Re: [galaxy-dev] [galaxy-iuc] Tool Shed packages for BLAST+ binaries
Hi Nicola! > Il giorno mer, 07/08/2013 alle 16.28 +0200, Bjoern Gruening ha scritto: > > > Also, we may wish to add a dependency on BOOST, e.g. > > > http://testtoolshed.g2.bx.psu.edu/view/iuc/package_boost_1_53 > > > once this is on the main Tool Shed. > > > > Ok, time to step up and migrate all the stuff to main. > > Thanks Bjoern, > I'd make us of it also for another tool I'm preparing (a wrapper for > Mugsy multiple aligner). > > Nicola Forgot to mention that most of my tool dependency packages are now in the Main Tool Shed under the IUC account. If I forget something to migrate, please ping me. A complete list can be found here: https://github.com/bgruening/galaxytools/tree/master/orphan_tool_dependencies Cheers, Bjoern ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] [galaxy-iuc] Tool Shed packages for BLAST+ binaries
Peter, I've created a Trello card for tracking the status of this issue. https://trello.com/c/32l2NZRn/1048-toolshed-investigate-possibility-of-recording-tool-dependencies-that-time-out-in-the-automated-testing-process --Dave B. On 8/14/13 09:40:03.000, Peter Cock wrote: On Wed, Aug 14, 2013 at 2:32 PM, Dave Bouvier wrote: Peter, The problem with testing the installation of package tool dependencies, especially but not limited to BLAST+, is that the time it takes to compile them exceeds the timeout for the automated testing framework, and so it terminates that build step. I am currently working on enhancing the actions tag to support a different install process depending on the target architecture, and hope to have that ready early next week. --Dave B. That's useful (and probably explains quite a few 'silent failures'). Could you make sure this time out failure and other install failures are visible on the Tool Shed as part of the test results? I think that is more urgent than tweaking the install target architecture. Thanks, Peter ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] [galaxy-iuc] Tool Shed packages for BLAST+ binaries
On Wed, Aug 14, 2013 at 2:32 PM, Dave Bouvier wrote: > Peter, > > The problem with testing the installation of package tool dependencies, > especially but not limited to BLAST+, is that the time it takes to compile > them exceeds the timeout for the automated testing framework, and so it > terminates that build step. I am currently working on enhancing the actions > tag to support a different install process depending on the target > architecture, and hope to have that ready early next week. > >--Dave B. That's useful (and probably explains quite a few 'silent failures'). Could you make sure this time out failure and other install failures are visible on the Tool Shed as part of the test results? I think that is more urgent than tweaking the install target architecture. Thanks, Peter ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] [galaxy-iuc] Tool Shed packages for BLAST+ binaries
Peter, The problem with testing the installation of package tool dependencies, especially but not limited to BLAST+, is that the time it takes to compile them exceeds the timeout for the automated testing framework, and so it terminates that build step. I am currently working on enhancing the actions tag to support a different install process depending on the target architecture, and hope to have that ready early next week. --Dave B. On 8/14/13 06:56:35.000, Peter Cock wrote: Hi Greg, I'm hoping you (or Dave) can throw a little light on why the NCBI BLAST+ nightly tests are not working again yet: http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/949fa0294c0d e.g. Fatal error: Exit code 127 () /bin/sh: 1: blastn: not found /bin/sh: 1: blastn: not found As of that commit, the ncbi_blast_plus repository depends on the new IUC repository