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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