Hi Greg,

I tried the manifest file and saw that the ordering is not correct. You
can see that on the last to repositories. Since, chemicaltoolbox is the
meta_repository it should be always the last one.

Cheers,
Bjoern

> Hello Bjoern,
> 
> 
> I have the export repository ( and optionally all repoository
> dependencies ) feature working on the test tool shed.  The feature
> allows you to chose a specific installable revision (if in the
> browser, by being on the Manage repository page for that revision or
> if using the API by passing the revision on the command line) for
> export.
> 
> 
> An example API call for this is ( from the ~/tool_shed/scripts/api
> directory):
> 
> 
> python ./export.py --url http://testtoolshed.g2.bx.psu.edu --name
> chemicaltoolbox --owner bgruening --revision 4133dbf7ff4d
> --export_repository_dependencies True --download_dir /tmp
> 
> 
> This will create a file named the following on your local disk:
> 
> 
> capsule_with_dependencies_testtoolshed.g2.bx.psu.edu_chemicaltoolbox_bgruening_4133dbf7ff4d.tar.gz
> 
> 
> If you extract it, you'll have the following:
> 
> 
> lily:repo gvk$ tar -xvf
> capsule_with_dependencies_testtoolshed.g2.bx.psu.edu_chemicaltoolbox_bgruening_4133dbf7ff4d.tar
>  
> x package_graphicsmagick_1_3-34f511310435.tar.gz
> x package_eigen_2_0-7293f118efef.tar.gz
> x package_atlas_3_10-68df9078bf69.tar.gz
> x package_chemfp_1_1-616ee8e4abf4.tar.gz
> x package_freetype_2_4-4e54e357ac25.tar.gz
> x package_lapack_3_4-a6b8f46acca7.tar.gz
> x package_bzlib_1_0-58a38de96f9b.tar.gz
> x package_eigen_3_1-b72b882b30b4.tar.gz
> x natural_product_likeness-da45aa9141cf.tar.gz
> x chemical_data_sources-c065b806ff8c.tar.gz
> x package_openbabel_2_3-3a993ff17df5.tar.gz
> x osra-e5e3d723a675.tar.gz
> x confab-df8c4f142ae3.tar.gz
> x package_boost_1_53-f5b13e56a321.tar.gz
> x molecule_datatypes-18ff2d6e1dca.tar.gz
> x package_numpy_1_7-40db34c904df.tar.gz
> x openbabel-b4ba90dcfde0.tar.gz
> x package_scipy_0_12-cd2e7872a8eb.tar.gz
> x package_matplotlib_1_2-dd81b71dff1b.tar.gz
> x package_scikit_learn_0_13-ad4341b759f2.tar.gz
> x ctb_machine_learning-bf0014ee0871.tar.gz
> x opsin-ee73c8d529b1.tar.gz
> x package_rdkit_2012_12-4663c03127f7.tar.gz
> x rdkit-aa46f08461f9.tar.gz
> x chemfp-ee02ddefe21b.tar.gz
> x silicos_it-1c218c2a4bd8.tar.gz
> x chemicaltoolbox-4133dbf7ff4d.tar.gz
> x simsearch-b4eaf75cac77.tar.gz
> x export_info.xml
> x manifest.xml
> 
> 
> The manifest.xml file defines the order in which the various tarballs
> should be uploaded to the tool shed.  It also includes the categories
> associated with each repository.  The dependency definitions within
> each of these tarballs that contain <repository> tags have had the
> tool_shed and change set_revision attributes eliminated, so when they
> are loaded into a tool shed, they should be automatically populated.
> 
> 
> I do not yet have the import feature implemented, but I'm working on
> it.  Even though the import is not finished, you may find the export
> useful in helping you migrate the chemicaltolbox over to the main tool
> shed.  However, I have not tested anything yet with regard to
> importing or uploading these tarball, so use a local tool shed first
> if you can!
> 
> 
> Let me know if you have any questions or bump into any problems!
> 
> 
> Here is the manifest.xml file for the chemicaltolbox repository:
> 
> 
> <?xml version="1.0"?>
> <repository name="package_graphicsmagick_1_3"
> type="tool_dependency_definition" username="bgruening">
>   <description>GraphicsMagick Image Processing System</description>
>     <long_description>GraphicsMagick is the swiss army knife of image
> processing and it provides a robust and efficient collection of tools
> and libraries which support reading, writing, and manipulating an
> image in over 88 major formats including important formats like DPX,
> GIF, JPEG, JPEG-2000, PNG, PDF, PNM, and TIFF.
