Mercurial > repos > bgruening > upload_testing
changeset 76:7f16481a1462
Merged 28.
| author | Dave Bouvier <dave@bx.psu.edu> |
|---|---|
| date | Wed, 20 Nov 2013 10:34:40 -0500 |
| parents | 886b67f8694d (diff) 207d85f220c1 (current diff) |
| children | dfd39244354f |
| files | tool_dependencies.xml |
| diffstat | 7 files changed, 78 insertions(+), 298 deletions(-) [+] |
line wrap: on
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--- 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) - -
--- 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 - - > $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>
--- 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.
--- 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>
--- 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 - -$$$$ -
--- 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 && cd potrace-1.11 && ./configure --with-libpotrace --prefix=$INSTALL_DIR/potrace/build && make && make install</action> - - <action type="shell_command">wget http://downloads.sourceforge.net/project/osra/gocr-patched/gocr-0.50pre-patched.tgz</action> - <action type="shell_command">tar xfvz gocr-0.50pre-patched.tgz && cd gocr-0.50pre-patched && ./configure --prefix=$INSTALL_DIR/gocr/build && make libs && 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 && cd tclap-1.2.1 && ./configure --prefix=$INSTALL_DIR/tclap/build && make && make install</action> - - - <action type="shell_command">wget http://mirror.checkdomain.de/gnu/ocrad/ocrad-0.21.tar.gz</action> - <action type="shell_command">tar xfvz ocrad-0.21.tar.gz && cd ocrad-0.21 && ./configure --prefix=$INSTALL_DIR/ocrad/build && make && 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 && cd cuneiform-linux-1.1.0 && mkdir build && cd build && cmake .. -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR/cuneiform/build/ && make && make install</action> + <action type="shell_command">tar xfz TPP-4.6.3.tgz</action> + <!-- doanload patched version of htmldoc to prevent a TPP crashed during compilation --> + <action type="download_file">https://github.com/bgruening/download_store/raw/master/htmldoc/htmldoc_1.8.27-8ubuntu1.debian.tar.gz</action> + <action type="shell_command">rm ./TPP-4.6.3/trans_proteomic_pipeline/extern/htmldoc.tgz</action> + <action type="shell_command">mv htmldoc_1.8.27-8ubuntu1.debian.tar.gz ./TPP-4.6.3/trans_proteomic_pipeline/extern/htmldoc.tgz</action> + <!-- + <action type="move_file" rename_to="htmldoc.tgz"> + <source>htmldoc-1.8.27-8.debian.patched.tar.gz</source> + <destination>./TPP-4.6.3/trans_proteomic_pipeline/extern/</destination> + </action> + --> + <action type="change_directory">./TPP-4.6.3/trans_proteomic_pipeline/src/</action> + <action type="shell_command">echo 'TPP_ROOT=$INSTALL_DIR/tpp/' > Makefile.config.incl</action> + <action type="shell_command">echo 'TPP_WEB=/tpp/' >> Makefile.config.incl</action> + <action type="shell_command">echo 'CGI_USER_DIR=$INSTALL_DIR/cgi-bin/' >> Makefile.config.incl</action> - - - <action type="shell_command">export PATH=$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=$INSTALL_DIR/cuneiform/build/install/include/ --with-cuneiform --with-cuneiform-lib=$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(.*) /(&) /' ../perl/tpp_models.pl</action> + <action type="shell_command">sed -i -e 's/qw(.*) /(&) /' ../CGI/show_nspbin.pl</action> + <action type="shell_command">sed -i -e 's/qw(.*) /(&) /' ../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/:$PERL5LIB && export PATH=$PERL_ROOT_DIR/bin/:$PATH && export PERL5LIB=$PERL_ROOT_DIR/lib/perl5:$PERL5LIB && make</action> + <action type="shell_command">make install</action> <action type="set_environment"> - <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$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>