Mercurial > repos > bgruening > osra
changeset 22:6cafe4f5d181 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/osra commit 74daed54894d9769a251a2ca6a46d96b7a27e461
| author | bgruening |
|---|---|
| date | Thu, 09 Nov 2017 03:41:26 -0500 |
| parents | 4c85de6856e9 |
| children | e41a468bc40d |
| files | osra.py osra.tar.bz2 osra.xml readme readme.md repository_dependencies.xml test-data/2008001635_153_chem.png test-data/2008001635_153_chem.smi test-data/CID_2244.pdf test-data/CID_2244.png test-data/CID_2244.sdf test-data/osra_on_CID2244.sdf test-data/patent.gif test_data/2008001635_153_chem.png test_data/2008001635_153_chem.smi test_data/CID_2244.png test_data/CID_2244.sdf tool_dependencies.xml |
| diffstat | 16 files changed, 211 insertions(+), 317 deletions(-) [+] |
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--- a/osra.py Tue Mar 01 10:38:59 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,27 +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[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) - -
--- a/osra.xml Tue Mar 01 10:38:59 2016 -0500 +++ b/osra.xml Thu Nov 09 03:41:26 2017 -0500 @@ -1,40 +1,38 @@ -<tool id="ctb_osra" name="Molecule recognition" version="0.3"> +<tool id="ctb_osra" name="Molecule recognition" version="2.1.0"> <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> + <requirement type="package" version="2.1.0">osra</requirement> </requirements> - <command interpreter='python'> + <command detect_errors="aggressive"> <![CDATA[ - ## 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 +osra + -f $oformat + '$infile' + -l `which osra | xargs dirname`/../share/spelling.txt + -a `which osra | xargs dirname`/../share/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 + $confidence + $adaptive + $thinning + > '$outfile' ]]> </command> <inputs> - <param name="infile" type="data" format="png,pdf" label="Image or PDF with molecules"/> + <param name="infile" type="data" format="pdf" label="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" /> + <param name="confidence" type="boolean" label="Print out confidence estimate" help=" (-p)" + truevalue="-p" falsevalue="" checked="true" /> + <param name="adaptive" type="boolean" label="Adaptive thresholding pre-processing, useful for low light/low contrast images" help="(-i)" + truevalue="-i" falsevalue="" checked="false" /> + <param name="thinning" type="boolean" label="Additional thinning/scaling down of low quality documents" help="(-j)" + truevalue="-j" falsevalue="" checked="false" /> </inputs> <outputs> - <data name="outfile" type="data" format="sdf"> + <data name="outfile" format="sdf"> <change_format> <when input="oformat" value="can" format="smi"/> </change_format> @@ -42,16 +40,16 @@ </outputs> <tests> <test> - <param name="infile" ftype="png" value="CID_2244.png"/> + <param name="infile" value="CID_2244.pdf" ftype="pdf"/> <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"/> + <!--test> + PNGs producing a core-dump in osra + <param name="infile" value="2008001635_153_chem.png"/> <param name="oformat" value="can"/> - <output name="outfile" ftype="sdf" file="2008001635_153_chem.smi"/> - </test> - + <output name="outfile" ftype="smi" file="2008001635_153_chem.smi"/> + </test--> </tests> <help> <![CDATA[ @@ -64,15 +62,17 @@ .. _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> + <citations> + <citation type="bibtex"> + @inproceedings{filippov2010improvements, + title={Improvements in Optical Structure Recognition Application}, + author={Filippov, Igor V and Nicklaus, Marc C and Kinney, John}, + booktitle={Document Analysis Systems Workshop}, + year={2010} + } + </citation> + </citations> </tool>
--- a/readme Tue Mar 01 10:38:59 2016 -0500 +++ /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.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/readme.md Thu Nov 09 03:41:26 2017 -0500 @@ -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.
--- a/repository_dependencies.xml Tue Mar 01 10:38:59 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -<?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="https://testtoolshed.g2.bx.psu.edu" /> -</repositories>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/CID_2244.sdf Thu Nov 09 03:41:26 2017 -0500 @@ -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 + +$$$$ +
--- a/test_data/2008001635_153_chem.smi Tue Mar 01 10:38:59 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -CCC(c1ccc(cc1)Br)OCCCO
--- a/test_data/CID_2244.sdf Tue Mar 01 10:38:59 2016 -0500 +++ /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 - -$$$$ -
--- a/tool_dependencies.xml Tue Mar 01 10:38:59 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,74 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="openbabel" version="2.3.2"> - <repository changeset_revision="4ec0d9c57ddd" name="package_openbabel_2_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="graphicsmagick" version="1.3.18"> - <repository changeset_revision="9b0d84b880e4" name="package_graphicsmagick_1_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="osra" version="2.0.0"> - <install version="1.0"> - <actions> - <!-- 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="4ec0d9c57ddd" name="package_openbabel_2_3" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> - <package name="openbabel" version="2.3.2" /> - </repository> - <repository changeset_revision="9b0d84b880e4" name="package_graphicsmagick_1_3" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> - <package name="graphicsmagick" version="1.3.18" /> - </repository> - </action> - - <!--compiling potrace-1.11 --> - <action type="download_file">https://depot.galaxyproject.org/software/potrace/potrace_1.11_src_all.tar.gz</action> - <action type="shell_command">tar xfvz potrace-1.11.tar.gz && cd potrace-1.11 && ./configure --with-libpotrace --prefix=$INSTALL_DIR/potrace/build && make && make install</action> - - <!--compiling gocr 0.50patched --> - <!-- not yet possible - <action type="download_file">http://www-e.uni-magdeburg.de/jschulen/ocr/gocr-0.50.tar.gz</action> - <action type="shell_command">tar xfvz gocr-0.50.tar.gz && cd gocr-0.50 && ./configure -|-prefix=$INSTALL_DIR/gocr/build && make libs && make all install</action> - --> - <action type="download_file">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 && cd gocr-0.50pre-patched && ./configure --prefix=$INSTALL_DIR/gocr/build && make libs && make all install</action> - - - <!--compiling tclap 1.2.1 --> - <action type="download_file">http://downloads.sourceforge.net/project/tclap/tclap-1.2.1.tar.gz</action> - <action type="shell_command">tar xfvz tclap-1.2.1.tar.gz && cd tclap-1.2.1 && ./configure --prefix=$INSTALL_DIR/tclap/build && make && make install</action> - - <!--compiling ocrad 0.21 --> - <action type="download_file">http://mirror.checkdomain.de/gnu/ocrad/ocrad-0.21.tar.gz</action> - <action type="shell_command">tar xfvz ocrad-0.21.tar.gz && cd ocrad-0.21 && ./configure --prefix=$INSTALL_DIR/ocrad/build && make && make install</action> - - <!--compiling cuneiform 1.1.0 --> - <action type="download_file">https://launchpad.net/cuneiform-linux/1.1/1.1/+download/cuneiform-linux-1.1.0.tar.bz2</action> - <action type="shell_command">tar xfvj cuneiform-linux-1.1.0.tar.bz2 && cd cuneiform-linux-1.1.0 && mkdir build && cd build && cmake .. -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR/cuneiform/build/ && make && 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/ && - ./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/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> - <!-- 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>We still have a handfull of requirements</readme> - </package> -</tool_dependency>