> </long_description>
>     <archive>package_graphicsmagick_1_3-34f511310435.tar.gz</archive>
>     <categories>
>       <category>Tool Dependency Packages</category>
>     </categories>
> </repository>
> 
> 
> <repository name="package_eigen_2_0" type="tool_dependency_definition"
> username="bgruening">
>   <description>Contains a tool dependency definition that downloads
> and extract version 2.0.x of the the eigen template
> library.</description>
>     <long_description>Eigen is a C++ template library for linear
> algebra: matrices, vectors, numerical solvers, and related
> algorithms.</long_description>
>     <archive>package_eigen_2_0-7293f118efef.tar.gz</archive>
>     <categories>
>       <category>Tool Dependency Packages</category>
>     </categories>
> </repository>
> 
> 
> <repository name="package_atlas_3_10"
> type="tool_dependency_definition" username="bgruening">
>   <description>Automatically Tuned Linear Algebra
> Software</description>
>     <long_description>The ATLAS (Automatically Tuned Linear Algebra
> Software) project is an ongoing research effort focusing on applying
> empirical techniques in order to provide portable performance. At
> present, it provides C and Fortran77 interfaces to a portably
> efficient BLAS implementation, as well as a few routines from LAPACK.
> 
> 
> http://math-atlas.sourceforge.net/</long_description>
>     <archive>package_atlas_3_10-68df9078bf69.tar.gz</archive>
>     <categories>
>       <category>Tool Dependency Packages</category>
>     </categories>
> </repository>
> 
> 
> <repository name="package_chemfp_1_1"
> type="tool_dependency_definition" username="bgruening">
>   <description>Contains a tool dependency definition that downloads
> and compiles version 1.1.x of the the chemfp package.</description>
>     <long_description>This repository is intended to be defined as a
> complex repository dependency within a separate repository.
> http://wiki.galaxyproject.org/DefiningRepositoryDependencies#Complex_repository_dependencies:_tool_dependency_definitions_that_contain_repository_dependency_definitions
> 
> 
> This is the version 1.1.x of chemfp.
> http://chemfp.com/
> 
> 
> chemfp provides toolkit independent generation of fingerprints and
> high-performance similarity search. The tools support the FPS
> fingerprint file format.</long_description>
>     <archive>package_chemfp_1_1-616ee8e4abf4.tar.gz</archive>
>     <categories>
>       <category>Tool Dependency Packages</category>
>     </categories>
> </repository>
> 
> 
> <repository name="package_freetype_2_4"
> type="tool_dependency_definition" username="bgruening">
>   <description>Contains a tool dependency definition that downloads
> and compiles version 2.4 of the freetype font library.</description>
>     <long_description>FreeType is a freely available software library
> to render fonts.
> 
> 
> It is written in C, designed to be small, efficient, highly
> customizable, and portable while capable of producing high-quality
> output (glyph images) of most vector and bitmap font formats.
> http://www.freetype.org/</long_description>
>     <archive>package_freetype_2_4-4e54e357ac25.tar.gz</archive>
>     <categories>
>       <category>Tool Dependency Packages</category>
>     </categories>
> </repository>
> 
> 
> <repository name="package_lapack_3_4"
> type="tool_dependency_definition" username="bgruening">
>   <description>Linear Algebra PACKage</description>
>     <long_description>Lapack provides routines for solving systems of
> simultaneous linear equations, least-squares solutions of linear
> systems of equations, eigenvalue problems, and singular value
> problems. 
> 
> 
> http://www.netlib.org
> 
> 
> You need a Fortran 90 compiler, e.g. gfortran, to build that
> package.</long_description>
>     <archive>package_lapack_3_4-a6b8f46acca7.tar.gz</archive>
>     <categories>
>       <category>Tool Dependency Packages</category>
>     </categories>
> </repository>
> 
> 
> <repository name="package_bzlib_1_0" type="tool_dependency_definition"
> username="bgruening">
>   <description>Contains a tool dependency definition that downloads
> and compiles version 1.0 of the bzlib library.</description>
>     <long_description>bzip2 is a freely available, patent free (see
> below), high-quality data compressor. It typically compresses files to
> within 10X to 15X of the best available techniques (the PPM family of
> statistical compressors), whilst being around twice as fast at
> compression and six times faster at decompression.
