| Previous changeset 0:b2040467dad2 (2014-05-06) Next changeset 2:0c393c9d3756 (2014-05-07) |
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Commit message:
Uploaded |
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added:
blockclust_workflow_clustering.ga blockclust_workflow_complete.ga |
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removed:
blockclust_workflow.ga readme.rst |
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| diff -r b2040467dad2 -r 25afbac62e0d blockclust_workflow.ga --- a/blockclust_workflow.ga Tue May 06 12:51:51 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,461 +0,0 @@\n-{\n- "a_galaxy_workflow": "true", \n- "annotation": "", \n- "format-version": "0.1", \n- "name": "BlockClustWorkflow", \n- "steps": {\n- "0": {\n- "annotation": "", \n- "id": 0, \n- "input_connections": {}, \n- "inputs": [\n- {\n- "description": "", \n- "name": "Input BAM file"\n- }\n- ], \n- "name": "Input dataset", \n- "outputs": [], \n- "position": {\n- "left": 267, \n- "top": 257.5\n- }, \n- "tool_errors": null, \n- "tool_id": null, \n- "tool_state": "{\\"name\\": \\"Input BAM file\\"}", \n- "tool_version": null, \n- "type": "data_input", \n- "user_outputs": []\n- }, \n- "1": {\n- "annotation": "", \n- "id": 1, \n- "input_connections": {\n- "tool_mode|reads_bam": {\n- "id": 0, \n- "output_name": "output"\n- }\n- }, \n- "inputs": [], \n- "name": "BlockClust", \n- "outputs": [\n- {\n- "name": "tags_bed", \n- "type": "bed"\n- }, \n- {\n- "name": "hclust_plot", \n- "type": "pdf"\n- }, \n- {\n- "name": "clusters", \n- "type": "bed"\n- }, \n- {\n- "name": 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| diff -r b2040467dad2 -r 25afbac62e0d blockclust_workflow_clustering.ga --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/blockclust_workflow_clustering.ga Wed May 07 04:59:28 2014 -0400 |
| [ |
| b'@@ -0,0 +1,282 @@\n+{\n+ "a_galaxy_workflow": "true", \n+ "annotation": "Until clustering step. 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"action_type": "HideDatasetAction", \n+ "output_name": "cluster_dist"\n+ }, \n+ "HideDatasetActioncluster_hclust": {\n+ "action_arguments": {}, \n+ "action_type": "HideDatasetAction", \n+ "output_name": "cluster_hclust"\n+ }, \n+ "HideDatasetActionsim_tab_out": {\n+ "action_arguments": {}, \n+ "action_type": "HideDatasetAction", \n+ "output_name": "sim_tab_out"\n+ }, \n+ "HideDatasetActiontags_bed": {\n+ "action_arguments": {}, \n+ "action_type": "HideDatasetAction", \n+ "output_name": "tags_bed"\n+ }\n+ }, \n+ "tool_errors": null, \n+ "tool_id": "toolshed.g2.bx.psu.edu/repos/rnateam/blockclust/blockclust/1.0.0", \n+ "tool_state": "{\\"tool_mode\\": \\"{\\\\\\"pred\\\\\\": {\\\\\\"pred_mode\\\\\\": {\\\\\\"__class__\\\\\\": \\\\\\"RuntimeValue\\\\\\"}, \\\\\\"enable_pred\\\\\\": \\\\\\"yes\\\\\\", \\\\\\"__current_case__\\\\\\": 0}, \\\\\\"operation\\\\\\": \\\\\\"clust\\\\\\", \\\\\\"reference\\\\\\": {\\\\\\"__class__\\\\\\": \\\\\\"RuntimeValue\\\\\\"}, 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| diff -r b2040467dad2 -r 25afbac62e0d blockclust_workflow_complete.ga --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/blockclust_workflow_complete.ga Wed May 07 04:59:28 2014 -0400 |
| [ |
