# HG changeset patch
# User rnateam
# Date 1399395111 14400
# Node ID b2040467dad211efafbf8d6b304edcad3b20eb2d
Uploaded
diff -r 000000000000 -r b2040467dad2 blockclust_workflow.ga
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/blockclust_workflow.ga Tue May 06 12:51:51 2014 -0400
@@ -0,0 +1,461 @@
+{
+ "a_galaxy_workflow": "true",
+ "annotation": "",
+ "format-version": "0.1",
+ "name": "BlockClustWorkflow",
+ "steps": {
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+ "annotation": "",
+ "id": 0,
+ "input_connections": {},
+ "inputs": [
+ {
+ "description": "",
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+ "name": "BlockClust",
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+ "type": "bed"
+ },
+ {
+ "name": "hclust_plot",
+ "type": "pdf"
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+ "outputs": [
+ {
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+ "type": "input"
+ }
+ ],
+ "position": {
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+ },
+ "post_job_actions": {
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+ "type": "tabular"
+ },
+ {
+ "name": "multiple_alignment_output",
+ "type": "tabular"
+ }
+ ],
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+}
\ No newline at end of file
diff -r 000000000000 -r b2040467dad2 readme.rst
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/readme.rst Tue May 06 12:51:51 2014 -0400
@@ -0,0 +1,278 @@
+
+
+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
diff -r 000000000000 -r b2040467dad2 repository_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/repository_dependencies.xml Tue May 06 12:51:51 2014 -0400
@@ -0,0 +1,8 @@
+
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