> http://www.bzip.org</long_description>
>     <archive>package_bzlib_1_0-58a38de96f9b.tar.gz</archive>
>     <categories>
>       <category>Tool Dependency Packages</category>
>     </categories>
> </repository>
> 
> 
> <repository name="package_eigen_3_1" type="tool_dependency_definition"
> username="bgruening">
>   <description>Contains a tool dependency definition that downloads,
> compiles and extracts version 3.1.x of the the eigen template
> library.</description>
>     <long_description>Eigen is a C++ template library for linear
> algebra: matrices, vectors, numerical solvers, and related
> algorithms.</long_description>
>     <archive>package_eigen_3_1-b72b882b30b4.tar.gz</archive>
>     <categories>
>       <category>Tool Dependency Packages</category>
>     </categories>
> </repository>
> 
> 
> <repository name="natural_product_likeness" type="unrestricted"
> username="bgruening">
>   <description>Natural product likeness scorer</description>
>     <long_description>The natural product likeness scorer implemented
> by Peter Ertl was originally devised to screen large compound
> libraries for natural product likeness in drug designing studies. His
> work is re-implemented using open source and open data to validate
> natural product likeness of theoretical metabolite structures in
> computer assisted structure elucidation.
> 
> 
> http://sourceforge.net/p/np-likeness</long_description>
>     <archive>natural_product_likeness-da45aa9141cf.tar.gz</archive>
>     <categories>
>       <category>Computational chemistry</category>
>     </categories>
> </repository>
> 
> 
> <repository name="chemical_data_sources" type="unrestricted"
> username="bgruening">
>   <description>Data sources for small molecules</description>
>     <archive>chemical_data_sources-c065b806ff8c.tar.gz</archive>
>     <categories>
>       <category>Data Source</category>
>     </categories>
> </repository>
> 
> 
> <repository name="package_openbabel_2_3"
> type="tool_dependency_definition" username="bgruening">
>   <description>Contains a tool dependency definition that downloads
> and compiles version 2.3.2 of the Open Babel package</description>
>     <long_description>This repository is intended to be defined as a
> complex repository dependency within a separate repository.
> http://wiki.galaxyproject.org/DefiningRepositoryDependencies#Complex_repository_dependencies:_tool_dependency_definitions_that_contain_repository_dependency_definitions
> 
> 
> This is the version 2.3.2 of Open Babel.
> http://openbabel.org
> 
> 
> Open Babel is a chemical toolbox designed to speak the many languages
> of chemical data. It's an open, collaborative project allowing anyone
> to search, convert, analyze, or store data from molecular modeling,
> chemistry, solid-state materials, biochemistry, or related areas.
> </long_description>
>     <archive>package_openbabel_2_3-3a993ff17df5.tar.gz</archive>
>     <categories>
>       <category>Tool Dependency Packages</category>
>     </categories>
> </repository>
> 
> 
> <repository name="osra" type="unrestricted" username="bgruening">
>   <description>OSRA - Optical Structure Recognition
> Application</description>
>     <long_description>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.</long_description>
>     <archive>osra-e5e3d723a675.tar.gz</archive>
>     <categories>
>       <category>Computational chemistry</category>
>     </categories>
> </repository>
> 
> 
> <repository name="confab" type="unrestricted" username="bgruening">
>   <description>Systematic conformation generator</description>
>     <long_description>Confab is an open source conformation generator
> whose goal is the systematic coverage of conformational
> space.</long_description>
>     <archive>confab-df8c4f142ae3.tar.gz</archive>
>     <categories>
>       <category>Computational chemistry</category>
>     </categories>
> </repository>
> 
> 
> <repository name="package_boost_1_53"
> type="tool_dependency_definition" username="bgruening">
>   <description>Contains a tool dependency definition that downloads
> and compiles version 1.53 of the boost C++ libraries</description>
>     <long_description>Boost provides free peer-reviewed portable C++
> source libraries.
