# HG changeset patch
# User bgruening
# Date 1396519652 14400
# Node ID 0b732f3cfad05c0b201c2bcfc56af8b919a4c70f
# Parent  de242914a56a5f80d4c2d888cab0194559b634ac
Uploaded

diff -r de242914a56a -r 0b732f3cfad0 MiClip.xml
--- a/MiClip.xml	Wed Mar 05 02:24:52 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,89 +0,0 @@
-<tool id="mi_clip" name="MiClip">
-    <description>Identify Binding Sites in CLIP-Seq Data</description>
-    <requirements>
-        <requirement type="binary">Rscript</requirement>
-        <requirement type="package" version="3.0.1">R_3_0_1</requirement>
-        <requirement type="package" version="1.2">miclip</requirement>
-        <requirement type="package" version="5.18.1">perl</requirement>
-        <requirement type="set_environment">MICLIP_SCRIPT_PATH</requirement>
-    </requirements>
-    <command interpreter="sh">
-        MiClip_wrapper.sh $input_file $control_file $mutation $paired $suffix $step $maxbin $model_cut $max_iter $convergence $emperical $output
-    </command>
-    <inputs>
-        <param name="input_file" type="data" format="sam" label="Input File" help="Input SAM File. Use Bam to Sam converter if Input file is in Bam format."/>
-        <param name="control_file" type="data" format="sam" optional="true" label="Control File" help="ex: Control experiment without crosslinking for distinguishing SNPs."/> 
-        <param name="mutation" type="select" label="Mutation Type" display="checkboxes" multiple="true" help="Select One or Multiple Mutations.">
-            <option value="T2C" selected="true">T-&gt;C</option>
-            <option value="T2A">T-&gt;A</option>
-            <option value="T2G">T-&gt;G</option>
-            <option value="C2A">C-&gt;A</option>
-            <option value="C2T">C-&gt;T</option>
-            <option value="C2G">C-&gt;G</option>
-            <option value="A2T">A-&gt;T</option>
-            <option value="A2G">A-&gt;G</option>
-            <option value="A2C">A-&gt;C</option>
-            <option value="G2A">G-&gt;A</option>
-            <option value="G2C">G-&gt;C</option>
-            <option value="G2T">G-&gt;T</option>
-            <option value="Ins">Ins</option>
-            <option value="Del">Del</option>
-        </param>
-
-        <param name="paired" type="boolean" checked="no" truevalue="TRUE" falsevalue="FALSE" label="Sequence is Pair-End" help=""/>
-        <param name="suffix" type="text" size="20" value="Forward,Backward" label="Suffix of Paired-End Read" help="Change only if Paired-End Reads. See Manual for more details."/>
-        <param name="step" type="integer" value="5" label="Bin Step Size" help="In the first HMM, all clusters will be divided into bins of the same length of step bp."/>
-        <param name="maxbin" type="integer" value="100" label="Max Number of Reads per Bin" help="Maximum number of Reads in a Bin or on a Base."/>
-        <param name="emperical" type="text" value="auto" label="Emperical" help="Used in model fitting in the first HMM. Default is 'auto'."/> 
-        <param name="model_cut" type="float" value="0.2" min="0.0" max="1.0" label="Mixure Model Cutoff" help="Cutoff for Fitting the mixture model in the Second HMM."/>
-        <param name="max_iter" type="integer" value="20" label="Max Number of HMM Iterations" help="The Maximum number of Iterations for both HMM iterations."/>
-        <param name="convergence" type="float" value="0.01" label="Convergence Cutoff" help="The Cutoff for reaching Convergence."/>
-    </inputs>
-    <outputs>
-        <data format="zip" name="output" />
-    </outputs>
-    <help>
-
-**Description**
-
-Cross-linking immunoprecipitation coupled with high-throughput sequencing (CLIP-Seq) has made it possible to identify targeting sites of RNA-binding proteins in various cell culture systems and tissue types on a genome-wide scale. Here we present MiClip,a novel model-based approach to identify high-confidence protein-RNA binding sites in CLIP-Seq datasets. This approach assigns confidence value to each binding site on a probabilistic basis. The MiClip package can be flexibly applied to analyze both HITS-CLIP data and PAR-CLIP data. 
