====== Trinotate ======

* Install **SignalP**
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Download from http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?signalp
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<code>
cat signalp-4.1c.Linux.tar.Z | uncompress | tar xvf -
mv signalp-4.1 /usr/local/bin/
nano -w /usr/local/bin/signalp-4.1/signalp
</code>
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<code>
###############################################################################
#               GENERAL SETTINGS: CUSTOMIZE TO YOUR SITE
###############################################################################

# full path to the signalp-4.1 directory on your system (mandatory)
BEGIN {
    $ENV{SIGNALP} = '/usr/local/bin/signalp-4.1';
}

# determine where to store temporary files (must be writable to all users)
my $outputDir = "/home/temp";

# max number of sequences per run (any number can be handled)
my $MAX_ALLOWED_ENTRIES=2000000;
</code>
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<code>
ln -s /usr/local/bin/signalp-4.1/signalp /usr/local/bin/
chown -R root:root /usr/local/bin/signalp-4.1
chmod -R 755 /usr/local/bin/signalp-4.1

cp /usr/local/bin/signalp-4.1/signalp.1 /usr/local/share/man/man1/
</code>
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Test (as USER)
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<code>
signalp -t euk -f short /usr/local/bin/signalp-4.1/test/euk10.fsa > euk10.fsa.short_out
diff euk10.fsa.short_out /usr/local/bin/signalp-4.1/test/euk10.fsa.short_out

signalp -t euk -f long /usr/local/bin/signalp-4.1/test/euk10.fsa > euk10.fsa.long_out
diff /usr/local/bin/signalp-4.1/test/euk10.fsa.long_out euk10.fsa.long_out

signalp -t euk -f all /usr/local/bin/signalp-4.1/test/euk10.fsa > euk10.fsa.all_out
diff /usr/local/bin/signalp-4.1/test/euk10.fsa.all_out euk10.fsa.all_out

signalp -t euk -f summary /usr/local/bin/signalp-4.1/test/euk10.fsa > euk10.fsa.summary_out
diff /usr/local/bin/signalp-4.1/test/euk10.fsa.summary_out euk10.fsa.summary_out

man signalp

signalp -h
</code>
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<code>
  Description: Predict signal peptide and cleavage site.

  Usage: /usr/local/bin/signalp -f <format>  -p <graphics-type> -k -s <networks> -t <organism-type> -m <fasta-file> -n <gff-file> -v -l <logfile> -u <value>  -U <value> -w -h -c <value> -T <temp dir> -V <fasta-file(s)>
  Options:
  -f   Setting the output format ('short', 'long', 'summary' or 'all'). Default: 'short'
  -g   Graphics 'png' or 'png+eps'. Default: 'Off'
  -k   Keep temporary directory. Default: 'Off'
  -s   Signal peptide networks to use ('best' or 'notm'). Default: 'best'
  -t   Organism type> (euk, gram+, gram-). Default: 'euk'
  -m   Make fasta file with mature sequence. Default: 'Off'
  -n   Make gff file of processed sequences. Default: 'Off'
  -T   Specify temporary file directory. Default: /home/temp
  -w   web predictions. Default: 'Off'
  -u   user defined D-cutoff for noTM networks
  -U   user defined D-cutoff for TM networks
  -M   Minimal predicted signal peptide length. Default: [10]
  -c   truncate to sequence length - 0 means no truncation. Default '70'
  -l   Logfile if -v is defined. Default: 'STDERR'
  -v   Verbose. Default: 'Off'
  -V   Print SignalP version and exit
  -h   Print this help information
</code>
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* Install **TMHMM**
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Download from http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?tmhmm
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<code>
cat tmhmm-2.0c.Linux.tar.gz | uncompress | tar xvf -
mv tmhmm-2.0c /usr/local/bin/
chown -R root:root /usr/local/bin/tmhmm-2.0c
chmod -R 755 /usr/local/bin/tmhmm-2.0c
nano -w /usr/local/bin/tmhmm-2.0c/bin/tmhmm
</code>
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<code>
#!/usr/bin/env perl

# This is version 2.0c of tmhmm
...
# full path to the main directory of the software
#$opt_basedir = "/usr/cbs/packages/tmhmm/2.0c/tmhmm-2.0c/";
$opt_basedir = "/usr/local/bin/tmhmm-2.0c/";
</code>
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<code>
nano -w /usr/local/bin/tmhmm-2.0c/bin/tmhmmformat.pl
</code>
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<code>
#!/usr/bin/env perl

