# HG changeset patch
# User rnateam
# Date 1423924115 18000
# Node ID 70170338b4f7ba0a9bd978c38343b6cd3b843df2
# Parent  78b364f5d93e7e3a48f50deaf3a44b17ce6a55b9
Uploaded

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
@@ -0,0 +1,461 @@
+{
+    "a_galaxy_workflow": "true", 
+    "annotation": "", 
+    "format-version": "0.1", 
+    "name": "BlockClustWorkflow", 
+    "steps": {
+        "0": {
+            "annotation": "", 
+            "id": 0, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "Input BAM file"
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 267, 
+                "top": 257.5
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"Input BAM file\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "1": {
+            "annotation": "", 
+            "id": 1, 
+            "input_connections": {
+                "tool_mode|reads_bam": {
+                    "id": 0, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "BlockClust", 
+            "outputs": [
+                {
+                    "name": "tags_bed", 
+                    "type": "bed"
+                }, 
+                {
+                    "name": "hclust_plot", 
+                    "type": "pdf"
+                }, 
+                {
+                    "name": "clusters", 
+                    "type": "bed"
+                }, 
+                {
+                    "name": "model_based_pred_bed", 
+                    "type": "bed"
+                }, 
+                {
+                    "name": "nearest_neighbour_pred_bed", 
+                    "type": "bed"
+                }, 
+                {
+                    "name": "sim_tab_out", 
+                    "type": "tabular"
+                }, 
+                {
+                    "name": "cluster_dist", 
+                    "type": "pdf"
+                }, 
+                {
+                    "name": "cluster_hclust", 
+                    "type": "pdf"
+                }
+            ], 
+            "position": {
+                "left": 524, 
+                "top": 323
+            }, 
+            "post_job_actions": {
+                "HideDatasetActioncluster_dist": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "cluster_dist"
+                }, 
+                "HideDatasetActioncluster_hclust": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "cluster_hclust"
+                }, 
+                "HideDatasetActionclusters": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "clusters"
+                }, 
+                "HideDatasetActionhclust_plot": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "hclust_plot"
+                }, 
+                "HideDatasetActionmodel_based_pred_bed": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "model_based_pred_bed"
+                }, 
+                "HideDatasetActionnearest_neighbour_pred_bed": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "nearest_neighbour_pred_bed"
+                }, 
+                "HideDatasetActionsim_tab_out": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "sim_tab_out"
+                }, 
+                "HideDatasetActiontags_bed": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "tags_bed"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "testtoolshed.g2.bx.psu.edu/repos/rnateam/blockclust/blockclust/1.0.0", 
+            "tool_state": "{\"tool_mode\": \"{\\\"operation\\\": \\\"pre\\\", \\\"reads_bam\\\": null, \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"mode\": \"{\\\"operation\\\": \\\"pre\\\", \\\"reads_bam\\\": null, \\\"__current_case__\\\": 0}\", \"__page__\": 0}", 
+            "tool_version": "1.0.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "2": {
+            "annotation": "", 
+            "id": 2, 
+            "input_connections": {
+                "input": {
+                    "id": 1, 
+                    "output_name": "tags_bed"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Sort", 
+            "outputs": [
+                {
+                    "name": "out_file1", 
+                    "type": "input"
+                }
+            ], 
+            "position": {
+                "left": 797, 
+                "top": 355
+            }, 
+            "post_job_actions": {
+                "HideDatasetActionout_file1": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "out_file1"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "sort1", 
+            "tool_state": "{\"__page__\": 0, \"style\": \"\\\"alpha\\\"\", \"column\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"1\\\"}\", \"__rerun_remap_job_id__\": null, \"order\": \"\\\"ASC\\\"\", \"input\": \"null\", \"column_set\": \"[{\\\"other_order\\\": \\\"ASC\\\", \\\"__index__\\\": 0, \\\"other_column\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"6\\\"}, \\\"other_style\\\": \\\"alpha\\\"}, {\\\"other_order\\\": \\\"ASC\\\", \\\"__index__\\\": 1, \\\"other_column\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"2\\\"}, \\\"other_style\\\": \\\"num\\\"}, {\\\"other_order\\\": \\\"ASC\\\", \\\"__index__\\\": 2, \\\"other_column\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"3\\\"}, \\\"other_style\\\": \\\"num\\\"}]\"}", 
