	 datafile. Find which on of both file is the newer (indexed or datafile).
	 If you want to create a new indexed file with from a new datafile, file check DATA UPDATE
	 in the README.
	 If you want to recreate an index from an old datafile, use -iforce option to force
	 the script to remove old index file and create a new one.

->ERROR: Cannot convert XX, hmmconvert binary does not exist or not executable : No such file or directory
	 Check that your bin/binaries/hmmconvert binary exists or the soft link you could have created is there.

=====================================================
I get less results with BlastProDom using my local InterProScan installation
than when I use EBI InterProScan. What's wrong?
=====================================================
Top
Actually this is not an error.
EBI InterProScan uses a larger file from ProDom (prodom.mul available for download from ProDom webiste)
which contains all the ProDom entries.
Standalone InterProScan uses a smaller file (prodom.ipr) which contains only ProDom entries integrated
into InterPro. That explains why on EBI web site appear some entries marked as 'unitegrated' which are not 
in prodom.ipr because they are not integrated into InterPro.


=====================================================
The SGI is an O2 running IRIX 6.5.12 and I am getting:
.../iprscan/bin/IRIX/hmmpfam: cannot execute
=====================================================
Top
Try type `uname` on your system and if the result is 'IRIX' do
the following (the distribution includes IRIX64 binaries):
1. `mv .../iprscan/bin/IRIX64 .../iprscan/bin/IRIX`
2. download & untar binaries for IRIX for hmmer from their
homepage;
`cp ..../bin/hmmpfam .../iprscan/bin/IRIX/`


=====================================================
Can I use more up to date source databases like PFAM 14.0 and
others?
=====================================================
Top
Just save the updated files under the same names and run index_data.pl manually.
The only problem is that you will be getting hits from signatures without corresponding 
InterPro records (referred as NULL as none integrated yet).

See: header of interpro.xml file.


=====================================================
How to replace EMBOSS tools to reformat
and translate nucleic sequences?
=====================================================
Top
Well, we integrated and developped new InterProScan using EMBOSS tools (two of them)
because they are fast, robust, free, maintained and used by a lot of people. 
But it is up to you if you don't want to used them. You can use your own tools to reformat
(not mandatory) or translate your sequences.
If you don't want to reformat sequence, you might have some problems with header of certain
sequences, they could produce error with certain applications.

Formatting sequences:
---------------------

  Open iprscan/conf/iprscan.conf file. Search for 'formatcmd'.
  The Original format sequence command is contained into a shell script calling
  seqret tool from EMBOSS package.
  This script reads the input sequences and write them to the InterProScan output sequence file.

     formatcmd=[%env IPRSCAN_HOME]/conf/seqret.sh  $in > $out

  So, to put your own formatting script (let's call it myscript):
  You can wrap it into a shell script, (like we did for seqret, have a look at the
  shell script to see how we did) or have a simple script taking options. You can put
  it in the bin directory as well(iprscan/bin).
  Also, [%env IPRSCAN_HOME] can be replaced by another path where your script is located.
  [%env IPRSCAN_HOME] referres to IPRSCAN_HOME environment variable which is the path where
  InterProScan is installed.

     formatcmd=[%env IPRSCAN_HOME]/[bin|conf]/myscript [options?] $in > $out

     [options] : It is the eventual option your script could need to get the input sequence
     as a parameter (e.g. -i, -input , -seqfile .....).
     NOTE: - Leave '$in' as it is. It is converted by InterProScan by the real path of the
	     input sequence file.
	     So the command would be : myscript -i $in > $out.
	   - Your script MUST be able to write the results on the standard output or to write
	     the results into a specified file. BUT IN ALL CASES, you must leave '$out' as it is,
	     the is the output file where the results will be, InterProScan will replace it by the
	     right name of the file. So, your different case could be:
		   myscript -i $in [ > $out | -o $out | -output $out | -out $out ...]


Translate sequences:
--------------------

  Open iprscan/conf/iprscan.conf file. Search for 'translatecmd'.
  The original translate sequences command is contained into a shell script calling
  sixpack tool form EMBOSS package.
  This script reads the input sequences and write the translated to the InterProScan translated output.

       translatecmd=[%env IPRSCAN_HOME]/conf/sixpack.sh -table $table -orfminsize $trlen  -outseq $out $in
 
  So, to put your own translating tool, you can either wrap it with a shell script which will call the right
  options (in case in your script needs some) or just litteraly write the whole command line.
  Your script can be installed either in conf or bin directory and executable.
  Also, [%env IPRSCAN_HOME] can be replaced by another path where your script is located.
  [%env IPRSCAN_HOME] referres to IPRSCAN_HOME environment variable which is the path where
  InterProScan is installed.
   
     translatecmd=[%env IPRSCAN_HOME]/[bin|conf]/myscript [options?]