| b'@@ -0,0 +1,462 @@\n+{\n+ "a_galaxy_workflow": "true", \n+ "annotation": "", \n+ "format-version": "0.1", \n+ "name": "BlockClustWorkflow_clustering", \n+ "steps": {\n+ "0": {\n+ "annotation": "", \n+ "id": 0, \n+ "input_connections": {}, \n+ "inputs": [\n+ {\n+ "description": "", \n+ "name": "Input BAM file"\n+ }\n+ ], \n+ "name": "Input dataset", \n+ "outputs": [], \n+ "position": {\n+ "left": 217, \n+ "top": 276.5\n+ }, \n+ "tool_errors": null, \n+ "tool_id": null, \n+ "tool_state": "{\\"name\\": \\"Input BAM file\\"}", \n+ "tool_version": null, \n+ "type": "data_input", \n+ "user_outputs": []\n+ }, \n+ "1": {\n+ "annotation": "", \n+ "id": 1, \n+ "input_connections": {\n+ "tool_mode|reads_bam": {\n+ "id": 0, \n+ "output_name": "output"\n+ }\n+ }, \n+ "inputs": [], \n+ "name": "BlockClust", \n+ "outputs": [\n+ {\n+ "name": "tags_bed", \n+ "type": "bed"\n+ }, \n+ {\n+ "name": "hclust_plot", \n+ "type": "pdf"\n+ }, \n+ {\n+ "name": "clusters", \n+ "type": "bed"\n+ }, \n+ {\n+ "name": "model_based_pred_bed", \n+ "type": "bed"\n+ }, \n+ {\n+ "name": "nearest_neighbour_pred_bed", \n+ "type": "bed"\n+ }, \n+ {\n+ "name": "sim_tab_out", \n+ "type": "tabular"\n+ }, \n+ {\n+ "name": "cluster_dist", \n+ "type": "pdf"\n+ }, \n+ {\n+ "name": "cluster_hclust", \n+ "type": "pdf"\n+ }\n+ ], \n+ "position": {\n+ "left": 446.5, \n+ "top": 233.5\n+ }, \n+ "post_job_actions": {\n+ "HideDatasetActioncluster_dist": {\n+ "action_arguments": {}, \n+ "action_type": "HideDatasetAction", \n+ "output_name": "cluster_dist"\n+ }, \n+ "HideDatasetActioncluster_hclust": {\n+ "action_arguments": {}, \n+ "action_type": "HideDatasetAction", \n+ "output_name": "cluster_hclust"\n+ }, \n+ "HideDatasetActionclusters": {\n+ "action_arguments": {}, \n+ "action_type": "HideDatasetAction", \n+ "output_name": "clusters"\n+ }, \n+ "HideDatasetActionhclust_plot": {\n+ "action_arguments": {}, \n+ "action_type": "HideDatasetAction", \n+ "output_name": "hclust_plot"\n+ }, \n+ "HideDatasetActionmodel_based_pred_bed": {\n+ "action_arguments": {}, \n+ "action_type": "HideDatasetAction", \n+ "output_name": "model_based_pred_bed"\n+ }, \n+ "HideDatasetActionnearest_neighbour_pred_bed": {\n+ "action_arguments": {}, \n+ "action_type": "HideDatasetAction", \n+ "output_name": "nearest_neighbour_pred_bed"\n+ }, \n+ "HideDatasetActionsim_tab_out": {\n+ "action_arguments": {}, \n+ "action_type": "HideDatasetAction", \n+ "output_name": "sim_tab_out"\n+ }, \n+ '..b'ing_thresholds_selector\\\\\\": \\\\\\"-E\\\\\\", \\\\\\"E\\\\\\": \\\\\\"0.1\\\\\\", \\\\\\"__current_case__\\\\\\": 1}\\", \\"cyk\\": \\"\\\\\\"False\\\\\\"\\", \\"__rerun_remap_job_id__\\": null}", \n+ "tool_version": "1.1.0.2", \n+ "type": "tool", \n+ "user_outputs": []\n+ }, \n+ "7": {\n+ "annotation": "", \n+ "id": 7, \n+ "input_connections": {\n+ "tool_mode|clusters_bed": {\n+ "id": 4, \n+ "output_name": "clusters"\n+ }, \n+ "tool_mode|cmsearch_out": {\n+ "id": 6, \n+ "output_name": "outfile"\n+ }, \n+ "tool_mode|sim_tab_in": {\n+ "id": 4, \n+ "output_name": "sim_tab_out"\n+ }\n+ }, \n+ "inputs": [], \n+ "name": "BlockClust", \n+ "outputs": [\n+ {\n+ "name": "tags_bed", \n+ "type": "bed"\n+ }, \n+ {\n+ "name": "hclust_plot", \n+ "type": "pdf"\n+ }, \n+ {\n+ "name": "clusters", \n+ "type": "bed"\n+ }, \n+ {\n+ "name": "model_based_pred_bed", \n+ "type": "bed"\n+ }, \n+ {\n+ "name": "nearest_neighbour_pred_bed", \n+ "type": "bed"\n+ }, \n+ {\n+ "name": "sim_tab_out", \n+ "type": "tabular"\n+ }, \n+ {\n+ "name": "cluster_dist", \n+ "type": "pdf"\n+ }, \n+ {\n+ "name": "cluster_hclust", \n+ "type": "pdf"\n+ }\n+ ], \n+ "position": {\n+ "left": 2165.5, \n+ "top": 313.5\n+ }, \n+ "post_job_actions": {\n+ "HideDatasetActionclusters": {\n+ "action_arguments": {}, \n+ "action_type": "HideDatasetAction", \n+ "output_name": "clusters"\n+ }, \n+ "HideDatasetActionhclust_plot": {\n+ "action_arguments": {}, \n+ "action_type": "HideDatasetAction", \n+ "output_name": "hclust_plot"\n+ }, \n+ "HideDatasetActionmodel_based_pred_bed": {\n+ "action_arguments": {}, \n+ "action_type": "HideDatasetAction", \n+ "output_name": "model_based_pred_bed"\n+ }, \n+ "HideDatasetActionnearest_neighbour_pred_bed": {\n+ "action_arguments": {}, \n+ "action_type": "HideDatasetAction", \n+ "output_name": "nearest_neighbour_pred_bed"\n+ }, \n+ "HideDatasetActionsim_tab_out": {\n+ "action_arguments": {}, \n+ "action_type": "HideDatasetAction", \n+ "output_name": "sim_tab_out"\n+ }, \n+ "HideDatasetActiontags_bed": {\n+ "action_arguments": {}, \n+ "action_type": "HideDatasetAction", \n+ "output_name": "tags_bed"\n+ }\n+ }, \n+ "tool_errors": null, \n+ "tool_id": "toolshed.g2.bx.psu.edu/repos/rnateam/blockclust/blockclust/1.0.0", \n+ "tool_state": "{\\"tool_mode\\": \\"{\\\\\\"cmsearch_out\\\\\\": null, \\\\\\"operation\\\\\\": \\\\\\"post\\\\\\", \\\\\\"clusters_bed\\\\\\": null, \\\\\\"__current_case__\\\\\\": 2, \\\\\\"sim_tab_in\\\\\\": null}\\", \\"__rerun_remap_job_id__\\": null, \\"__page__\\": 0}", \n+ "tool_version": "1.0.0", \n+ "type": "tool", \n+ "user_outputs": []\n+ }\n+ }\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r b2040467dad2 -r 25afbac62e0d readme.rst --- a/readme.rst Tue May 06 12:51:51 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b"@@ -1,278 +0,0 @@\n-\n-\n-This package is a Galaxy workflow for BlockClust pipeline.\n-\n-\n-======\n-Galaxy\n-======\n-\n-`Galaxy <http://galaxyproject.org/>`_ is an open, web-based platform for data intensive research.\n-All tools can be combined in workflows without any need of programming skills. \n-Furthermore the platform can be extended with more tools at any time.\n-Each tool has its own information about what it does and how the input is supposed to look like.\n-You can make data available for Galaxy by uploading local files or downloading online content.\n-Inputfiles, workflowsteps and results are stored in a history where you can view them or reaccess them later.\n-It is possible to share workflows and histories with other users or make the public available.\n-Saved workflows can be used with new input files or just to rerun an analyses which ensures repeatability.\n-\n-\n-\n-Getting Started\n-===============\n-\n-BlockClust can be installed on all common Unix systems. \n-However, it is developed on Linux and I don't have access to OS X. You are welcome to help improving this documentation, just contact_ me.\n-\n-For any additional information, especially cluster configuration or general Galaxy_ questions, \n-please have a look at the Galaxy Wiki.