+            "tool_version": "1.0.3", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "3": {
+            "annotation": "", 
+            "id": 3, 
+            "input_connections": {
+                "input": {
+                    "id": 2, 
+                    "output_name": "out_file1"
+                }
+            }, 
+            "inputs": [], 
+            "name": "blockbuster", 
+            "outputs": [
+                {
+                    "name": "output", 
+                    "type": "tabular"
+                }
+            ], 
+            "position": {
+                "left": 970, 
+                "top": 225
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "testtoolshed.g2.bx.psu.edu/repos/rnateam/blockbuster/blockbuster/0.1", 
+            "tool_state": "{\"distance\": \"\\\"40\\\"\", \"scale\": \"\\\"0.5\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"print\": \"\\\"2\\\"\", \"tagFilter\": \"\\\"0\\\"\", \"merge\": \"\\\"0\\\"\", \"minBlockHeight\": \"\\\"1.0\\\"\", \"input\": \"null\", \"minClusterHeight\": \"\\\"50.0\\\"\"}", 
+            "tool_version": "0.1", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "4": {
+            "annotation": "", 
+            "id": 4, 
+            "input_connections": {
+                "tool_mode|input_bbo": {
+                    "id": 3, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool BlockClust", 
+                    "name": "tool_mode"
+                }
+            ], 
+            "name": "BlockClust", 
+            "outputs": [
+                {
+                    "name": "tags_bed", 
+                    "type": "bed"
+                }, 
+                {
+                    "name": "hclust_plot", 
+                    "type": "pdf"
+                }, 
+                {
+                    "name": "clusters", 
+                    "type": "bed"
+                }, 
+                {
+                    "name": "model_based_pred_bed", 
+                    "type": "bed"
+                }, 
+                {
+                    "name": "nearest_neighbour_pred_bed", 
+                    "type": "bed"
+                }, 
+                {
+                    "name": "sim_tab_out", 
+                    "type": "tabular"
+                }, 
+                {
+                    "name": "cluster_dist", 
+                    "type": "pdf"
+                }, 
+                {
+                    "name": "cluster_hclust", 
+                    "type": "pdf"
+                }
+            ], 
+            "position": {
+                "left": 1232, 
+                "top": 321
+            }, 
+            "post_job_actions": {
+                "HideDatasetActioncluster_dist": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "cluster_dist"
+                }, 
+                "HideDatasetActioncluster_hclust": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "cluster_hclust"
+                }, 
+                "HideDatasetActionclusters": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "clusters"
+                }, 
+                "HideDatasetActionnearest_neighbour_pred_bed": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "nearest_neighbour_pred_bed"
+                }, 
+                "HideDatasetActionsim_tab_out": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "sim_tab_out"
+                }, 
+                "HideDatasetActiontags_bed": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "tags_bed"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "testtoolshed.g2.bx.psu.edu/repos/rnateam/blockclust/blockclust/1.0.0", 
+            "tool_state": "{\"tool_mode\": \"{\\\"pred\\\": {\\\"pred_mode\\\": \\\"model_based\\\", \\\"enable_pred\\\": \\\"yes\\\", \\\"__current_case__\\\": 0}, \\\"operation\\\": \\\"clust\\\", \\\"reference\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 1, \\\"input_bbo\\\": null}\", \"__rerun_remap_job_id__\": null, \"mode\": \"{\\\"operation\\\": \\\"clust\\\", \\\"reference\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 1, \\\"input_bbo\\\": null}\", \"__page__\": 0}", 
+            "tool_version": "1.0.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "5": {
+            "annotation": "", 
+            "id": 5, 
+            "input_connections": {
+                "input": {
+                    "id": 4, 
+                    "output_name": "clusters"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Extract Genomic DNA", 
+            "outputs": [
+                {
+                    "name": "out_file1", 
+                    "type": "input"
+                }
+            ], 
+            "position": {
+                "left": 1495, 
+                "top": 248
+            }, 
+            "post_job_actions": {
+                "HideDatasetActionout_file1": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "out_file1"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "Extract genomic DNA 1", 
+            "tool_state": "{\"out_format\": \"\\\"fasta\\\"\", \"__page__\": 0, \"interpret_features\": \"\\\"yes\\\"\", \"__rerun_remap_job_id__\": null, \"seq_source\": \"{\\\"index_source\\\": \\\"cached\\\", \\\"__current_case__\\\": 0}\", \"input\": \"null\"}", 