     [options] : It is the eventual option your script could need to get the input sequence
     as a parameter (e.g. -i, -input , -seqfile .....).
     NOTE: - Leave '$in' and $out as they are. It is converted by InterProScan by the real path of the
	     input and output file.
	   - Additionaly, you can precise (or not) a translation table (see http://www.ebi.ac.uk/cgi-bin/mutations/trtables.cgi)
	     and also a minimum length for the translated sequence (-table and -orfminsize in our exmaple).
	     BUT, if you have such option for table code value and minimum orf length, you will have to use $table and $trlen
	     as value for the options of your scirpt as InterProScan will replace them automatically when reading the
	     configuration file (e.g. : myscript -i $in -out $out -tablevalue $table -minlengthforORF $trlen).

If you have problem, contact interhelp@ebi.ac.uk
	

=====================================================
I have EMBOSS package installed and
also seqret and sixpack but I get errors
from InterProScan about them.
What is the problem?
=====================================================
Top
Check environment variable  called EMBOSS_ROOT and EMBOSS_ACDROOT in seqret and sixpack
shell scripts located into your iprscan/conf directory. Make sure that these values point
to the right directory. EMBOSS_ROOT is the root directory where your EMBOSS package is
installed and EMBOSS_ACDROOT is the directory where acd directory (needed for all EMBOSS
applications) is needed.

=====================================================
I would like to avoid removing of some
session directories InterProScan created.
Can I do it quickly?
=====================================================
Top
Yes :) of course, editing iprscan/conf/tooldefault.conf. Search for 'dirmode' tag
and put the rights you want (default is 775).
You can change the umask values as well.


=====================================================
I would like to configure some limits for maximum of input sequences given by the user.
Is this possible?
=====================================================
Top
Yes. You can do it when you install InterProScan or if you skipped it during installation
you can do it manually editing iprscan.conf file.
You can limit:

    - Maximum number of proteic input sequences changing value of 'maxinputseqs.aa'.
    - Maximum number of nucleic input sequences changing value of 'maxinputseqs.nt'.
    - Maximum length of nucleic input sequences changing value of 'maxseqlen.nt'.
    - Minimum length of proteic input sequences changing value of 'minseqlen.aa'.

and also give the default value of the minimum length for an ORF ('minorfsize') when nucleic
sequences are translated, thus that the default codon table value to use for translation
('codon.table').

=====================================================
I don't really understand how the configuration files work.
Is it possible to change something or edit them?
=====================================================
Top
Yes they have been made for it :).
Configuration files are based on 'tags' that are expandable when InterProScan is reading them.
What we call a tag? For example in the following lines :

workserver=http://fido.ebi.ac.uk:4000
workurl=[%workserver]/iprscan/iprscan?tool=iprscan&jobid=....

workserver is a key and http://fido.ebi.ac.uk:4000 is the value. In the next line,
[%workserver] is a tag. So when InterProScan reads a configuration file, it reads it as key-value pair
file. When it see something on the line looking like '[%.....]', it understands it as a tag and try to
to expand/replace it in its memory and searches if it already seen this key somewhere. If yes, it replace
the tag '[%...]' by its value, otherwise it replace it by nothing. That's why, each time you want to use
a tag in a value to avoid repeat it, you HAVE TO SET IT correctly before as file are read from top to bottom.

In that case, workurl will be :
http://fido.ebi.ac.uk:4000/iprscan/iprscan?tool=iprscan&jobid=....
after expanding.

InterProScan support conditions in its tags. Here is a list. To know how to write them correctly,
you will have to read the code of Config.pm module (iprscan/lib/Dispatcher/Config.pm).

-%env      -> referres to environment variable hash table in Perl (%ENV).
-%if       -> you can do some condition into your tags.
-%switch   -> you can have mutiple choices (same as basic switch condition in programing).
-%random   -> calls the srand Per subroutine.
-%YYYY     -> translates it as the actual year.
-%MM       -> translates it as the current month of the year.
-%DD       -> translates it as the current day of the month.
-%hh       -> translates it as the current hour of the day.
-%mm       -> translates it as the current minutes of the hour.
-%ss       -> translates it as the current second of the minute.
-%hostname -> translates it as the hostname of the machine.
-%pid      -> translates it with the process id of the program.
-%uname    -> translates it with the operating system name.

