# HG changeset patch
# User Dave Bouvier <dave@bx.psu.edu>
# Date 1384961680 18000
# Node ID 7f16481a1462b16caaea08f8a68391bd87abdee3
# Parent  886b67f8694d7c5c150d00c84a2b742bde03a88e# Parent  207d85f220c132bb870380142b6bbd910137e061
Merged 28.

diff -r 207d85f220c1 -r 7f16481a1462 osra.py
--- a/osra.py	Mon May 27 13:30:02 2013 +0200
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,26 +0,0 @@
-#!usr/bin/env python
-
-import os, sys
-import subprocess
-
-"""
-    OSRA_DATA_FILES is set during the toolshed Installation
-    If it is not set, use the standard configuration of OSRA. 
-    That means we need to delete argument 4-7.
-    That script is a hack, because we do not know the content of OSRA_DATA_FILES at xml evaluation time.
-
-    osra -f $oformat $infile 
-        -l \$OSRA_DATA_FILES/spelling.txt -a \$OSRA_DATA_FILES/superatom.txt
-        > $outfile
-"""
-
-if not os.path.exists(sys.argv[6]):
-    # OSRA_DATA_FILES path is not set or the spelling file is not existent
-    sys.argv.pop(7) # superatom.txt path
-    sys.argv.pop(6) # -a
-    sys.argv.pop(5) # speling.txt path
-    sys.argv.pop(4) # -l
-
-subprocess.call(sys.argv[1:], stdout=sys.stdout)
-
-
diff -r 207d85f220c1 -r 7f16481a1462 osra.xml
--- a/osra.xml	Mon May 27 13:30:02 2013 +0200
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,46 +0,0 @@
-<tool id="osra" name="Molecule recognition" version="0.3">
-    <description>in Images or PDF documents (OSRA)</description>
-    <requirements>
-        <requirement type="package" version="2.0.0">osra</requirement>
-    </requirements>
-    <command interpreter="python">
-        ## OSRA_DATA_FILES is set during the toolshed Installation
-        ## if it is not set, use the standard configuration and hope the best
-        osra.py -f $oformat $infile 
-        -l \$OSRA_DATA_FILES/spelling.txt -a \$OSRA_DATA_FILES/superatom.txt
-        
-        ## further additions of OSRA parameter should go after -l and -a
-        ## because -l and -a can be removed by the python wrapper
-        
-        &gt; $outfile
-    </command>
-    <inputs>
-        <param format="png,pdf" label="Image or PDF with molecules" name="infile" type="data" />
-        <param label="Output molecule format" name="oformat" type="select">
-            <option value="can">SMILES</option>
-            <option value="sdf">SDF</option>
-        </param>
-    </inputs>
-    <outputs>
-        <data format="sdf" name="outfile" type="data">
-            <change_format>
-                <when format="smi" input="oformat" value="can" />
-            </change_format>
-        </data>
-    </outputs>
-    <tests>
-        <test>
-            <param ftype="png" name="infile" value="CID_2244.png" />
-            <param name="oformat" value="sdf" />
-            <output file="osra_on_CID2244.sdf" ftype="sdf" name="outfile" />
-        </test>
-    </tests>
-    <help>
-
-**What it does**
-
-OSRA detects molecules in images and converts them to standard molecule formats. 
-
-
-    </help>
-</tool>
diff -r 207d85f220c1 -r 7f16481a1462 readme
--- a/readme	Mon May 27 13:30:02 2013 +0200
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,20 +0,0 @@
-OSRA: Optical Structure Recognition Application
-
-OSRA is a utility designed to convert graphical representations of chemical 
-structures, as they appear in journal articles, patent documents, textbooks, 
-trade magazines etc., into SMILES (Simplified Molecular Input Line Entry 
-Specification - see http://en.wikipedia.org/wiki/SMILES) or 
-SD files - a computer recognizable molecular structure format. 
-OSRA can read a document in any of the over 90 graphical formats parseable by 
-ImageMagick - including GIF, JPEG, PNG, TIFF, PDF, PS etc., and generate 
-the SMILES or SDF representation of the molecular structure images encountered 
-within that document.
-
-Note that any software designed for optical recognition is unlikely to be 
-perfect, and the output produced might, and probably will, contain errors, 
-so curation by a human knowledgeable in chemical structures is highly recommended.
