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3 This package is a Galaxy workflow for BlockClust pipeline.
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5
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6 ======
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7 Galaxy
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8 ======
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9
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10 `Galaxy <http://galaxyproject.org/>`_ is an open, web-based platform for data intensive research.
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11 All tools can be combined in workflows without any need of programming skills.
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12 Furthermore the platform can be extended with more tools at any time.
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13 Each tool has its own information about what it does and how the input is supposed to look like.
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14 You can make data available for Galaxy by uploading local files or downloading online content.
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15 Inputfiles, workflowsteps and results are stored in a history where you can view them or reaccess them later.
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16 It is possible to share workflows and histories with other users or make the public available.
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17 Saved workflows can be used with new input files or just to rerun an analyses which ensures repeatability.
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18
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19
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20
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21 Getting Started
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22 ===============
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23
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24 BlockClust can be installed on all common Unix systems.
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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.
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26
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27 For any additional information, especially cluster configuration or general Galaxy_ questions,
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28 please have a look at the Galaxy Wiki.
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29
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30 - http://wiki.galaxyproject.org/
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31
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32 - http://wiki.galaxyproject.org/Admin/
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33
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34 - http://galaxyproject.org/search/web/
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35
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36 .. _contact: https://github.com/bgruening
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37 .. _Galaxy: http://galaxyproject.org/
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38
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39 Prerequisites::
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40
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41 * Python 2.6 or 2.7
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42 * standard C compiler, C++ and Fortran compiler
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43 * Autotools
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44 * CMake
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45 * cairo development files (used for PNG depictions)
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46 * python development files
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47 * Java Runtime Environment (JRE, used by OPSIN and NPLS)
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48
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49 To install all of the prerequisites you can run the following command, depending on your OS:
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50
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51 - Debian based systems: apt-get install build-essential gfortran cmake mercurial libcairo2-dev python-dev
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52 - Fedora: yum install make automake gcc gcc-c++ gcc-gfortran cmake mercurial libcairo2-devel python-devel
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53 - OS X (MacPorts_): port install gcc cmake automake mercurial cairo-devel
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54
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55 .. _MacPorts: http://www.macports.org/
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56
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57
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58 ===================
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59 Galaxy installation
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60 ===================
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61
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62
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63 0. Create a sand-boxed Python using virtualenv_ (not necessary but recommended)::
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64
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65 wget https://raw.github.com/pypa/virtualenv/master/virtualenv.py
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66 python ./virtualenv.py --no-site-packages galaxy_env
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67 . ./galaxy_env/bin/activate
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68
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69 .. _virtualenv: http://www.virtualenv.org/
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70
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71
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72 1. Clone the latest `Galaxy platform`_::
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73
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74 hg clone https://bitbucket.org/galaxy/galaxy-central/
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75
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76 .. _Galaxy platform: http://wiki.galaxyproject.org/Admin/Get%20Galaxy
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77
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78 2. Navigate to the galaxy-central folder and update it::
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79
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80 cd ~/galaxy-central
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81 hg pull
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82 hg update
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83
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84 This step is not necessary if you have a fresh checkout. Anyway, it is good to know ;)
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85
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86 3. Create folders for toolshed and dependencies::
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87
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88 mkdir ~/shed_tools
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89 mkdir ~/galaxy-central/tool_deps
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90
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91 4. Create configuration file::
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92
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93 cp ~/galaxy-central/universe_wsgi.ini.sample ~/galaxy-central/universe_wsgi.ini
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94
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95 5. Open universe_wsgi.ini and change the dependencies directory::
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96
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97 LINUX: gedit ~/galaxy-central/universe_wsgi.ini
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98 OS X: open -a TextEdit ~/galaxy-central/universe_wsgi.ini
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99
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100 6. Search for ``tool_dependency_dir = None`` and change it to ``tool_dependency_dir = ./tool_deps``, remove the ``#`` if needed
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101
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102 7. Remove the ``#`` in front of ``tool_config_file`` and ``tool_path``
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103
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104 8. (Re-)Start the galaxy daemon::
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105
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106 sh run.sh --reload
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107
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108 In deamon mode all logs will be written to main.log in your Galaxy Home directory. You can also use::
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109
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110 run.sh
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111
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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.
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113
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114 After launching galaxy is accessible via the browser at ``http://localhost:8080/``.
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115
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116
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117
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118 =======================
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119 Tool Shed configuration
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120 =======================
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121
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122 - Register a new user account in your Galaxy instance: Top Panel → User → Register
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123 - Become an admin
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124 - open ``universe_wsgi.ini`` in your favourite text editor (gedit universe_wsgi.ini)
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125 - search ``admin_users = None`` and change it to ``admin_users = EMAIL_ADDRESS`` (your Galaxy Username)
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126 - remove the ``#`` if needed
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127 - restart Galaxy
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128
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129 ::
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130
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131 sh run.sh --reload
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132
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133
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134 =======================
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135 BlockClust installation
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136 =======================
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137
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138 BlockClust will automatically download and compile all requirements,
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139 like EDeN, samtools and so on. It can take up to 1-2 hours.