package_blast_plus_2_2_26 which now depends on the IUC repository package_boost_1_53, which depends on Bjoern's package_bzlib_1_0, i.e. this chain: http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus -> http://testtoolshed.g2.bx.psu.edu/view/iuc/package_blast_plus_2_2_26 -> http://testtoolshed.g2.bx.psu.edu/view/iuc/package_boost_1_53 -> http://testtoolshed.g2.bx.psu.edu/view/bgruening/package_bzlib_1_0 Sadly the (Test) Tool Shed isn't showing me any install logs, so I am hoping *you* have access to them. I've also requested individual package repositories (i.e. type "Tool dependency definition") be tested nightly for installation problems: https://trello.com/c/HVGrShnC/1042-tool-shed-should-test-installation-of-packages Meanwhile, I have tried this locally - the dependencies seem to install, but the BLAST+ package says "Installed, missing tool dependencies". It looks like the BLAST+ make fails, but I don't know how/if I can see this from the Galaxy Admin web-interface. I can see the logs at the command line, $ tail -n 30 blast+/2.2.26+/iuc/package_blast_plus_2_2_26/9ff9bfdcd04f/INSTALLATION.log make[1]: Leaving directory `/opt/galaxy-dist/database/tmp/tmp-toolshed-mtdutx4hN/ncbi-blast-2.2.26+-src/c++/GCC412-Debug64/build' # # cd c++ && ./configure --with-boost=$BOOST_ROOT_DIR --prefix=/opt/galaxy-dist-shed-tools/blast+/2.2.26+/iuc/package_blast_plus_2_2_26/9ff9bfdcd04f && make && make install STDERR basename: missing operand Try `basename --help' for more information. configure: WARNING: Untested Boost version; may prove incompatible. configure: WARNING: If so, please re-run this script with the flag --without-boost. make[1]: [/opt/galaxy-dist/database/tmp/tmp-toolshed-mtdutx4hN/ncbi-blast-2.2.26+-src/c++/src/db/Makefile.in] Error 1 (ignored) make[1]: [/opt/galaxy-dist/database/tmp/tmp-toolshed-mtdutx4hN/ncbi-blast-2.2.26+-src/c++/src/db/Makefile.in] Error 1 (ignored) make[1]: [/opt/galaxy-dist/database/tmp/tmp-toolshed-mtdutx4hN/ncbi-blast-2.2.26+-src/c++/src/ctools/Makefile.in] Error 1 (ignored) make[1]: [/opt/galaxy-dist/database/tmp/tmp-toolshed-mtdutx4hN/ncbi-blast-2.2.26+-src/c++/src/ctools/Makefile.in] Error 1 (ignored) make[1]: [/opt/galaxy-dist/database/tmp/tmp-toolshed-mtdutx4hN/ncbi-blast-2.2.26+-src/c++/src/misc/Makefile.in] Error 1 (ignored) make[1]: [/opt/galaxy-dist/database/tmp/tmp-toolshed-mtdutx4hN/ncbi-blast-2.2.26+-src/c++/src/misc/Makefile.in] Error 1 (ignored) make[1]: [/opt/galaxy-dist/database/tmp/tmp-toolshed-mtdutx4hN/ncbi-blast-2.2.26+-src/c++/src/gui/Makefile.in] Error 1 (ignored) make[1]: [/opt/galaxy-dist/database/tmp/tmp-toolshed-mtdutx4hN/ncbi-blast-2.2.26+-src/c++/src/gui/Makefile.in] Error 1 (ignored) make[1]: [/opt/galaxy-dist/database/tmp/tmp-toolshed-mtdutx4hN/ncbi-blast-2.2.26+-src/c++/src/sample/Makefile.in] Error 1 (ignored) make[1]: [/opt/galaxy-dist/database/tmp/tmp-toolshed-mtdutx4hN/ncbi-blast-2.2.26+-src/c++/src/sample/Makefile.in] Error 1 (ignored) make[1]: [/opt/galaxy-dist/database/tmp/tmp-toolshed-mtdutx4hN/ncbi-blast-2.2.26+-src/c++/src/internal/Makefile.in] Error 1 (ignored) make[1]: [/opt/galaxy-dist/database/tmp/tmp-toolshed-mtdutx4hN/ncbi-blast-2.2.26+-src/c++/src/internal/Makefile.in] Error 1 (ignored) make[2]: [/opt/galaxy-dist/database/tmp/tmp-toolshed-mtdutx4hN/ncbi-blast-2.2.26+-src/c++/src/corelib/test/Makefile.in] Error 1 (ignored) make[2]: [/opt/galaxy-dist/database/tmp/tmp-toolshed-mtdutx4hN/ncbi-blast-2.2.26+-src/c++/src/corelib/test/Makefile.in] Error 1 (ignored) /bin/sh: /usr/bin/touch: No such file or directory make[3]: *** [sources.usr] Error 127 make[2]: *** [sources.usr.locked] Error 2 make[1]: *** [all_r.real] Error 5 make: *** [all] Error 2 # I just checked the BOOST bit worked by manually compiling BLAST+, $ echo 'BOOST_ROOT_DIR=/opt/galaxy-dist-shed-tools/boost/1.53.0/iuc/package_boost_1_53/a72f8efe9201/boost; export BOOST_ROOT_DIR' $ ./configure --with-boost=$BOOST_ROOT_DIR --prefix=/opt/galaxy-dist-shed-t