-
-http://cactus.nci.nih.gov/osra/
-
-The wrapper comes with an automatic installation of all dependencies through the
-galaxy toolshed.
diff -r 207d85f220c1 -r 7f16481a1462 repository_dependencies.xml
--- a/repository_dependencies.xml	Mon May 27 13:30:02 2013 +0200
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-<repositories description="This requires the Molecule datatype definitions (e.g. SMILES, InChI, SD-format).">
-    <repository changeset_revision="c5383bd4d006" name="molecule_datatypes" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
-    
-</repositories>
diff -r 207d85f220c1 -r 7f16481a1462 test_data/CID_2244.png
Binary file test_data/CID_2244.png has changed
diff -r 207d85f220c1 -r 7f16481a1462 test_data/CID_2244.sdf
--- a/test_data/CID_2244.sdf	Mon May 27 13:30:02 2013 +0200
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,155 +0,0 @@
-2244
-  -OEChem-05151212332D
-
- 21 21  0     0  0  0  0  0  0999 V2000
-    3.7320   -0.0600    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
-    6.3301    1.4400    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
-    4.5981    1.4400    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
-    2.8660   -1.5600    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
-    4.5981   -0.5600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-    5.4641   -0.0600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-    4.5981   -1.5600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-    6.3301   -0.5600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-    5.4641   -2.0600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-    6.3301   -1.5600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-    5.4641    0.9400    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-    2.8660   -0.5600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-    2.0000   -0.0600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-    4.0611   -1.8700    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
-    6.8671   -0.2500    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
-    5.4641   -2.6800    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
-    6.8671   -1.8700    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
-    2.3100    0.4769    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
-    1.4631    0.2500    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
-    1.6900   -0.5969    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
-    6.3301    2.0600    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
-  1  5  1  0  0  0  0
-  1 12  1  0  0  0  0
-  2 11  1  0  0  0  0
-  2 21  1  0  0  0  0
-  3 11  2  0  0  0  0
-  4 12  2  0  0  0  0
-  5  6  1  0  0  0  0
-  5  7  2  0  0  0  0
-  6  8  2  0  0  0  0
-  6 11  1  0  0  0  0
-  7  9  1  0  0  0  0
-  7 14  1  0  0  0  0
-  8 10  1  0  0  0  0
-  8 15  1  0  0  0  0
-  9 10  2  0  0  0  0
-  9 16  1  0  0  0  0
- 10 17  1  0  0  0  0
- 12 13  1  0  0  0  0
- 13 18  1  0  0  0  0
- 13 19  1  0  0  0  0
- 13 20  1  0  0  0  0
-M  END
-> <PUBCHEM_COMPOUND_CID>
-2244
-
-> <PUBCHEM_COMPOUND_CANONICALIZED>
-1
-
-> <PUBCHEM_CACTVS_COMPLEXITY>
-212
-
-> <PUBCHEM_CACTVS_HBOND_ACCEPTOR>
-4
-
-> <PUBCHEM_CACTVS_HBOND_DONOR>
-1
-
-> <PUBCHEM_CACTVS_ROTATABLE_BOND>
-3
-
-> <PUBCHEM_CACTVS_SUBSKEYS>
-AAADccBwOAAAAAAAAAAAAAAAAAAAAAAAAAAwAAAAAAAAAAABAAAAGgAACAAADASAmAAyDoAABgCIAiDSCAACCAAkIAAIiAEGCMgMJzaENRqCe2Cl4BEIuYeIyCCOAAAAAAAIAAAAAAAAABAAAAAAAAAAAA==
-
-> <PUBCHEM_IUPAC_OPENEYE_NAME>
-2-acetoxybenzoic acid
-
-> <PUBCHEM_IUPAC_CAS_NAME>
-2-acetyloxybenzoic acid
-
-> <PUBCHEM_IUPAC_NAME>
-2-acetyloxybenzoic acid
-
-> <PUBCHEM_IUPAC_SYSTEMATIC_NAME>
