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repository_dependencies.xml |
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blockclust_workflow.ga readme.rst |
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| diff -r 78b364f5d93e -r 70170338b4f7 blockclust_workflow.ga --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/blockclust_workflow.ga Sat Feb 14 09:28:35 2015 -0500 |
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| b'@@ -0,0 +1,461 @@\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": "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": 524, \n+ "top": 323\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+ "H'..b' \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": 2049, \n+ "top": 433\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": "testtoolshed.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, \\"mode\\": \\"{\\\\\\"cmsearch_out\\\\\\": null, \\\\\\"operation\\\\\\": \\\\\\"post\\\\\\", \\\\\\"clusters_bed\\\\\\": null, \\\\\\"__current_case__\\\\\\": 2, \\\\\\"sim_tab_in\\\\\\": 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' |
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| diff -r 78b364f5d93e -r 70170338b4f7 readme.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/readme.rst Sat Feb 14 09:28:35 2015 -0500 |
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| @@ -0,0 +1,243 @@ + + +This package is a Galaxy workflow for BlockClust pipeline. + + +====== +Galaxy +====== + +`Galaxy <http://galaxyproject.org/>`_ is an open, web-based platform for data intensive research. +All tools can be combined in workflows without any need of programming skills. +Furthermore the platform can be extended with more tools at any time. +Each tool has its own information about what it does and how the input is supposed to look like. +You can make data available for Galaxy by uploading local files or downloading online content. +Inputfiles, workflowsteps and results are stored in a history where you can view them or reaccess them later. +It is possible to share workflows and histories with other users or make the public available. +Saved workflows can be used with new input files or just to rerun an analyses which ensures repeatability. + + + +Getting Started +=============== + +BlockClust can be installed on all common Unix systems. +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. + +For any additional information, especially cluster configuration or general Galaxy_ questions, +please have a look at the Galaxy Wiki. + +- http://wiki.galaxyproject.org/ + +- http://wiki.galaxyproject.org/Admin/ + +- http://galaxyproject.org/search/web/ + +.. _contact: https://github.com/bgruening +.. _Galaxy: http://galaxyproject.org/ + +Prerequisites:: + +* Python 2.6 or 2.7 +* standard C compiler, C++ and Fortran compiler +* Autotools +* CMake +* cairo development files (used for PNG depictions) +* python development files +* Java Runtime Environment (JRE, used by OPSIN and NPLS) + +To install all of the prerequisites you can run the following command, depending on your OS: + +- Debian based systems: apt-get install build-essential gfortran cmake mercurial libcairo2-dev python-dev +- Fedora: yum install make automake gcc gcc-c++ gcc-gfortran cmake mercurial libcairo2-devel python-devel +- OS X (MacPorts_): port install gcc cmake automake mercurial cairo-devel + +.. _MacPorts: http://www.macports.org/ + + +=================== +Galaxy installation +=================== + + +0. Create a sand-boxed Python using virtualenv_ (not necessary but recommended):: + + wget https://raw.github.com/pypa/virtualenv/master/virtualenv.py + python ./virtualenv.py --no-site-packages galaxy_env + . ./galaxy_env/bin/activate + +.. _virtualenv: http://www.virtualenv.org/ + + +1. Clone the latest `Galaxy platform`_:: + + hg clone https://bitbucket.org/galaxy/galaxy-central/ + +.. _Galaxy platform: http://wiki.galaxyproject.org/Admin/Get%20Galaxy + +2. Navigate to the galaxy-central folder and update it:: + + cd ~/galaxy-central + hg pull + hg update + + This step is not necessary if you have a fresh checkout. Anyway, it is good to know ;) + +3. Create folders for toolshed and dependencies:: + + mkdir ~/shed_tools + mkdir ~/galaxy-central/tool_deps + +4. Create configuration file:: + + cp ~/galaxy-central/universe_wsgi.ini.sample ~/galaxy-central/universe_wsgi.ini + +5. Open universe_wsgi.ini and change the dependencies directory:: + + LINUX: gedit ~/galaxy-central/universe_wsgi.ini + OS X: open -a TextEdit ~/galaxy-central/universe_wsgi.ini + +6. Search for ``tool_dependency_dir = None`` and change it to ``tool_dependency_dir = ./tool_deps``, remove the ``#`` if needed + +7. Remove the ``#`` in front of ``tool_config_file`` and ``tool_path`` + +8. (Re-)Start the galaxy daemon:: + + sh run.sh --reload + + In deamon mode all logs will be written to main.log in your Galaxy Home directory. You can also use:: + + run.sh + + 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. + +After launching