Mercurial > repos > rnateam > blockclust_workflow

comparison readme.rst @ 9:70170338b4f7 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author rnateam
date Sat, 14 Feb 2015 09:28:35 -0500
parents
children
comparison
equal deleted inserted replaced
8:78b364f5d93e 9:70170338b4f7
1
2
3 This package is a Galaxy workflow for BlockClust pipeline.
4
5
6 ======
7 Galaxy
8 ======
9
10 `Galaxy <http://galaxyproject.org/>`_ is an open, web-based platform for data intensive research.
11 All tools can be combined in workflows without any need of programming skills.
12 Furthermore the platform can be extended with more tools at any time.
13 Each tool has its own information about what it does and how the input is supposed to look like.
14 You can make data available for Galaxy by uploading local files or downloading online content.
15 Inputfiles, workflowsteps and results are stored in a history where you can view them or reaccess them later.
16 It is possible to share workflows and histories with other users or make the public available.
17 Saved workflows can be used with new input files or just to rerun an analyses which ensures repeatability.
18
19
20
21 Getting Started
22 ===============
23
24 BlockClust can be installed on all common Unix systems.
25 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.
26
27 For any additional information, especially cluster configuration or general Galaxy_ questions,
28 please have a look at the Galaxy Wiki.
29
30 - http://wiki.galaxyproject.org/
31
32 - http://wiki.galaxyproject.org/Admin/
33
34 - http://galaxyproject.org/search/web/
35
36 .. _contact: https://github.com/bgruening
37 .. _Galaxy: http://galaxyproject.org/
38
39 Prerequisites::
40
41 * Python 2.6 or 2.7
42 * standard C compiler, C++ and Fortran compiler
43 * Autotools
44 * CMake
45 * cairo development files (used for PNG depictions)
46 * python development files
47 * Java Runtime Environment (JRE, used by OPSIN and NPLS)
48
49 To install all of the prerequisites you can run the following command, depending on your OS:
50
51 - Debian based systems: apt-get install build-essential gfortran cmake mercurial libcairo2-dev python-dev
52 - Fedora: yum install make automake gcc gcc-c++ gcc-gfortran cmake mercurial libcairo2-devel python-devel
53 - OS X (MacPorts_): port install gcc cmake automake mercurial cairo-devel
54
55 .. _MacPorts: http://www.macports.org/
56
57
58 ===================
59 Galaxy installation
60 ===================
61
62
63 0. Create a sand-boxed Python using virtualenv_ (not necessary but recommended)::
64
65 wget https://raw.github.com/pypa/virtualenv/master/virtualenv.py
66 python ./virtualenv.py --no-site-packages galaxy_env
67 . ./galaxy_env/bin/activate
68
69 .. _virtualenv: http://www.virtualenv.org/
70
71
72 1. Clone the latest `Galaxy platform`_::
73
74 hg clone https://bitbucket.org/galaxy/galaxy-central/
75
76 .. _Galaxy platform: http://wiki.galaxyproject.org/Admin/Get%20Galaxy
77
78 2. Navigate to the galaxy-central folder and update it::
79
80 cd ~/galaxy-central
81 hg pull
82 hg update
83
84 This step is not necessary if you have a fresh checkout. Anyway, it is good to know ;)
85
86 3. Create folders for toolshed and dependencies::
87
88 mkdir ~/shed_tools
89 mkdir ~/galaxy-central/tool_deps
90
91 4. Create configuration file::
92
93 cp ~/galaxy-central/universe_wsgi.ini.sample ~/galaxy-central/universe_wsgi.ini
94
95 5. Open universe_wsgi.ini and change the dependencies directory::
96
97 LINUX: gedit ~/galaxy-central/universe_wsgi.ini
98 OS X: open -a TextEdit ~/galaxy-central/universe_wsgi.ini
99
100 6. Search for ``tool_dependency_dir = None`` and change it to ``tool_dependency_dir = ./tool_deps``, remove the ``#`` if needed
101
102 7. Remove the ``#`` in front of ``tool_config_file`` and ``tool_path``
103
104 8. (Re-)Start the galaxy daemon::
105
106 sh run.sh --reload
107
108 In deamon mode all logs will be written to main.log in your Galaxy Home directory. You can also use::
109
110 run.sh
111
112 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.