-2-acetyloxybenzoic acid
-
-> <PUBCHEM_IUPAC_TRADITIONAL_NAME>
-2-acetoxybenzoic acid
-
-> <PUBCHEM_IUPAC_INCHI>
-InChI=1S/C9H8O4/c1-6(10)13-8-5-3-2-4-7(8)9(11)12/h2-5H,1H3,(H,11,12)
-
-> <PUBCHEM_IUPAC_INCHIKEY>
-BSYNRYMUTXBXSQ-UHFFFAOYSA-N
-
-> <PUBCHEM_XLOGP3>
-1.2
-
-> <PUBCHEM_EXACT_MASS>
-180.042259
-
-> <PUBCHEM_MOLECULAR_FORMULA>
-C9H8O4
-
-> <PUBCHEM_MOLECULAR_WEIGHT>
-180.15742
-
-> <PUBCHEM_OPENEYE_CAN_SMILES>
-CC(=O)OC1=CC=CC=C1C(=O)O
-
-> <PUBCHEM_OPENEYE_ISO_SMILES>
-CC(=O)OC1=CC=CC=C1C(=O)O
-
-> <PUBCHEM_CACTVS_TPSA>
-63.6
-
-> <PUBCHEM_MONOISOTOPIC_WEIGHT>
-180.042259
-
-> <PUBCHEM_TOTAL_CHARGE>
-0
-
-> <PUBCHEM_HEAVY_ATOM_COUNT>
-13
-
-> <PUBCHEM_ATOM_DEF_STEREO_COUNT>
-0
-
-> <PUBCHEM_ATOM_UDEF_STEREO_COUNT>
-0
-
-> <PUBCHEM_BOND_DEF_STEREO_COUNT>
-0
-
-> <PUBCHEM_BOND_UDEF_STEREO_COUNT>
-0
-
-> <PUBCHEM_ISOTOPIC_ATOM_COUNT>
-0
-
-> <PUBCHEM_COMPONENT_COUNT>
-1
-
-> <PUBCHEM_CACTVS_TAUTO_COUNT>
-1
-
-> <PUBCHEM_COORDINATE_TYPE>
-1
-5
-255
-
-> <PUBCHEM_BONDANNOTATIONS>
-5  6  8
-5  7  8
-6  8  8
-7  9  8
-8  10  8
-9  10  8
-
-$$$$
-
diff -r 207d85f220c1 -r 7f16481a1462 tool_dependencies.xml
--- a/tool_dependencies.xml	Mon May 27 13:30:02 2013 +0200
+++ b/tool_dependencies.xml	Wed Nov 20 10:34:40 2013 -0500
@@ -1,64 +1,95 @@
+<?xml version="1.0"?>
 <tool_dependency>
-    <package name="openbabel" version="2.3.2">
-        <repository changeset_revision="ccda1b8ebc72" name="package_openbabel_2_3" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
+    <package name="libgd" version="2.1.0">
+        <repository changeset_revision="55e3d764c6c2" name="package_libgd_2_1" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="perl" version="5.18.1">
+        <repository changeset_revision="ab58b9f990c5" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
-    <package name="graphicsmagick" version="1.3.18">
-        <repository changeset_revision="34f511310435" name="package_graphicsmagick_1_3" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
+    <package name="expat" version="2.1.0">
+        <repository changeset_revision="8fc96166cddd" name="package_expat_2_1" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
-    <package name="osra" version="2.0.0">
+    <package name="bzlib" version="1.0.6">
+        <repository changeset_revision="04e1967b1722" name="package_bzlib_1_0" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="libpng" version="1.2.5">
+        <repository changeset_revision="a80a3062f066" name="package_libpng_1_2" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="trans_proteomic_pipeline" version="4.6.3">
         <install version="1.0">
             <actions>
-                <action type="download_by_url">http://downloads.sourceforge.net/project/osra/osra/2.0.0/osra-2.0.0.tgz</action>
-
+                <action type="setup_perl_environment">
+                    <repository changeset_revision="ab58b9f990c5" name="package_perl_5_18" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                        <package name="perl" version="5.18.1" />
+                    </repository>
+                    <repository changeset_revision="8fc96166cddd" name="package_expat_2_1" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                        <package name="expat" version="2.1.0" />
+                    </repository>
+                    <!-- allow downloading and installing an Perl package from cpan.org-->
+                   
+                    <package>http://search.cpan.org/CPAN/authors/id/T/TO/TODDR/XML-Parser-2.41.tar.gz</package>
+                    <!-- Also possible but not reproducible, due to the fact that always the latest version is installed.