galaxy is accessible via the browser at ``http://localhost:8080/``. + + + +======================= +Tool Shed configuration +======================= + +- Register a new user account in your Galaxy instance: Top Panel → User → Register +- Become an admin + - open ``universe_wsgi.ini`` in your favourite text editor (gedit universe_wsgi.ini) + - search ``admin_users = None`` and change it to ``admin_users = EMAIL_ADDRESS`` (your Galaxy Username) + - remove the ``#`` if needed +- restart Galaxy + +:: + + sh run.sh --reload + + +======================= +BlockClust installation +======================= + +BlockClust will automatically download and compile all requirements, +like EDeN, samtools and so on. It can take up to 1-2 hours. + + +Installation via webbrowser +=========================== + +- go to the `admin page`_ +- select *Search and browse tool sheds* +- Galaxy test tool shed > Sequence Analysis > blockclust_workflow +- install + +.. _admin page: http://localhost:8080/admin + + +=============== +Troubleshooting +=============== +You can navigate to the blockclust_workflow repository in your browser and repair manually: +Top Panel → Admin → Manage installed tool shed repositories → blockclust_workflow → Repository Actions → Repair repository + +------ + + +On slow computers and during the compilation of large software libraries, like R, +the Tool Shed can run into a timeout and kills the installation. +That problem is known and should be fixed in the near future. + +If you encouter a timeout or 'hung' during the installation you can increase the ``threadpool_kill_thread_limit`` in your universe_wsgi.ini file. + + +------ + +**Database locking errors** + +Please note that Galaxy per default uses a SQLite database. Sqlite is not intended for production use. +With multiple users or complex components, like that workflow, you will see database locking errors. +We highly recommend to use PostgreSQL for any kind of production system. + + +.. _Galaxy wiki: http://wiki.galaxyproject.org/ + + +Workflows +========= + +The BlockClust workflow is located in the `Tool Shed`:: + + http://toolshed.g2.bx.psu.edu/view/rnateam/blockclust_workflow + +To import successfully installed the workflow to all your users you need to go to the admin panel, choose the worklow and import it. +For more information have a look at the Galaxy wiki:: + + http://wiki.galaxyproject.org/ToolShedWorkflowSharing#Finding_workflows_in_tool_shed_repositories + +Please **note** that Galaxy per default uses a SQLite database. Sqlite is not intended for production use. +With multiple users or complex components, like that workflow, you will see database locking errors. +We highly recommend to use PostgreSQL for any kind of production system. + + + +Sample Data +=========== + + + +Citation +======== + +If you use this workflow directly, or a derivative of it, or the associated +wrappers for Galaxy, in work leading to a scientific publication, +please cite: + +Pavankumar Videm, Dominic Rose, Fabrizio Costa, and Rolf Backofen. "BlockClust: efficient clustering and classification of non-coding RNAs from short read RNA-seq profiles." Bioinformatics 30, no. 12 (2014): i274-i282. + + + +Additional References +===================== + + + +Availability +============ + +This workflow is available on the main Galaxy Tool Shed: + + http://toolshed.g2.bx.psu.edu/view/rnateam/blockclust_workflow + +Development is being done on github: + +https://github.com/bgruening/galaxytools/tree/master/workflows/blockclust + + +Dependencies +============ + +These dependencies should be resolved automatically via the Galaxy Tool Shed: + +* http://testtoolshed.g2.bx.psu.edu/view/iuc/package_samtools_0_1_19 +* http://testtoolshed.g2.bx.psu.edu/view/iuc/package_r_3_0_1 +* http://testtoolshed.g2.bx.psu.edu/view/iuc/msa_datatypes +* http://testtoolshed.g2.bx.psu.edu/view/iuc/package_infernal_1_1rc4 +* http://testtoolshed.g2.bx.psu.edu/view/rnateam/blockbuster +* http://testtoolshed.g2.bx.psu.edu/view/bgruening/package_eden_1_1 +* http://testtoolshed.g2.bx.psu.edu/view/iuc/package_mcl_12_135 |
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| diff -r 78b364f5d93e -r 70170338b4f7 repository_dependencies.xml --- a/repository_dependencies.xml Thu Feb 12 12:19:22 2015 -0500 +++ b/repository_dependencies.xml Sat Feb 14 09:28:35 2015 -0500 |
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| @@ -3,6 +3,6 @@ <repository changeset_revision="6ecd674b5b62" name="blockclust" owner="rnateam" toolshed="https://toolshed.g2.bx.psu.edu" /> <!--<repository name="segemehl" owner="rnateam" />--> <repository changeset_revision="6ae946589f04" name="blockbuster" owner="rnateam" toolshed="https://toolshed.g2.bx.psu.edu" /> - <repository changeset_revision="55bb96edfc07" name="infernal" owner="bgruening" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="fac157e22e1b" name="infernal" owner="bgruening" toolshed="https://toolshed.g2.bx.psu.edu" /> <!--<repository name="graphclust" owner="rnateam" />--> </repositories> |