\n-\n-- http://wiki.galaxyproject.org/\n-\n-- http://wiki.galaxyproject.org/Admin/\n-\n-- http://galaxyproject.org/search/web/\n-\n-.. _contact: https://github.com/bgruening\n-.. _Galaxy: http://galaxyproject.org/\n-\n-Prerequisites::\n-\n-* Python 2.6 or 2.7\n-* standard C compiler, C++ and Fortran compiler\n-* Autotools\n-* CMake\n-* cairo development files (used for PNG depictions)\n-* python development files\n-* Java Runtime Environment (JRE, used by OPSIN and NPLS)\n-\n-To install all of the prerequisites you can run the following command, depending on your OS:\n-\n-- Debian based systems: apt-get install build-essential gfortran cmake mercurial libcairo2-dev python-dev\n-- Fedora: yum install make automake gcc gcc-c++ gcc-gfortran cmake mercurial libcairo2-devel python-devel\n-- OS X (MacPorts_): port install gcc cmake automake mercurial cairo-devel\n-\n-.. _MacPorts: http://www.macports.org/\n-\n-\n-===================\n-Galaxy installation\n-===================\n-\n-\n-0. Create a sand-boxed Python using virtualenv_ (not necessary but recommended)::\n-\n- wget https://raw.github.com/pypa/virtualenv/master/virtualenv.py\n-\tpython ./virtualenv.py --no-site-packages galaxy_env\n-\t. ./galaxy_env/bin/activate\n-\n-.. _virtualenv: http://www.virtualenv.org/\n-\n-\n-1. Clone the latest `Galaxy platform`_::\n-\n-\thg clone https://bitbucket.org/galaxy/galaxy-central/\n-\n-.. _Galaxy platform: http://wiki.galaxyproject.org/Admin/Get%20Galaxy\n-\n-2. Navigate to the galaxy-central folder and update it::\n-\t\n-\tcd ~/galaxy-central\n-\thg pull\n-\thg update\n- \n- This step is not necessary if you have a fresh checkout. Anyway, it is good to know ;)\n-\n-3. Create folders for toolshed and dependencies::\n-\n-\tmkdir ~/shed_tools\n-\tmkdir ~/galaxy-central/tool_deps\n-\n-4. Create configuration file::\n-\n-\tcp ~/galaxy-central/universe_wsgi.ini.sample ~/galaxy-central/universe_wsgi.ini\n-\n-5. Open universe_wsgi.ini and change the dependencies directory::\n-\n-\tLINUX: gedit ~/galaxy-central/universe_wsgi.ini\n-\tOS X: open -a TextEdit ~/galaxy-central/universe_wsgi.ini\n-\n-6. Search for ``tool_dependency_dir = None`` and change it to ``tool_dependency_dir = ./tool_deps``, remove the ``#`` if needed\n-\n-7. Remove the ``#`` in front of ``tool_config_file`` and ``tool_path``\n-\n-8. (Re-)Start the galaxy daemon::\n-\n-\tsh run.sh --reload\n-\t\n- In deamon mode all logs will be written to main.log in your Galaxy Home directory. You can also use::\n- \n-\trun.sh \n-\n- During the first startup Galaxy will prepare your database. That can take some time. Have a look at the log file if you want to know what happens.\n-\n-After launching galaxy is accessible via the browser at ``http://localhost:8080/``.\n-\n-\n-\n-=======================\n-Tool Shed configuration\n-=======================\n"..b"lysis > blockclust_workflow\n-- install chemicaltoolbox\n-\n-.. _admin page: http://localhost:8080/admin\n-\n-\n-\n-===============\n-Troubleshooting\n-===============\n-\n-If you have any trouble or the installation did not finish properly, do not hesitate to contact me. However, if the \n-installation fails during the Galaxy installation, you can have a look at the `Galaxy wiki`_. If the ChemicalToolBoX installation fails, \n-you can try to run::\n-\n-\tpython ./scripts/api/repair_tool_shed_repository.py --api YOUR_API_KEY -l http://localhost:8080 --url http://toolshed.g2.bx.psu.edu/ -o rnateam -r e9b2400cc569 --name blockclust_workflow\n-\n-That will rerun all failed installation routines. Alternatively, you can navigate to the ChemicalToolBoX repository in \n-your browser and repair manually: \n-Top Panel \xe2\x86\x92 Admin \xe2\x86\x92 Manage installed tool shed repositories \xe2\x86\x92 chemicaltoolbox \xe2\x86\x92 Repository Actions \xe2\x86\x92 Repair repository\n-\n-------\n-\n-\n-On slow computers and during the compilation of large software libraries, like R, \n-the Tool Shed can run into a timeout and kills the installation.