Re: [galaxy-dev] [galaxy-iuc] Tool Shed packages for BLAST+ binaries
Hi Peter, no nothing BLAST+ related. Greg highjacked that thread to inform me about the new export functionality. I will stop posting here. Cheers, Bjoern > Hi Bjoern, > > Was this reply on the wrong thread - or is there > something here related to the BLAST+ binaries? > > Thanks, > > Peter > > On Wed, Aug 14, 2013 at 10:29 AM, Bjoern Gruening > wrote: > > 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. > >> > >> ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] [galaxy-iuc] Tool Shed packages for BLAST+ binaries
Hi Bjoern, Was this reply on the wrong thread - or is there something here related to the BLAST+ binaries? Thanks, Peter On Wed, Aug 14, 2013 at 10:29 AM, Bjoern Gruening wrote: > 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. >> >> ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] [galaxy-iuc] Tool Shed packages for BLAST+ binaries
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 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: > > > > type="tool_dependency_definition" username="bgruening"> > GraphicsMagick Image Processing System > 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. > > package_graphicsmagick_1_3-34f511310435.tar.gz > > Tool Dependency Packages > > > > > username="bgruening"> > Contains a tool dependency definition that downloads > and extract version 2.0.x of the the eigen template > library. > Eigen is a C++ template library for linear > algebra: matrices, vectors, numerical solvers, and related > algorithms. > package_eigen_2_0-7293f118efef.tar.gz > > Tool Dependency Packages > > > > > type="tool_dependency_definition" username="bgruening"> > Automatically Tuned Linear Algebra > Software > 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/ > package_atlas_3_10-68df9078bf69.tar.gz > > Tool Dependency Packages > > > > > type="tool_dependency_definition" username="bgruening"> > Contains a tool dependency definition that downloads > and compiles version 1.1.x of the t
Re: [galaxy-dev] [galaxy-iuc] Tool Shed packages for BLAST+ binaries
Thanks Bjoern, My hope is that the current export process will help you with whatever you are manually migrating. If you export the chemicaltoolbox and all of it's dependencies, you will have a nice tarball of each repository that you want to manually upload to the main tool shed. Of course, you'll need to be looged in as the owner that you want for each of the uploaded repositories. The order that you'll want to upload each of them manually is defined in the manifest.xml file, so that should help as well. And automatically populating the "unpopulated" toolshed and changeset_revision attributes for tags should make things easier. Thanks! Greg On Aug 7, 2013, at 11:20 AM, Bjoern Gruening wrote: > 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 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: >> >> >> >> > type="tool_dependency_definition" username="bgruening"> >> GraphicsMagick Image Processing System >>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. >> >>package_graphicsmagick_1_3-34f511310435.tar.gz >> >> Tool Dependency Packages >> >> >> >> >> > username="bgruening"> >> Contains a tool dependency definition that downloads >> and extract version 2.0.x of the the eigen template >> library. >>Eigen is a C++ template library for linear >> algebra: matrices, vectors, numerical solvers, and related >> algorithms. >>package_eigen_2_0
Re: [galaxy-dev] [galaxy-iuc] Tool Shed packages for BLAST+ binaries