# This is version 2.0c of tmhmmformat.pl
</code>
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<code>
ln -s /usr/local/bin/tmhmm-2.0c/bin/tmhmm /usr/local/bin/
ln -s /usr/local/bin/tmhmm-2.0c/bin/tmhmmformat.pl /usr/local/bin/
ln -s /usr/local/bin/tmhmm-2.0c/bin/decodeanhmm.Linux_x86_64 /usr/local/bin/tmhmm-2.0c/bin/decodeanhmm
ln -s /usr/local/bin/tmhmm-2.0c/bin/decodeanhmm /usr/local/bin/
</code>
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Test (as USER)
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<code>
nano -w seq.fasta
</code>
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<code>
>5H2A_CRIGR you can have comments after the ID
MEILCEDNTSLSSIPNSLMQVDGDSGLYRNDFNSRDANSSDASNWTIDGENRTNLSFEGYLPPTCLSILHL
QEKNWSALLTAVVIILTIAGNILVIMAVSLEKKLQNATNYFLMSLAIADMLLGFLVMPVSMLTILYGYRWP
LPSKLCAVWIYLDVLFSTASIMHLCAISLDRYVAIQNPIHHSRFNSRTKAFLKIIAVWTISVGVSMPIPVF
GLQDDSKVFKQGSCLLADDNFVLIGSFVAFFIPLTIMVITYFLTIKSLQKEATLCVSDLSTRAKLASFSFL
PQSSLSSEKLFQRSIHREPGSYTGRRTMQSISNEQKACKVLGIVFFLFVVMWCPFFITNIMAVICKESCNE
HVIGALLNVFVWIGYLSSAVNPLVYTLFNKTYRSAFSRYIQCQYKENRKPLQLILVNTIPALAYKSSQLQA
GQNKDSKEDAEPTDNDCSMVTLGKQQSEETCTDNINTVNEKVSCV
</code>
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<code>
tmhmm seq.fasta
</code>
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<code>
# 5H2A_CRIGR Length: 471
# 5H2A_CRIGR Number of predicted TMHs:  7
# 5H2A_CRIGR Exp number of AAs in TMHs: 159.47336
# 5H2A_CRIGR Exp number, first 60 AAs:  0.01677
# 5H2A_CRIGR Total prob of N-in:        0.00629
5H2A_CRIGR      TMHMM2.0        outside      1    76
5H2A_CRIGR      TMHMM2.0        TMhelix     77    99
5H2A_CRIGR      TMHMM2.0        inside     100   111
5H2A_CRIGR      TMHMM2.0        TMhelix    112   134
5H2A_CRIGR      TMHMM2.0        outside    135   148
5H2A_CRIGR      TMHMM2.0        TMhelix    149   171
5H2A_CRIGR      TMHMM2.0        inside     172   191
5H2A_CRIGR      TMHMM2.0        TMhelix    192   214
5H2A_CRIGR      TMHMM2.0        outside    215   233
5H2A_CRIGR      TMHMM2.0        TMhelix    234   256
5H2A_CRIGR      TMHMM2.0        inside     257   324
5H2A_CRIGR      TMHMM2.0        TMhelix    325   347
5H2A_CRIGR      TMHMM2.0        outside    348   356
5H2A_CRIGR      TMHMM2.0        TMhelix    357   379
5H2A_CRIGR      TMHMM2.0        inside     380   471
</code>
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<code>
tmhmm --short < seq.fasta >tmhmm.out
</code>
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<code>
5H2A_CRIGR      len=471 ExpAA=159.47    First60=0.02    PredHel=7       Topology=o77-99i112-134o149-171i192-214o234-256i325-347o357-379i
</code>
</WRAP>
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<code>
cat seq.fasta  | decodeanhmm -f /usr/local/bin/tmhmm-2.0c/lib/TMHMM2.0.options -modelfile /usr/local/bin/tmhmm-2.0c/lib//TMHMM2.0.model
</code>
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<code>
/usr/local/bin/tmhmm-2.0c/lib//TMHMM2.0.model
decodeanhmm 1.1g
Copyright (C) 1998 by Anders Krogh
Mon Nov 18 10:56:39 2013

Model in file "/usr/local/bin/tmhmm-2.0c/lib//TMHMM2.0.model" parsed successfully.
>5H2A_CRIGR you can have comments after the ID
%len 471
%lett A:29 C:14 D:20 E:18 F:25 G:18 H:6 I:37 K:23 L:55 M:14 N:28 P:17 Q:19 R:15 S:50 T:27 V:34 W:7 Y:15
%score BG 1983.221633 (4.210662 per character)
%score FW 1939.519064 (4.117875 per character)
%score NB(0) 1945.771111 (4.131149 per character)
%score LO(0) 37.450523 (0.079513 per character)
%pred NB(0): o 1 76, M 77 99, i 100 111, M 112 134, o 135 148, M 149 171, i 172 191, M 192 214, o 215 233, M 234 256, i 257 324, M 325 347, o 348 356, M 357 379, i 380 471
   MEILCEDNTSLSSIPNSLMQVDGDSGLYRNDFNSRDANSSDASNWTIDGENRTNLSFEGYLPPTCLSILHLQ
?0 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

   EKNWSALLTAVVIILTIAGNILVIMAVSLEKKLQNATNYFLMSLAIADMLLGFLVMPVSMLTILYGYRWPLP
?0 ooooMMMMMMMMMMMMMMMMMMMMMMMiiiiiiiiiiiiMMMMMMMMMMMMMMMMMMMMMMMoooooooooo