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140
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141
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142 Installation via Galaxy API (recommended)
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143 =========================================
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144
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145 - Generate an `API Key`_
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146 - Run the installation script::
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147
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148 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
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149
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150 The -r argument specifies the version of ChemicalToolBoX. You can get the latest revsion number from the
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151 `test tool shed`_ or with the following command::
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152
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153 hg identify http://toolshed.g2.bx.psu.edu/repos/bgruening/chemicaltoolbox
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154
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155 You can watch the installation status under: Top Panel → Admin → Manage installed tool shed repositories
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156
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157
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158 .. _API Key: http://wiki.galaxyproject.org/Admin/API#Generate_the_Admin_Account_API_Key
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159 .. _`test tool shed`: http://testtoolshed.g2.bx.psu.edu/
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160
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161
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162 Installation via webbrowser
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163 ===========================
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164
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165 - go to the `admin page`_
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166 - select *Search and browse tool sheds*
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167 - Galaxy test tool shed > Sequence Analysis > blockclust_workflow
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168 - install chemicaltoolbox
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169
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170 .. _admin page: http://localhost:8080/admin
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171
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172
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173
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174 ===============
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175 Troubleshooting
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176 ===============
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177
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178 If you have any trouble or the installation did not finish properly, do not hesitate to contact me. However, if the
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179 installation fails during the Galaxy installation, you can have a look at the `Galaxy wiki`_. If the ChemicalToolBoX installation fails,
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180 you can try to run::
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181
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182 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
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183
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184 That will rerun all failed installation routines. Alternatively, you can navigate to the ChemicalToolBoX repository in
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185 your browser and repair manually:
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186 Top Panel → Admin → Manage installed tool shed repositories → chemicaltoolbox → Repository Actions → Repair repository
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187
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188 ------
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189
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190
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191 On slow computers and during the compilation of large software libraries, like R,
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192 the Tool Shed can run into a timeout and kills the installation.
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193 That problem is known and should be fixed in the near future.
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194
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195 If you encouter a timeout or 'hung' during the installation you can increase the ``threadpool_kill_thread_limit`` in your universe_wsgi.ini file.
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196
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197
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198 ------
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199
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200 **Database locking errors**
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201
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202 Please note that Galaxy per default uses a SQLite database. Sqlite is not intended for production use.
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203 With multiple users or complex components, like that workflow, you will see database locking errors.
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204 We highly recommend to use PostgreSQL for any kind of production system.
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205
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206
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207 .. _Galaxy wiki: http://wiki.galaxyproject.org/
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208
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209
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210 Workflows
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211 =========
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212
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213 An example workflow is located in the `Tool Shed`::
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214
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215 http://testtoolshed.g2.bx.psu.edu/view/rnateam/blockclust_workflow
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216
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217 You can install the workflow with the API::
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218
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219 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
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220
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221 or as described above via webbrowser. You have now successfully installed the workflow,
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222 to import it to all your users you need to go to the admin panel, choose the worklow and import it.
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223 For more information have a look at the Galaxy wiki::
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224
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225 http://wiki.galaxyproject.org/ToolShedWorkflowSharing#Finding_workflows_in_tool_shed_repositories
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226
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227 Please **note** that Galaxy per default uses a SQLite database. Sqlite is not intended for production use.
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228 With multiple users or complex components, like that workflow, you will see database locking errors.
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229 We highly recommend to use PostgreSQL for any kind of production system.
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230
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231
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232
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233 Sample Data
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234 ===========
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235
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236
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237
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238 Citation
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239 ========
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240
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241 If you use this workflow directly, or a derivative of it, or the associated
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242 wrappers for Galaxy, in work leading to a scientific publication,
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243 please cite:
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244
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245 P. Videm at al...
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246
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247
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248
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249 Additional References
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250 =====================
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251
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252
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253
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254 Availability
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255 ============
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256
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257 This workflow is available on the main Galaxy Tool Shed:
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258
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259 http://testtoolshed.g2.bx.psu.edu/view/rnateam/blockclust_workflow
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260
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261 Development is being done on github:
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262
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263 https://github.com/bgruening/galaxytools/tree/master/workflows/blockclust
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265
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266 Dependencies
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267 ============
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268
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269 These dependencies should be resolved automatically via the Galaxy Tool Shed:
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270
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271 * http://testtoolshed.g2.bx.psu.edu/view/iuc/package_samtools_0_1_19
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272 * http://testtoolshed.g2.bx.psu.edu/view/iuc/package_r_3_0_1
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273 * http://testtoolshed.g2.bx.psu.edu/view/rnateam/package_segemehl_0_1_6
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274 * http://testtoolshed.g2.bx.psu.edu/view/iuc/msa_datatypes
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275 * http://testtoolshed.g2.bx.psu.edu/view/iuc/package_infernal_1_1rc4
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276 * http://testtoolshed.g2.bx.psu.edu/view/rnateam/blockbuster
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277 * http://testtoolshed.g2.bx.psu.edu/view/bgruening/package_eden_1_1
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278 * http://testtoolshed.g2.bx.psu.edu/view/iuc/package_mcl_12_135
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