-
-
-------
-
-**Manual**
-GalaxyManual_
-
-.. _GalaxyManual: http://galaxy.swmed.edu/galaxy/static/galaxy_manual.pdf
-
-MiniClipDemo_
-
-.. _MiniClipDemo: http://galaxy.swmed.edu/galaxy/u/tpers1/p/miniclipwalkthrough
-
-Vignette.pdf_ 
-
-.. _Vignette.pdf: http://galaxy.swmed.edu/galaxy/static/MiClip_vignette.pdf
-
-Manual.pdf_ 
-
-.. _Manual.pdf: http://galaxy.swmed.edu/galaxy/static/MiClip-manual.pdf
-
-
-------
-
-**Source**
-
-MiClip_R_Package_
-
-.. _MiClip_R_Package: http://galaxy.swmed.edu/galaxy/static/MiClip.tar.gz
-
-------
-
-**Author** 
-
-Tao Wang. 
-For any suggestions or inquiries please contact Tao.Wang@UTSouthwestern.edu
-
-
-    </help>
-</tool>
diff -r de242914a56a -r 0b732f3cfad0 MiClip_wrapper.sh
--- a/MiClip_wrapper.sh	Wed Mar 05 02:24:52 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,10 +0,0 @@
-R --vanilla --slave --args $1 $2 $3 $4 $5 $6 $7 $8 $9 ${10} ${11} < /HOME/galaxy/galaxy-dist/tools/MiClip/MiClip.R > dump
-if [ -f ${__tool_data_path__}clusters.csv ]
- then
-   zip temp ${__tool_data_path__}log.txt
-   zip temp ${__tool_data_path__}*.csv
-   mv ${__tool_data_path__}temp.zip ${12}
- else 
-   cat dump >&2
-fi
-
diff -r de242914a56a -r 0b732f3cfad0 osra.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/osra.py	Thu Apr 03 06:07:32 2014 -0400
@@ -0,0 +1,27 @@
+#!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[7]):
+    # 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
+
+sys.argv[0] = 'osra'
+subprocess.call(sys.argv, stdout=sys.stdout)
+
+
diff -r de242914a56a -r 0b732f3cfad0 osra.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/osra.xml	Thu Apr 03 06:07:32 2014 -0400
@@ -0,0 +1,74 @@
+<tool id="ctb_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>
+        <requirement type="package" version="2.3.2">openbabel</requirement>
+        <requirement type="package" version="1.3.18">graphicsmagick</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
+        
+        $confidence
+        $adaptive
+        $thinning
+        
+        > $outfile
+    </command>
+    <inputs>
+        <param name="infile" type="data" format="png,pdf" label="Image or PDF with molecules"/>
+        <param name="oformat" type="select" label="Output molecule format">
+            <option value="can">SMILES</option>
+            <option value="sdf">SDF</option>
+        </param>
+        <param name="confidence" type="boolean" label="Print out confidence estimate (-p)" truevalue="-p" falsevalue="" checked="true" />
+        <param name="adaptive" type="boolean" label="Adaptive thresholding pre-processing, useful for low light/low contrast images (-i)" truevalue="-i" falsevalue="" checked="false" />
+        <param name="thinning" type="boolean" label="Additional thinning/scaling down of low quality documents (-j)" truevalue="-j" falsevalue="" checked="false" />
+
+    </inputs>
+    <outputs>
+        <data name="outfile" type="data" format="sdf">
+            <change_format>
+                <when input="oformat" value="can" format="smi"/>
+            </change_format>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="infile" ftype="png" value="CID_2244.png"/>
+            <param name="oformat" value="sdf"/>
+            <output name="outfile" ftype="sdf" file="osra_on_CID2244.sdf"/>
+        </test>
+        <test>
+            <param name="infile" ftype="png" value="2008001635_153_chem.png"/>
+            <param name="oformat" value="can"/>
+            <output name="outfile" ftype="sdf" file="2008001635_153_chem.smi"/>
+        </test>
+        
+    </tests>
+    <help>
+
+.. class:: infomark
+
+**What this tool does**
+
+OSRA_ (Optical Structure Recognition Application) is a utility designed to convert graphical representations of chemical structures into SMILES or SDF. It generates the SMILES or SDF representation of any molecular structure image within a document which is parseable by GraphicMagick.