> http://www.boost.org/</long_description>
>     <archive>package_boost_1_53-f5b13e56a321.tar.gz</archive>
>     <categories>
>       <category>Tool Dependency Packages</category>
>     </categories>
> </repository>
> 
> 
> <repository name="molecule_datatypes" type="unrestricted"
> username="bgruening">
>   <description>Datatypes and converter for
> cheminformatics</description>
>     <long_description>Molecule datatypes and converters. Including
> SDF, MOL, SMILES, InChI, MOL2, PDB ...</long_description>
>     <archive>molecule_datatypes-18ff2d6e1dca.tar.gz</archive>
>     <categories>
>       <category>Computational chemistry</category>
>         <category>Convert Formats</category>
>     </categories>
> </repository>
> 
> 
> <repository name="package_numpy_1_7" type="tool_dependency_definition"
> username="bgruening">
>   <description>Contains a tool dependency definition that downloads
> and compiles version 1.7 of the the python numpy package</description>
>     <long_description>This repository is intended to be defined as a
> complex repository dependency within a separate repository.
> http://wiki.galaxyproject.org/DefiningRepositoryDependencies#Complex_repository_dependencies:_tool_dependency_definitions_that_contain_repository_dependency_definitions
> 
> 
> This is the version 1.7 of numpy.
> www.numpy.org/
> 
> 
> NumPy is the fundamental package for scientific computing with
> Python.</long_description>
>     <archive>package_numpy_1_7-40db34c904df.tar.gz</archive>
>     <categories>
>       <category>Tool Dependency Packages</category>
>     </categories>
> </repository>
> 
> 
> <repository name="openbabel" type="unrestricted" username="bgruening">
>   <description>Open Babel tools</description>
>     <long_description>Open Babel is a chemical toolbox designed to
> speak the many languages of chemical data. It's an open, collaborative
> project allowing anyone to search, convert, analyze, or store data
> from molecular modeling, chemistry, solid-state materials,
> biochemistry, or related areas. </long_description>
>     <archive>openbabel-b4ba90dcfde0.tar.gz</archive>
>     <categories>
>       <category>Computational chemistry</category>
>     </categories>
> </repository>
> 
> 
> <repository name="package_scipy_0_12"
> type="tool_dependency_definition" username="bgruening">
>   <description>Scientific Tools for Python</description>
>     <long_description>SciPy is open-source software for mathematics,
> science, and engineering. The SciPy library is built to work with
> NumPy arrays, and provides many user-friendly and efficient numerical
> routines such as routines for numerical integration and
> optimization.</long_description>
>     <archive>package_scipy_0_12-cd2e7872a8eb.tar.gz</archive>
>     <categories>
>       <category>Tool Dependency Packages</category>
>     </categories>
> </repository>
> 
> 
> <repository name="package_matplotlib_1_2" type="unrestricted"
> username="bgruening">
>   <description>Contains a tool dependency definition that downloads
> and compiles version 1.2.x of the the python matplotlib
> package.</description>
>     <long_description>This repository is intended to be defined as a
> complex repository dependency within a separate repository.
> http://wiki.galaxyproject.org/DefiningRepositoryDependencies#Complex_repository_dependencies:_tool_dependency_definitions_that_contain_repository_dependency_definitions
> 
> 
> This is the version 1.2.x of matplotlib.
> www.matplotlib.org/
> 
> 
> matplotlib is a python 2D plotting library which produces publication
> quality figures.</long_description>
>     <archive>package_matplotlib_1_2-dd81b71dff1b.tar.gz</archive>
>     <categories>
>       <category>Tool Dependency Packages</category>
>     </categories>
> </repository>
> 
> 
> <repository name="package_scikit_learn_0_13"
> type="tool_dependency_definition" username="bgruening">
>   <description>Contains a tool dependency definition that downloads
> and compiles version 0.13.x of the the scikit-learn
> package.</description>
>     <long_description>Easy-to-use and general-purpose machine learning
> in Python
> 
> 
> Scikit-learn integrates machine learning algorithms in the
> tightly-knit scientific Python world, building upon numpy, scipy, and
> matplotlib. As a machine-learning module, it provides versatile tools
> for data mining and analysis in any field of science and engineering.
> It strives to be simple and efficient, accessible to everybody, and
> reusable in various contexts.