+            "tool_version": "2.2.3", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "6": {
+            "annotation": "", 
+            "id": 6, 
+            "input_connections": {
+                "seqdb": {
+                    "id": 5, 
+                    "output_name": "out_file1"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Search covariance model(s)", 
+            "outputs": [
+                {
+                    "name": "outfile", 
+                    "type": "tabular"
+                }, 
+                {
+                    "name": "multiple_alignment_output", 
+                    "type": "tabular"
+                }
+            ], 
+            "position": {
+                "left": 1753, 
+                "top": 247
+            }, 
+            "post_job_actions": {
+                "HideDatasetActionmultiple_alignment_output": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "multiple_alignment_output"
+                }, 
+                "HideDatasetActionoutfile": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "outfile"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "testtoolshed.g2.bx.psu.edu/repos/bgruening/infernal/infernal_cmsearch/1.1.0.2", 
+            "tool_state": "{\"A\": \"\\\"False\\\"\", \"nohmm\": \"\\\"False\\\"\", \"--acyk\": \"\\\"False\\\"\", \"bottomonly\": \"\\\"False\\\"\", \"g\": \"\\\"False\\\"\", \"inclusion_thresholds_opts\": \"{\\\"inclusion_thresholds_selector\\\": \\\"\\\", \\\"__current_case__\\\": 3}\", \"__page__\": 0, \"max\": \"\\\"False\\\"\", \"notrunc\": \"\\\"False\\\"\", \"mid\": \"\\\"False\\\"\", \"seqdb\": \"null\", \"toponly\": \"\\\"False\\\"\", \"cm_opts\": \"{\\\"database\\\": null, \\\"__current_case__\\\": 0, \\\"cm_opts_selector\\\": \\\"db\\\"}\", \"reporting_thresholds_opts\": \"{\\\"reporting_thresholds_selector\\\": \\\"\\\", \\\"__current_case__\\\": 3}\", \"cyk\": \"\\\"False\\\"\", \"__rerun_remap_job_id__\": null}", 
+            "tool_version": "1.1.0.2", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "7": {
+            "annotation": "", 
+            "id": 7, 
+            "input_connections": {
+                "tool_mode|clusters_bed": {
+                    "id": 4, 
+                    "output_name": "clusters"
+                }, 
+                "tool_mode|cmsearch_out": {
+                    "id": 6, 
+                    "output_name": "outfile"
+                }, 
+                "tool_mode|sim_tab_in": {
+                    "id": 4, 
+                    "output_name": "sim_tab_out"
+                }
+            }, 
+            "inputs": [], 
+            "name": "BlockClust", 
+            "outputs": [
+                {
+                    "name": "tags_bed", 
+                    "type": "bed"
+                }, 
+                {
+                    "name": "hclust_plot", 
+                    "type": "pdf"
+                }, 
+                {
+                    "name": "clusters", 
+                    "type": "bed"
+                }, 
+                {
+                    "name": "model_based_pred_bed", 
+                    "type": "bed"
+                }, 
+                {
+                    "name": "nearest_neighbour_pred_bed", 
+                    "type": "bed"
+                }, 
+                {
+                    "name": "sim_tab_out", 
+                    "type": "tabular"
+                }, 
+                {
+                    "name": "cluster_dist", 
+                    "type": "pdf"
+                }, 
+                {
+                    "name": "cluster_hclust", 
+                    "type": "pdf"
+                }
+            ], 
+            "position": {
+                "left": 2049, 
+                "top": 433
+            }, 
+            "post_job_actions": {
+                "HideDatasetActionclusters": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "clusters"
+                }, 
+                "HideDatasetActionhclust_plot": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "hclust_plot"
+                }, 
+                "HideDatasetActionmodel_based_pred_bed": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "model_based_pred_bed"
+                }, 
+                "HideDatasetActionnearest_neighbour_pred_bed": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "nearest_neighbour_pred_bed"
+                }, 
+                "HideDatasetActionsim_tab_out": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "sim_tab_out"
+                }, 
+                "HideDatasetActiontags_bed": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "tags_bed"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "testtoolshed.g2.bx.psu.edu/repos/rnateam/blockclust/blockclust/1.0.0", 
+            "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}", 
+            "tool_version": "1.0.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }
+    }
+}
\ No newline at end of file
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
@@ -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 
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
@@ -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>