+
+.. _OSRA: http://cactus.nci.nih.gov/osra/
+
+-----
+
+.. class:: infomark
+
+**Cite**
+
+Igor V Filippov and Marc C Nicklaus - `Optical Structure Recognition Software To Recover Chemical Information: OSRA, An Open Source Solution`_
+
+.. _`Optical Structure Recognition Software To Recover Chemical Information: OSRA, An Open Source Solution`: http://pubs.acs.org/doi/abs/10.1021/ci800067r
+    </help>
+</tool>
diff -r de242914a56a -r 0b732f3cfad0 readme
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/readme	Thu Apr 03 06:07:32 2014 -0400
@@ -0,0 +1,20 @@
+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 de242914a56a -r 0b732f3cfad0 repository_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/repository_dependencies.xml	Thu Apr 03 06:07:32 2014 -0400
@@ -0,0 +1,4 @@
+<?xml version="1.0"?>
+<repositories description="This requires the Molecule datatype definitions (e.g. SMILES, InChI, SD-format).">
+    <repository changeset_revision="8714f927a6ee" name="molecule_datatypes" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+</repositories>
diff -r de242914a56a -r 0b732f3cfad0 test_data/2008001635_153_chem.png
Binary file test_data/2008001635_153_chem.png has changed
diff -r de242914a56a -r 0b732f3cfad0 test_data/2008001635_153_chem.smi
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test_data/2008001635_153_chem.smi	Thu Apr 03 06:07:32 2014 -0400
@@ -0,0 +1,1 @@
+CCC(c1ccc(cc1)Br)OCCCO
diff -r de242914a56a -r 0b732f3cfad0 test_data/CID_2244.png
Binary file test_data/CID_2244.png has changed
diff -r de242914a56a -r 0b732f3cfad0 test_data/CID_2244.sdf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test_data/CID_2244.sdf	Thu Apr 03 06:07:32 2014 -0400
@@ -0,0 +1,155 @@
+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 de242914a56a -r 0b732f3cfad0 tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Mar 05 02:24:52 2014 -0500
+++ b/tool_dependencies.xml	Thu Apr 03 06:07:32 2014 -0400
@@ -1,49 +1,74 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="libxml2" version="2.9.1">
-        <repository changeset_revision="cff446402e07" name="package_libxml2_2_9_1" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="iconv" version="1.14">
-        <repository changeset_revision="5b87c1521e4d" name="package_iconv_1_14" owner="iracooke" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    <package name="openbabel" version="2.3.2">
+        <repository changeset_revision="8426be5149ce" name="package_openbabel_2_3" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
-    <package name="openssl" version="1.0">
-        <repository changeset_revision="d3f9ae5d3727" name="package_openssl_1_0" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    <package name="graphicsmagick" version="1.3.18">
+        <repository changeset_revision="2fd4eb971ba5" name="package_graphicsmagick_1_3" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
-
-    <package name="ruby" version="2.0">
+    <package name="osra" version="2.0.0">
         <install version="1.0">
             <actions>
-                <action type="download_by_url">http://cache.ruby-lang.org/pub/ruby/2.0/ruby-2.0.0-p451.tar.gz</action>
+                <!-- first action is always downloading -->
+                <action type="download_by_url">http://downloads.sourceforge.net/project/osra/osra/2.0.0/osra-2.0.0.tgz</action>
+
+                <!-- populate the environment variables from the dependend repos -->
                 <action type="set_environment_for_install">
-                    <repository changeset_revision="cff446402e07" name="package_libxml2_2_9_1" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu">
-                        <package name="libxml2" version="2.9.1" />
+                    <repository changeset_revision="8426be5149ce" name="package_openbabel_2_3" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                        <package name="openbabel" version="2.3.2" />
                     </repository>
-                    <repository changeset_revision="5b87c1521e4d" name="package_iconv_1_14" owner="iracooke" toolshed="http://testtoolshed.g2.bx.psu.edu">
-                        <package name="iconv" version="1.14" />
-                    </repository>
-                    <repository changeset_revision="d3f9ae5d3727" name="package_openssl_1_0" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
-                        <package name="openssl" version="1.0" />