> 
> 
> http://scikit-learn.org/</long_description>
>     <archive>package_scikit_learn_0_13-ad4341b759f2.tar.gz</archive>
>     <categories>
>       <category>Tool Dependency Packages</category>
>     </categories>
> </repository>
> 
> 
> <repository name="ctb_machine_learning" type="unrestricted"
> username="bgruening">
>   <description>machine learning scripts for the
> chemicaltoolbox</description>
>     <long_description>This repository contains small tools dealing
> with machine learning techniques inside the
> chemicaltoolbox.</long_description>
>     <archive>ctb_machine_learning-bf0014ee0871.tar.gz</archive>
>     <categories>
>       <category>Computational chemistry</category>
>     </categories>
> </repository>
> 
> 
> <repository name="opsin" type="unrestricted" username="bgruening">
>   <description>Open Parser for Systematic IUPAC
> nomenclature</description>
>     <long_description>OPSIN is library for IUPAC name-to-structure
> conversion offering high recall and precision on organic chemical
> nomenclature.
> https://bitbucket.org/dan2097/opsin</long_description>
>     <archive>opsin-ee73c8d529b1.tar.gz</archive>
>     <categories>
>       <category>Computational chemistry</category>
>     </categories>
> </repository>
> 
> 
> <repository name="package_rdkit_2012_12"
> type="tool_dependency_definition" username="bgruening">
>   <description>Contains a tool dependency definition that downloads
> and compiles version 2012-12 of the RDKit cheminformatics and
> machine-learning package.</description>
>     <long_description>A collection of cheminformatics and
> machine-learning software written in C++ and Python.
> 
> 
> The core algorithms and data structures are written in C++. Wrappers
> are provided to use the toolkit from either Python or Java.
> 
> 
> Additionally, the RDKit distribution includes a PostgreSQL-based
> cartridge that allows molecules to be stored in relational database
> and retrieved via substructure and similarity searches.
> http://www.rdkit.org/</long_description>
>     <archive>package_rdkit_2012_12-4663c03127f7.tar.gz</archive>
>     <categories>
>       <category>Tool Dependency Packages</category>
>     </categories>
> </repository>
> 
> 
> <repository name="rdkit" type="unrestricted" username="bgruening">
>   <description>RDKit tools.</description>
>     <long_description>Various tools that are using the RDKit
> library.</long_description>
>     <archive>rdkit-aa46f08461f9.tar.gz</archive>
>     <categories>
>       <category>Computational chemistry</category>
>     </categories>
> </repository>
> 
> 
> <repository name="chemfp" type="unrestricted" username="bgruening">
>   <description>Chemfp tools.</description>
>     <long_description>chemfp is a set of tools for working with
> cheminformatics fingerprints in the FPS format.</long_description>
>     <archive>chemfp-ee02ddefe21b.tar.gz</archive>
>     <categories>
>       <category>Computational chemistry</category>
>     </categories>
> </repository>
> 
> 
> <repository name="silicos_it" type="unrestricted"
> username="bgruening">
>   <description>silicos</description>
>     <archive>silicos_it-1c218c2a4bd8.tar.gz</archive>
>     <categories>
>       <category>Computational chemistry</category>
>     </categories>
> </repository>
> 
> 
> <repository name="chemicaltoolbox" type="unrestricted"
> username="bgruening">
>   <description>ChemicalToolBoX Metapackage</description>
>     <long_description>That metapackage will install several
> cheminformatic tool wrappers (e.g. chemfp, openbabel, osra, confab,
> rdkit)</long_description>
>     <archive>chemicaltoolbox-4133dbf7ff4d.tar.gz</archive>
>     <categories>
>       <category>Computational chemistry</category>
>     </categories>
> </repository>
> 
> 
> <repository name="simsearch" type="unrestricted" username="bgruening">
>   <description>Similarity search with openbabel or
> chemfp</description>
>     <long_description>Similarity search with openbabel or
> chemfp</long_description>
>     <archive>simsearch-b4eaf75cac77.tar.gz</archive>
>     <categories>
>       <category>Computational chemistry</category>
>     </categories>
> </repository>
> 
> 
> 
> 
>  
> On Aug 7, 2013, at 10:28 AM, Bjoern Gruening
> <bjoern.gruen...@gmail.com> wrote:
> 
> > 
> > Ok, time to step up and migrate all the stuff to main.
> > 
> > Cheers,
> > Bjoern
> > 
> 
> 


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