Mercurial > repos > bgruening > osra

changeset 7:edff5c162649

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Uploaded
author bgruening
date Sat, 11 May 2013 17:13:11 -0400
parents 26189cd2a940
children dfa05117e30a
files readme repository_dependencies.xml
diffstat 2 files changed, 2 insertions(+), 147 deletions(-) [+]
line wrap: on
line diff
--- a/readme	Fri Apr 26 11:08:46 2013 -0400
+++ b/readme	Sat May 11 17:13:11 2013 -0400
@@ -16,150 +16,5 @@
 
 http://cactus.nci.nih.gov/osra/
 
-
 The wrapper comes with an automatic installation of all dependencies through the
-galaxy toolshed. If you do not want to use that feature you can compile OSRA with
-the following instructions.
-
-
-########################################
-#                                      #
-#           OSRA Setup                 #
-# currently a small patch is requiered #
-#                                      #
-########################################
-
-Save the following file to 'osra-1.4.0-configure.patch' and store it next 
-to that script below.
-
--------------------------------------------------------
---- configure	2013-03-18 18:14:00.888605219 +0100
-+++ configure_ori	2013-03-18 18:13:48.396605759 +0100
-@@ -4178,7 +4178,8 @@
- 
- # Check whether --with-tclap-include was given.
- if test "${with_tclap_include+set}" = set; then :
--  withval=$with_tclap_include;
-+    withval=$with_tclap_include;
-+    CPPFLAGS="-I${withval} ${CPPFLAGS}"
- else
-   with_tclap_include="auto"
- fi
--------------------------------------------------------
-
-#!/usr/bin/bash
-#osra installation
-
-cdir=`pwd`
-
-wget http://sourceforge.net/projects/graphicsmagick/files/graphicsmagick/1.3.18/GraphicsMagick-1.3.18.tar.gz
-tar xfvz GraphicsMagick-1.3.18.tar.gz
-cd GraphicsMagick-1.3.18
-./configure --prefix=`pwd`/build --enable-shared=yes
-make
-make install
-cd ..
-
-export PATH=$PATH:/home/bag/projects/osra/GraphicsMagick-1.3.18/build/bin/
-
-wget http://potrace.sourceforge.net/download/potrace-1.11.tar.gz
-tar xfvz potrace-1.11.tar.gz
-cd potrace-1.11
-./configure --with-libpotrace --prefix=`pwd`/build
-make
-make install
-cd ..
-
-wget http://downloads.sourceforge.net/project/osra/gocr-patched/gocr-0.50pre-patched.tgz
-tar xfvz gocr-0.50pre-patched.tgz
-cd gocr-0.50pre-patched
-./configure --prefix=`pwd`/build
-make libs
-make all install
-cd ..
-
-wget http://downloads.sourceforge.net/project/tclap/tclap-1.2.1.tar.gz
-tar xfvz tclap-1.2.1.tar.gz
-cd tclap-1.2.1
-./configure --prefix=`pwd`/build
-make
-make install
-cd ..
-
-wget http://mirror.checkdomain.de/gnu/ocrad/ocrad-0.21.tar.gz
-tar xfvz ocrad-0.21.tar.gz
-cd ocrad-0.21
-./configure --prefix=`pwd`/build
-make
-make install
-cd ..
-
-wget http://downloads.sourceforge.net/project/openbabel/openbabel/2.3.2/openbabel-2.3.2.tar.gz
-tar xfvz openbabel-2.3.2.tar.gz
-cd openbabel-2.3.2
-mkdir build
-cd build
-cmake .. -DCMAKE_INSTALL_PREFIX=`pwd`/install/
-make
-make install
-cd ../..
-
-#wget http://tesseract-ocr.googlecode.com/files/tesseract-ocr-3.02.02.tar.gz
-#tar xfvz tesseract-ocr-3.02.02.tar.gz
-#cd tesseract-ocr
-#./configure --prefix=`pwd`/build
-#make
-#make install
-#cd ..
-
-
-wget https://launchpad.net/cuneiform-linux/1.1/1.1/+download/cuneiform-linux-1.1.0.tar.bz2
-tar xfvj cuneiform-linux-1.1.0.tar.bz2
-cd cuneiform-linux-1.1.0
-mkdir build
-cd build
-cmake .. -DCMAKE_INSTALL_PREFIX=`pwd`/install/
-make
-make install
-cd ../..
-
-
-wget http://downloads.sourceforge.net/project/osra/osra/1.4.0/osra-1.4.0.tgz
-tar xfvz osra-1.4.0.tgz
-patch osra-1.4.0/configure < osra-1.4.0-configure.patch
-cd osra-1.4.0
-
-./configure --with-tclap-include=$cdir/tclap-1.2.1/build/include/ \
---with-potrace-include=$cdir/potrace-1.11/build/include/ \
---with-potrace-lib=$cdir/potrace-1.11/build/lib/ \
---with-gocr-include=$cdir/gocr-0.50pre-patched/build/include/gocr/ \
---with-gocr-lib=$cdir/gocr-0.50pre-patched/build/lib/ \
---with-ocrad-include=$cdir/ocrad-0.21/build/include/ \
---with-ocrad-lib=$cdir/ocrad-0.21/build/lib/ \
---with-cuneiform-include=$cdir/cuneiform-linux-1.1.0/build/install/include/ \
---with-cuneiform \
---with-cuneiform-lib=$cdir/cuneiform-linux-1.1.0/build/install/lib/ \
---with-openbabel-include=$cdir/openbabel-2.3.2/build/install/include/openbabel-2.0/ \
---with-openbabel-lib=$cdir/openbabel-2.3.2/build/install/lib/ \
---with-graphicsmagick-lib=$cdir/GraphicsMagick-1.3.18/build/lib/ \
---with-graphicsmagick-include=$cdir/GraphicsMagick-1.3.18/build/include/GraphicsMagick/ \
---prefix=`pwd`/bin/ 
-#--enable-static-linking --disable-graphicsmagick-config
-make
-make install
-
-export LD_LIBRARY_PATH=$cdir/GraphicsMagick-1.3.18/build/lib/:$cdir/GraphicsMagick-1.3.18/build/lib:$cdir/potrace-1.11/build/lib/
-./bin/bin/osra
-
-
-#--with-tesseract-include=$cdir/tclap-1.2.1/build/include/
-#--with-tesseract
-#--with-tesseract-lib
-
-
-
-
-
-
-
-
+galaxy toolshed.
--- a/repository_dependencies.xml	Fri Apr 26 11:08:46 2013 -0400
+++ b/repository_dependencies.xml	Sat May 11 17:13:11 2013 -0400
@@ -1,4 +1,4 @@
 <?xml version="1.0"?>
 <repositories description="This requires the Molecule datatype definitions (e.g. SMILES, InChI, SD-format).">
-    <repository toolshed="http://testtoolshed.g2.bx.psu.edu/" name="molecule_datatypes" owner="bgruening" changeset_revision="e533de975501" />
+    <repository toolshed="http://testtoolshed.g2.bx.psu.edu/" name="molecule_datatypes" owner="bgruening" changeset_revision="1a070566e9c6" />
 </repositories>