Repository 'blockclust_workflow'
hg clone https://toolshed.g2.bx.psu.edu/repos/rnateam/blockclust_workflow

Changeset 9:70170338b4f7 (2015-02-14)
Previous changeset 8:78b364f5d93e (2015-02-12) Next changeset 10:69fd3011b1a9 (2018-12-10)
Commit message:
Uploaded
modified:
repository_dependencies.xml
added:
blockclust_workflow.ga
readme.rst
b
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
[
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'
b
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
b
@@ -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 
b
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
b
@@ -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>