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} +} \ No newline at end of file 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 @@ -1,278 +0,0 @@ - - -This package is a Galaxy workflow for BlockClust pipeline. - - -====== -Galaxy -====== - -`Galaxy `_ 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 Galaxy API (recommended) -========================================= - -- Generate an `API Key`_ -- Run the installation script:: - - python ./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 ChemicalToolBoX - -The -r argument specifies the version of ChemicalToolBoX. You can get the latest revsion number from the -`test tool shed`_ or with the following command:: - - hg identify http://toolshed.g2.bx.psu.edu/repos/bgruening/chemicaltoolbox - -You can watch the installation status under: Top Panel → Admin → Manage installed tool shed repositories - - -.. _API Key: http://wiki.galaxyproject.org/Admin/API#Generate_the_Admin_Account_API_Key -.. _`test tool shed`: http://testtoolshed.g2.bx.psu.edu/ - - -Installation via webbrowser -=========================== - -- go to the `admin page`_ -- select *Search and browse tool sheds* -- Galaxy test tool shed > Sequence Analysis > blockclust_workflow -- install chemicaltoolbox - -.. _admin page: http://localhost:8080/admin - - - -=============== -Troubleshooting -=============== - -If you have any trouble or the installation did not finish properly, do not hesitate to contact me. However, if the -installation fails during the Galaxy installation, you can have a look at the `Galaxy wiki`_. If the ChemicalToolBoX installation fails, -you can try to run:: - - python ./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 - -That will rerun all failed installation routines. Alternatively, you can navigate to the ChemicalToolBoX repository in -your browser and repair manually: -Top Panel → Admin → Manage installed tool shed repositories → chemicaltoolbox → 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 -========= - -An example workflow is located in the `Tool Shed`:: - - http://testtoolshed.g2.bx.psu.edu/view/rnateam/blockclust_workflow - -You can install the workflow with the API:: - - python ./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 - -or as described above via webbrowser. You have now successfully installed the workflow, -to import it 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: - -P. Videm at al... - - - -Additional References -===================== - - - -Availability -============ - -This workflow is available on the main Galaxy Tool Shed: - - http://testtoolshed.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/rnateam/package_segemehl_0_1_6 -* 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