   SKLCAVWIYLDVLFSTASIMHLCAISLDRYVAIQNPIHHSRFNSRTKAFLKIIAVWTISVGVSMPIPVFGLQ
?0 ooooMMMMMMMMMMMMMMMMMMMMMMMiiiiiiiiiiiiiiiiiiiiMMMMMMMMMMMMMMMMMMMMMMMoo

   DDSKVFKQGSCLLADDNFVLIGSFVAFFIPLTIMVITYFLTIKSLQKEATLCVSDLSTRAKLASFSFLPQSS
?0 oooooooooooooooooMMMMMMMMMMMMMMMMMMMMMMMiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii

   LSSEKLFQRSIHREPGSYTGRRTMQSISNEQKACKVLGIVFFLFVVMWCPFFITNIMAVICKESCNEHVIGA
?0 iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiMMMMMMMMMMMMMMMMMMMMMMMoooooooooMMMM

   LLNVFVWIGYLSSAVNPLVYTLFNKTYRSAFSRYIQCQYKENRKPLQLILVNTIPALAYKSSQLQAGQNKDS
?0 MMMMMMMMMMMMMMMMMMMiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii

   KEDAEPTDNDCSMVTLGKQQSEETCTDNINTVNEKVSCV
?0 iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii

</code>
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\\
* Install **RNAMMER**
\\
\\
Install Hmmer v2
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<code>
wget ftp://selab.janelia.org/pub/software/hmmer/2.3.2/hmmer-2.3.2.tar.gz
tar -xvzf hmmer-2.3.2.tar.gz
cd hmmer-2.3.2/
./configure
make
make check
cd ..
mv hmmer-2.3.2 /usr/local/bin/
chown -R root:root /usr/local/bin/hmmer-2.3.2
chmod -R 755 /usr/local/bin/hmmer-2.3.2
ln -s /usr/local/bin/hmmer-2.3.2/src/hmmsearch /usr/local/bin/hmmsearch2

hmmsearch2 -h
</code>
</WRAP>
\\
Download from http://www.cbs.dtu.dk/cgi-bin/sw_request?rnammer
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<code>
mkdir rnammer-1.2
cd rnammer-1.2/
cat ../rnammer-1.2.src.tar.Z | uncompress | tar xvf -
cd ..
mv rnammer-1.2 /usr/local/bin/
chown -R root:root /usr/local/bin/rnammer-1.2
chmod -R 755 /usr/local/bin/rnammer-1.2
ln -s /usr/local/bin/rnammer-1.2/rnammer /usr/local/bin/

nano -w /usr/local/bin/rnammer-1.2/rnammer
</code>
</WRAP>
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<code>
## PROGRAM CONFIGURATION BEGIN

# the path of the program
my $INSTALL_PATH = "/usr/local/bin/rnammer-1.2";

# The library in which HMMs can be found
my $HMM_LIBRARY = "$INSTALL_PATH/lib";
my $XML2GFF = "$INSTALL_PATH/xml2gff";
my $XML2FSA = "$INSTALL_PATH/xml2fsa";

# The location of the RNAmmer core module
my $RNAMMER_CORE     = "$INSTALL_PATH/core-rnammer";

# path to hmmsearch of HMMER package
chomp ( my $uname = `uname`);
my $HMMSEARCH_BINARY;
my $PERL;
if ( $uname eq "Linux" ) {
        $HMMSEARCH_BINARY = "/usr/local/bin/hmmsearch2";
        $PERL = "/usr/bin/perl";
} elsif ( $uname eq "IRIX64" ) {
        $HMMSEARCH_BINARY = "/usr/local/bin/hmmsearch2";
        $PERL = "/usr/sbin/perl";
} else {
        die "unknown platform\n";
}
</code>
</WRAP>
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<code>
nano -w core-rnammer [remove --cpu ]

cp /usr/local/bin/rnammer-1.2/man/rnammer.1 /usr/local/share/man/man1/
</code>
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Test (as USER)
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<code>
mkdir example
cd example/
cp /usr/local/bin/rnammer-1.2/example/ecoli.fsa ./
rnammer -S bac -m lsu,ssu,tsu -xml ecoli.xml -gff ecoli.gff -h ecoli.hmmreport < ecoli.fsa
</code>
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check against /usr/local/bin/rnammer-1.2/example/example
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NOTE: In command 
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<code>
$TRINOTATE_HOME/util/rnammer_support/RnammerTranscriptome.pl --transcriptome Trinity.fasta --path_to_rnammer /usr/bin/software/rnammer_v1.2/rnammer
</code>
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use /usr/local/bin/rnammer as rnammer path
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* Install **Trinotate**
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\\
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<code>
sudo apt-get install sqlite3 libdbd-sqlite3-perl

wget http://garr.dl.sourceforge.net/project/trinotate/Trinotate_r20131110.tar.gz
tar -xvzf Trinotate_r20131110.tar.gz
mv Trinotate_r20131110 /usr/local/bin/
chown -R root:root /usr/local/bin/Trinotate_r20131110
chmod -R 755 /usr/local/bin/Trinotate_r20131110
ln -s /usr/local/bin/Trinotate_r20131110 /usr/local/bin/trinotate
</code>
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