\n-That problem is known and should be fixed in the near future.\n-\n-If you encouter a timeout or 'hung' during the installation you can increase the ``threadpool_kill_thread_limit`` in your universe_wsgi.ini file.\n-\n-\n-------\n-\n-**Database locking errors**\n-\n-Please note that Galaxy per default uses a SQLite database. Sqlite is not intended for production use. \n-With multiple users or complex components, like that workflow, you will see database locking errors. \n-We highly recommend to use PostgreSQL for any kind of production system.\n-\n-\n-.. _Galaxy wiki: http://wiki.galaxyproject.org/\n-\n-\n-Workflows\n-=========\n-\n-An example workflow is located in the `Tool Shed`::\n-\n-\t http://testtoolshed.g2.bx.psu.edu/view/rnateam/blockclust_workflow\n-\n-You can install the workflow with the API::\n-\n-\tpython ./scripts/api/install_tool_shed_repositories.py --api YOUR_API_KEY -l http://localhost:8080 --url http://toolshed.g2.bx.psu.edu/ -o rnateam -r e9b2400cc569 --name blockclust_workflow --tool-deps --repository-deps --panel-section-name BlockClust\n-\n-or as described above via webbrowser. You have now successfully installed the workflow, \n-to import it to all your users you need to go to the admin panel, choose the worklow and import it.\n-For more information have a look at the Galaxy wiki::\n-\n-\thttp://wiki.galaxyproject.org/ToolShedWorkflowSharing#Finding_workflows_in_tool_shed_repositories\n-\n-Please **note** that Galaxy per default uses a SQLite database. Sqlite is not intended for production use. \n-With multiple users or complex components, like that workflow, you will see database locking errors. \n-We highly recommend to use PostgreSQL for any kind of production system.\n-\n-\n-\n-Sample Data\n-===========\n-\n-\n-\n-Citation\n-========\n-\n-If you use this workflow directly, or a derivative of it, or the associated\n-wrappers for Galaxy, in work leading to a scientific publication,\n-please cite:\n-\n-P. Videm at al...\n-\n-\n-\n-Additional References\n-=====================\n-\n-\n-\n-Availability\n-============\n-\n-This workflow is available on the main Galaxy Tool Shed:\n-\n- http://testtoolshed.g2.bx.psu.edu/view/rnateam/blockclust_workflow \n-\n-Development is being done on github:\n-\n-https://github.com/bgruening/galaxytools/tree/master/workflows/blockclust\n-\n-\n-Dependencies\n-============\n-\n-These dependencies should be resolved automatically via the Galaxy Tool Shed:\n-\n-* http://testtoolshed.g2.bx.psu.edu/view/iuc/package_samtools_0_1_19 \n-* http://testtoolshed.g2.bx.psu.edu/view/iuc/package_r_3_0_1\n-* http://testtoolshed.g2.bx.psu.edu/view/rnateam/package_segemehl_0_1_6 \n-* http://testtoolshed.g2.bx.psu.edu/view/iuc/msa_datatypes \n-* http://testtoolshed.g2.bx.psu.edu/view/iuc/package_infernal_1_1rc4 \n-* http://testtoolshed.g2.bx.psu.edu/view/rnateam/blockbuster \n-* http://testtoolshed.g2.bx.psu.edu/view/bgruening/package_eden_1_1\n-* http://testtoolshed.g2.bx.psu.edu/view/iuc/package_mcl_12_135 \n" |