+                        <package>XML::Parser</package>
+                    -->
+                   <package>http://search.cpan.org/CPAN/authors/id/L/LD/LDS/CGI.pm-3.43.tar.gz</package>
+                </action>
+                <action type="change_directory">..</action>
+                <action type="download_file">https://downloads.sourceforge.net/project/sashimi/Trans-Proteomic%20Pipeline%20%28TPP%29/TPP%20v4.6%20%28occupy%29%20rev%203/TPP-4.6.3.tgz</action>
+                <!-- populate the environment variables from the dependend repos -->
                 <action type="set_environment_for_install">
-                    <repository changeset_revision="ccda1b8ebc72" name="package_openbabel_2_3" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu/">
-                        <package name="openbabel" version="2.3.2" />
+                    <repository changeset_revision="55e3d764c6c2" name="package_libgd_2_1" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                        <package name="libgd" version="2.1.0" />
                     </repository>
-                    <repository changeset_revision="34f511310435" name="package_graphicsmagick_1_3" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu/">
-                        <package name="graphicsmagick" version="1.3.18" />
+                    <repository changeset_revision="a80a3062f066" name="package_libpng_1_2" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                        <package name="libpng" version="1.2.5" />
+                    </repository>
+                    <repository changeset_revision="04e1967b1722" name="package_bzlib_1_0" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                        <package name="bzlib" version="1.0.6" />
                     </repository>
                 </action>
-                <action type="shell_command">wget http://potrace.sourceforge.net/download/potrace-1.11.tar.gz</action>
-                <action type="shell_command">tar xfvz potrace-1.11.tar.gz &amp;&amp; cd potrace-1.11 &amp;&amp; ./configure --with-libpotrace --prefix=$INSTALL_DIR/potrace/build &amp;&amp; make &amp;&amp; make install</action>
-
-                <action type="shell_command">wget http://downloads.sourceforge.net/project/osra/gocr-patched/gocr-0.50pre-patched.tgz</action>
-                <action type="shell_command">tar xfvz gocr-0.50pre-patched.tgz &amp;&amp; cd gocr-0.50pre-patched &amp;&amp; ./configure --prefix=$INSTALL_DIR/gocr/build &amp;&amp; make libs &amp;&amp; make all install</action>
-
-
-                
-                <action type="shell_command">wget http://downloads.sourceforge.net/project/tclap/tclap-1.2.1.tar.gz</action>
-                <action type="shell_command">tar xfvz tclap-1.2.1.tar.gz &amp;&amp; cd tclap-1.2.1 &amp;&amp; ./configure --prefix=$INSTALL_DIR/tclap/build &amp;&amp; make &amp;&amp; make install</action>
-
-                
-                <action type="shell_command">wget http://mirror.checkdomain.de/gnu/ocrad/ocrad-0.21.tar.gz</action>
-                <action type="shell_command">tar xfvz ocrad-0.21.tar.gz &amp;&amp; cd ocrad-0.21 &amp;&amp; ./configure --prefix=$INSTALL_DIR/ocrad/build &amp;&amp; make &amp;&amp; make install</action>
-
-                
-                <action type="shell_command">wget https://launchpad.net/cuneiform-linux/1.1/1.1/+download/cuneiform-linux-1.1.0.tar.bz2</action>
-                <action type="shell_command">tar xfvj cuneiform-linux-1.1.0.tar.bz2 &amp;&amp; cd cuneiform-linux-1.1.0 &amp;&amp; mkdir build &amp;&amp; cd build &amp;&amp; cmake .. -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR/cuneiform/build/ &amp;&amp; make &amp;&amp; make install</action>
+                <action type="shell_command">tar xfz TPP-4.6.3.tgz</action>
+                <!-- doanload patched version of htmldoc to prevent a TPP crashed during compilation -->
+                <action type="download_file">https://github.com/bgruening/download_store/raw/master/htmldoc/htmldoc_1.8.27-8ubuntu1.debian.tar.gz</action>
+                <action type="shell_command">rm ./TPP-4.6.3/trans_proteomic_pipeline/extern/htmldoc.tgz</action>
+                <action type="shell_command">mv htmldoc_1.8.27-8ubuntu1.debian.tar.gz ./TPP-4.6.3/trans_proteomic_pipeline/extern/htmldoc.tgz</action>
+                <!--
+                <action type="move_file" rename_to="htmldoc.tgz">