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 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: > > > > type="tool_dependency_definition" username="bgruening"> > GraphicsMagick Image Processing System > 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. > > package_graphicsmagick_1_3-34f511310435.tar.gz > > Tool Dependency Packages > > > > > username="bgruening"> > Contains a tool dependency definition that downloads > and extract version 2.0.x of the the eigen template > library. > Eigen is a C++ template library for linear > algebra: matrices, vectors, numerical solvers, and related > algorithms. > package_eigen_2_0-7293f118efef.tar.gz > > Tool Dependency Packages > > > > > type="tool_dependency_definition" username="bgruening"> > Automatically Tuned Linear Algebra > Software > 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/ > package_atlas_3_10-68df9078bf69.tar.gz > > Tool Dependency Packages > > > > > type="tool_dependency_definition" username="bgruening"> > Contains a tool dependency definition that downloads > and compiles version 1.1.x of the the chemfp package. > This rep
Re: [galaxy-dev] [galaxy-iuc] Tool Shed packages for BLAST+ binaries
Il giorno mer, 07/08/2013 alle 16.28 +0200, Bjoern Gruening ha scritto: > > Also, we may wish to add a dependency on BOOST, e.g. > > http://testtoolshed.g2.bx.psu.edu/view/iuc/package_boost_1_53 > > once this is on the main Tool Shed. > > Ok, time to step up and migrate all the stuff to main. Thanks Bjoern, I'd make us of it also for another tool I'm preparing (a wrapper for Mugsy multiple aligner). Nicola -- Nicola Soranzo, Ph.D. CRS4 Bioinformatics Program Loc. Piscina Manna 09010 Pula (CA), Italy http://www.bioinformatica.crs4.it/ ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] [galaxy-iuc] Tool Shed packages for BLAST+ binaries
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 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: GraphicsMagick Image Processing System 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. package_graphicsmagick_1_3-34f511310435.tar.gz Tool Dependency Packages Contains a tool dependency definition that downloads and extract version 2.0.x of the the eigen template library. Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms. package_eigen_2_0-7293f118efef.tar.gz Tool Dependency Packages Automatically Tuned Linear Algebra Software 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/ package_atlas_3_10-68df9078bf69.tar.gz Tool Dependency Packages Contains a tool dependency definition that downloads and compiles version 1.1.x of the the chemfp package. 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. package_chemfp_1_1-616ee8e4abf4.tar.gz Tool Dependency Packages Contains a tool dependency definition that downloads and compiles ver
Re: [galaxy-dev] [galaxy-iuc] Tool Shed packages for BLAST+ binaries
Hi Peter, > Hi Greg et al, > > For the NCBI BLAST+ wrappers, Nicola has suggested we split > out the binaries themselves into a separate Tool Shed package, > e.g. package_blast_plus_2_2_26 and similar for the later releases. > > https://github.com/peterjc/galaxy_blast/issues/7 > > I think this is a good idea. Yes, me too! > I'd like to check if there are any complications foreseeable from > the fact that the NCBI BLAST+ wrappers were migrated out of > the Galaxy core and therefore have migration scripts we need > to consider. > > Potentially this could be held under the shared IUC account > as planned for other commonly used packages? Or would > the migration issues require it to also live under devteam? > > Also, we may wish to add a dependency on BOOST, e.g. > http://testtoolshed.g2.bx.psu.edu/view/iuc/package_boost_1_53 > once this is on the main Tool Shed. Ok, time to step up and migrate all the stuff to main. Cheers, Bjoern > Regards, > > Peter > ___ > galaxy-iuc mailing list > galaxy-...@lists.bx.psu.edu > http://lists.bx.psu.edu/listinfo/galaxy-iuc ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
