Hi Greg, wonderful will test it locally asap and report any error. The most urgent packages I will migrate manually for the time being. I promised it far to long.
Thanks Greg!!! 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 > > > > ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. 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