113
114 After launching galaxy is accessible via the browser at ``http://localhost:8080/``.
115
116
117
118 =======================
119 Tool Shed configuration
120 =======================
121
122 - Register a new user account in your Galaxy instance: Top Panel → User → Register
123 - Become an admin
124 - open ``universe_wsgi.ini`` in your favourite text editor (gedit universe_wsgi.ini)
125 - search ``admin_users = None`` and change it to ``admin_users = EMAIL_ADDRESS`` (your Galaxy Username)
126 - remove the ``#`` if needed
127 - restart Galaxy
128
129 ::
130
131 sh run.sh --reload
132
133
134 =======================
135 BlockClust installation
136 =======================
137
138 BlockClust will automatically download and compile all requirements,
139 like EDeN, samtools and so on. It can take up to 1-2 hours.
140
141
142 Installation via webbrowser
143 ===========================
144
145 - go to the `admin page`_
146 - select *Search and browse tool sheds*
147 - Galaxy test tool shed > Sequence Analysis > blockclust_workflow
148 - install
149
150 .. _admin page: http://localhost:8080/admin
151
152
153 ===============
154 Troubleshooting
155 ===============
156 You can navigate to the blockclust_workflow repository in your browser and repair manually:
157 Top Panel → Admin → Manage installed tool shed repositories → blockclust_workflow → Repository Actions → Repair repository
158
159 ------
160
161
162 On slow computers and during the compilation of large software libraries, like R,
163 the Tool Shed can run into a timeout and kills the installation.
164 That problem is known and should be fixed in the near future.
165
166 If you encouter a timeout or 'hung' during the installation you can increase the ``threadpool_kill_thread_limit`` in your universe_wsgi.ini file.
167
168
169 ------
170
171 **Database locking errors**
172
173 Please note that Galaxy per default uses a SQLite database. Sqlite is not intended for production use.
174 With multiple users or complex components, like that workflow, you will see database locking errors.
175 We highly recommend to use PostgreSQL for any kind of production system.
176
177
178 .. _Galaxy wiki: http://wiki.galaxyproject.org/
179
180
181 Workflows
182 =========
183
184 The BlockClust workflow is located in the `Tool Shed`::
185
186 http://toolshed.g2.bx.psu.edu/view/rnateam/blockclust_workflow
187
188 To import successfully installed the workflow to all your users you need to go to the admin panel, choose the worklow and import it.
189 For more information have a look at the Galaxy wiki::
190
191 http://wiki.galaxyproject.org/ToolShedWorkflowSharing#Finding_workflows_in_tool_shed_repositories
192
193 Please **note** that Galaxy per default uses a SQLite database. Sqlite is not intended for production use.
194 With multiple users or complex components, like that workflow, you will see database locking errors.
195 We highly recommend to use PostgreSQL for any kind of production system.
196
197
198
199 Sample Data
200 ===========
201
202
203
204 Citation
205 ========
206
207 If you use this workflow directly, or a derivative of it, or the associated
208 wrappers for Galaxy, in work leading to a scientific publication,
209 please cite:
210
211 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.
212
213
214
215 Additional References
216 =====================
217
218
219
220 Availability
221 ============
222
223 This workflow is available on the main Galaxy Tool Shed:
224
225 http://toolshed.g2.bx.psu.edu/view/rnateam/blockclust_workflow
226
227 Development is being done on github:
228
229 https://github.com/bgruening/galaxytools/tree/master/workflows/blockclust
230
231
232 Dependencies
233 ============
234
235 These dependencies should be resolved automatically via the Galaxy Tool Shed:
236
237 * http://testtoolshed.g2.bx.psu.edu/view/iuc/package_samtools_0_1_19
238 * http://testtoolshed.g2.bx.psu.edu/view/iuc/package_r_3_0_1
239 * http://testtoolshed.g2.bx.psu.edu/view/iuc/msa_datatypes
240 * http://testtoolshed.g2.bx.psu.edu/view/iuc/package_infernal_1_1rc4
241 * http://testtoolshed.g2.bx.psu.edu/view/rnateam/blockbuster
242 * http://testtoolshed.g2.bx.psu.edu/view/bgruening/package_eden_1_1
243 * http://testtoolshed.g2.bx.psu.edu/view/iuc/package_mcl_12_135