changeset 1:25afbac62e0d draft

Uploaded
author rnateam
date Wed, 07 May 2014 04:59:28 -0400 (2014-05-07)
parents b2040467dad2
children 0c393c9d3756
files blockclust_workflow.ga blockclust_workflow_clustering.ga blockclust_workflow_complete.ga readme.rst
diffstat 4 files changed, 744 insertions(+), 739 deletions(-) [+]
line wrap: on
line diff
--- a/blockclust_workflow.ga	Tue May 06 12:51:51 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,461 +0,0 @@
-{
-    "a_galaxy_workflow": "true", 
-    "annotation": "", 
-    "format-version": "0.1", 
-    "name": "BlockClustWorkflow", 
-    "steps": {
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-            "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": {
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-                "top": 323
-            }, 
-            "post_job_actions": {
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-                    "action_type": "HideDatasetAction", 
-                    "output_name": "cluster_hclust"
-                }, 
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-                }, 
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-                    "output_name": "hclust_plot"
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-                    "action_type": "HideDatasetAction", 
-                    "output_name": "out_file1"
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-                    "output_name": "out_file1"
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-                    "type": "tabular"
-                }
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-                    "type": "bed"
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-            "position": {
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\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/blockclust_workflow_clustering.ga	Wed May 07 04:59:28 2014 -0400
@@ -0,0 +1,282 @@
+{
+    "a_galaxy_workflow": "true", 
+    "annotation": "Until clustering step. No post processing included.", 
+    "format-version": "0.1", 
+    "name": "BlockClustWorkflow_clustering", 
+    "steps": {
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+            "annotation": "", 
+            "id": 0, 
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+            "inputs": [
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+                }
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+                "top": 282.5
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+            "type": "data_input", 
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+            "id": 1, 
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+                    "output_name": "output"
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+            "outputs": [
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+                    "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"
+                }
+            ], 
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+                "top": 239.5
+            }, 
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+                    "action_type": "HideDatasetAction", 
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+                "left": 740, 
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+                    "output_name": "out_file1"
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+            "type": "tool", 
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+                }
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+            "inputs": [], 
+            "name": "blockbuster", 
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+                    "type": "tabular"
+                }
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+                    "output_name": "output"
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+            "tool_version": "0.1", 
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+            "annotation": "", 
+            "id": 4, 
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+                "tool_mode|input_bbo": {
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+                    "name": "tool_mode"
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+                    "action_type": "HideDatasetAction", 
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+}
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/blockclust_workflow_complete.ga	Wed May 07 04:59:28 2014 -0400
@@ -0,0 +1,462 @@
+{
+    "a_galaxy_workflow": "true", 
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+            "outputs": [
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+                    "type": "tabular"
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+                    "type": "pdf"
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+                    "name": "cluster_hclust", 
+                    "type": "pdf"
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+                    "description": "runtime parameter for tool Search covariance model(s)", 
+                    "name": "cm_opts"
+                }
+            ], 
+            "name": "Search covariance model(s)", 
+            "outputs": [
+                {
+                    "name": "outfile", 
+                    "type": "tabular"
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+                {
+                    "name": "multiple_alignment_output", 
+                    "type": "tabular"
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+            "post_job_actions": {
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+                    "action_type": "HideDatasetAction", 
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+    }
+}
\ No newline at end of file
--- 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 <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 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