With all of these features, you should be able to modify/configure InterProScan and applications
as you want.


=====================================================
I am using a queueing system, I looked at the
configuration file but I don't understand what
are the special tag 'optqueue' and 'optresource'
=====================================================
Top
'optqueue' is the queue name to use for an application
for example and optresource is the name of a resource
to use for this application. If you don't know what are
this terms, contact you system administrator.

Each time an application is launched, InterProScan reads its
configuration file, and launches the job. To launch the job, it
looks what is the method to do it. Queue or Local implementation?
This is mentionned in the tag 'queue' of each applications.
Then, if the queue is a queue like LSF for example (lsf42.conf)
then it launches the application using lsf command and specific queue
name and resource on the command line if specified in the application
configuration file (search for 'resource' and 'queue.name').
Thus in the command line of lsf, optqueue is replaced by the value
of the 'queue.name' tag (for this application) and optresource is then
replaced by 'resource' tag (for this application).


=====================================================
InterProScan gives me a report file containing
some errors from FingerPRINTScan that are weird
like : ERROR: Calculation has exceeded maximum allowed complexity
Fingerprint PRICHEXTENSN matches this sequence
=====================================================
Top
This is not a real error, this is just a warning. Don't worry about it.


=====================================================
I would like to apply a time limit to running jobs
How can I do it?
=====================================================
Top
If is quite simple. Edit iprscan.conf and put 'job.time.limit' to 1.
Then configure the two following tags, 'poolinterval' (sleeping time in seconds
between two checking jobs) and maxpollrounds (number of checking jobs).

NOTE: BE AWARE THAT THIS CONFIGUATION IS NOT POSSIBLE WITH INSTALLTIONS USING
----- 'local' QUEUE!!! (MAYBE LATER).

=====================================================
I would like to have some different right on the session directory
to avoid other people to look in my session directory.
=====================================================
Top
Easy ;)!! Actually, the rights for the date and session directories
is stored in tooldefault.conf file under 'dirmode' tag. Default
value for this tag is 777 and the umask is set to 000. So this means
that anybody can creates/remove any directory under iprscan/tmp.
If you want to protect session directory, open iprscan.conf and
edit 'usermode' to put the value you want. If not value is set,
iprscan will use the default one stored in tooldefault.conf.

======================================================
I would like to use more than one cpu for my hmmer searches
using InterProScan. Is it possible to configure it?
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Top
Yes of course. Applications using hmmpfam or hmmsearch are configurable.
You just need to update/change the tag 'cpu_opt' in the applicaton's
configuration file you want to update/change.
Configuration file supporting this option are listed below :

- gene3d.conf      (GENE3D)
- hmmpanther.conf  (Panther)
- hmmpir.conf      (PIR superfamily)
- hmmpfam.conf     (Pfam)
- hmmsmart.conf    (Smart)
- hmmtigr.conf     (Tigr)
- superfamily.conf (SCOP/SUPERFAMILY)

If this tag 'cpu_opt' value is empty (default) the '--cpu' option is not used.

NOTE: By default, PIR is set to '--cpu 1'. 
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How to use taxonomy filtering?
How does it work?
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Top
The taxonomy filtering is based on InterPro entry taxonomy.
InterProScan does it current work, searching your sequence against
InterPro members databases. When all analysis are done, InterProScan
perform a post processing of the results based on the taxonomy found
for each InterPro entries found for your sequence(s).

e.g:

Your sequence (RS16_ECOLI) is analysed against Pfam and ProDom.
Hits returned are :

Pfam   : PF00886 
ProDom : PD003791

and associated InterPro entries:

IPR000307

Taxonomy for IPR000307 is listed below.

Arabidopsis thaliana
Archaea
Arthropoda
Bacteria
Caenorhabditis elegans
Chordata
Cyanobacteria
Eukaryota
Fruit Fly
Fungi
Green Plants
Human
Metazoa
Mouse
Nematoda
Other Eukaryotes
Plastid Group
Rice spp.
Saccharomyces cerevisiae
Synechocystis PCC 6803

For each hits, 2 different cases can happen.
AND rule :
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    If all the taxonomy selected by the user is not present in the InterPro entry,
    then the hit (PF00886, or PD003791) is rejected and not shown as result.
OR rule :
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    If one of the taxonomy name selected by the user is present on the InterPro entry,
    then the hit (PF00886, or PD003791) is conserved and shown to the user.
   
NOTE:  If you do not wish to use taxonomy and make it unavailable for users, just edit iprscan.conf
       and set the value 0 for the tag 'taxonomy.use'.