+                    <repository changeset_revision="2fd4eb971ba5" name="package_graphicsmagick_1_3" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                        <package name="graphicsmagick" version="1.3.18" />
                     </repository>
                 </action>
 
-                <!-- Fails on OSX due to lack of openssl. -->
-                <action type="autoconf">--disable-install-doc</action>
+                <!--compiling potrace-1.11 -->
+                <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=$INSTALL_DIR/potrace/build &amp;&amp; make &amp;&amp; make install</action>
+
+                <!--compiling gocr 0.50patched -->
+                <!-- not yet possible 
+                <action type="shell_command">wget http://www-e.uni-magdeburg.de/jschulen/ocr/gocr-0.50.tar.gz</action>
+                <action type="shell_command">tar xfvz gocr-0.50.tar.gz &amp;&amp; cd gocr-0.50 &amp;&amp; ./configure -|-prefix=$INSTALL_DIR/gocr/build &amp;&amp; make libs &amp;&amp; make all install</action>
+                -->
+                <action type="shell_command">wget http://downloads.sourceforge.net/project/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=$INSTALL_DIR/gocr/build &amp;&amp; make libs &amp;&amp; make all install</action>
+
+
+                <!--compiling tclap 1.2.1 -->
+                <action type="shell_command">wget http://downloads.sourceforge.net/project/tclap/tclap-1.2.1.tar.gz</action>
+                <action type="shell_command">tar xfvz tclap-1.2.1.tar.gz &amp;&amp; cd tclap-1.2.1 &amp;&amp; ./configure --prefix=$INSTALL_DIR/tclap/build &amp;&amp; make &amp;&amp; make install</action>
+
+                <!--compiling ocrad 0.21 -->
+                <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=$INSTALL_DIR/ocrad/build &amp;&amp; make &amp;&amp; make install</action>
+
+                <!--compiling cuneiform 1.1.0 -->
+                <action type="shell_command">wget https://launchpad.net/cuneiform-linux/1.1/1.1/+download/cuneiform-linux-1.1.0.tar.bz2</action>
+                <action type="shell_command">tar xfvj cuneiform-linux-1.1.0.tar.bz2 &amp;&amp; cd cuneiform-linux-1.1.0 &amp;&amp; mkdir build &amp;&amp; cd build &amp;&amp; cmake .. -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR/cuneiform/build/ &amp;&amp; make &amp;&amp; make install</action>
+
+                <!--And finally OSRA 1.4.0-->
+                <!-- Extending the PATH is needed for OSRA -->
+                <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>
+
+                <action type="shell_command">rm $INSTALL_DIR/tclap/ -r</action>
+                <!--<action type="shell_command">rm $INSTALL_DIR/openbabel/ -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="set_environment">
+                    <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[GRAPHICSMAGICK_ROOT_DIR]/lib/</environment_variable>
+                    <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/potrace/build/lib/</environment_variable>
                     <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
-                    <environment_variable action="set_to" name="RUBYLIB">$INSTALL_DIR/lib/</environment_variable>
-                    <environment_variable action="set_to" name="RUBY_HOME">$INSTALL_DIR</environment_variable>
-                    <environment_variable action="set_to" name="GALAXY_RUBY_HOME">$INSTALL_DIR</environment_variable>
-                    <!--<environment_variable name="LD_LIBRARY_PATH" action="prepend_to">$ENV[PYTHONPATH_NUMPY]</environment_variable>-->
+                    <!-- OSRA_DATA_FILES is only used by the galaxy wrapper and is not part of OSRA -->
+                    <environment_variable action="set_to" name="OSRA_DATA_FILES">$INSTALL_DIR/share</environment_variable>
                 </action>
             </actions>
         </install>
-        <readme>
-            This installs ruby 2.0.x. Ruby is a dynamic, open source programming language with a focus on simplicity and productivity.
-            It has an elegant syntax that is natural to read and easy to write.
-            https://www.ruby-lang.org/
-
-            RUBYHOME and RUBYLIB will be set and with GALAXY_RUBY_HOME you can access the root installation directory.
-        </readme>
+        <readme>We still have a handfull of requirements</readme>
     </package>
 </tool_dependency>