+                    <source>htmldoc-1.8.27-8.debian.patched.tar.gz</source>
+                    <destination>./TPP-4.6.3/trans_proteomic_pipeline/extern/</destination>
+                </action>
+                -->
+                <action type="change_directory">./TPP-4.6.3/trans_proteomic_pipeline/src/</action>
+                <action type="shell_command">echo 'TPP_ROOT=$INSTALL_DIR/tpp/' &gt; Makefile.config.incl</action>
+                <action type="shell_command">echo 'TPP_WEB=/tpp/' &gt;&gt; Makefile.config.incl</action>
+                <action type="shell_command">echo 'CGI_USER_DIR=$INSTALL_DIR/cgi-bin/' &gt;&gt; Makefile.config.incl</action>
 
-                
-                
-                <action type="shell_command">export PATH=$PATH:$GRAPHICSMAGICK_ROOT_DIR/bin/ &amp;&amp; 
-                    ./configure --with-tclap-include=$INSTALL_DIR/tclap/build/include/ --with-potrace-include=$INSTALL_DIR/potrace/build/include/ --with-potrace-lib=$INSTALL_DIR/potrace/build/lib/ --with-gocr-include=$INSTALL_DIR/gocr/build/include/gocr/ --with-gocr-lib=$INSTALL_DIR/gocr/build/lib/ --with-ocrad-include=$INSTALL_DIR/ocrad/build/include/ --with-ocrad-lib=$INSTALL_DIR/ocrad/build/lib/ --with-cuneiform-include=$INSTALL_DIR/cuneiform/build/install/include/ --with-cuneiform --with-cuneiform-lib=$INSTALL_DIR/cuneiform/build/install/lib/ --with-openbabel-include=$OPENBABEL_INCLUDE_DIR/openbabel-2.0/ --with-openbabel-lib=$OPENBABEL_LIB_DIR --with-graphicsmagick-lib=$GRAPHICSMAGICK_ROOT_DIR/lib/ --with-graphicsmagick-include=$GRAPHICSMAGICK_ROOT_DIR/include/GraphicsMagick/ --prefix=$INSTALL_DIR </action>
-                <action type="shell_command">make</action>
-                <action type="shell_command">make install</action>
+                <!--
+                    TPP is fails with a error due to an deprecated use of qw()
+                    See the rant @ http://blogs.perl.org/users/rurban/2010/09/qw-in-list-context-deprecated.html
+                -->
+                <action type="shell_command">sed -i -e 's/qw(.*) /(&amp;) /' ../perl/tpp_models.pl</action>
+                <action type="shell_command">sed -i -e 's/qw(.*) /(&amp;) /' ../CGI/show_nspbin.pl</action>
+                <action type="shell_command">sed -i -e 's/qw(.*) /(&amp;) /' ../perl/exporTPP.pl</action>
 
-                <action type="shell_command">rm $INSTALL_DIR/tclap/ -r</action>
-                
-                <action type="shell_command">rm $INSTALL_DIR/gocr/ -r</action>
-                <action type="shell_command">rm $INSTALL_DIR/ocrad/ -r</action>
-                <action type="shell_command">rm $INSTALL_DIR/cuneiform/ -r</action>
-
+                <action type="shell_command">export PERL5LIB=$INSTALL_DIR/lib/perl5/:$PERL5LIB &amp;&amp; export PATH=$PERL_ROOT_DIR/bin/:$PATH &amp;&amp; export PERL5LIB=$PERL_ROOT_DIR/lib/perl5:$PERL5LIB &amp;&amp; make</action>
+                <action type="shell_command">make install</action>
                 <action type="set_environment">
-                    <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$GRAPHICSMAGICK_ROOT_DIR/lib/</environment_variable>
-                    <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/potrace/build/lib/</environment_variable>
-                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
-                    
-                    <environment_variable action="set_to" name="OSRA_DATA_FILES">$INSTALL_DIR/share</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/tpp/bin</environment_variable>
+                    <environment_variable action="prepend_to" name="PERL5LIB">$INSTALL_DIR/lib/perl5</environment_variable>
+                    <environment_variable action="set_to" name="TPP_ROOT_PATH">$INSTALL_DIR</environment_variable>
                 </action>
             </actions>
         </install>
-        <readme>We still have a handfull of requirements</readme>
+        <readme>
+            Installs and complils the trans proteomic pipeline in version 4.6.3.
+            The Trans-Proteomic Pipeline (TPP) is a collection of integrated tools for MS/MS proteomics, developed at the SPC.
+
+            http://tools.proteomecenter.org/
+
+            Dependencies: e2fslibs-dev (e2fsprogs-devel)
+
+            PATH will be set.
+            TPP_ROOT_PATH will point to the root path of the installation.
+        </readme>
     </package>
 </tool_dependency>