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annotate readme.md @ 13:fdc984e79f40 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
author galaxyp
date Thu, 27 Aug 2020 19:43:01 -0400
parents 2a5a6ff18f9e
children abffdfee3021
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5c56387ff06a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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1 Galaxy wrapper for OpenMS
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2 =========================
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3
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4 OpenMS is an open-source software C++ library for LC/MS data management and analyses.
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5 It offers an infrastructure for the rapid development of mass spectrometry related software.
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6 OpenMS is free software available under the three clause BSD license and runs under Windows, MacOSX and Linux.
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7
5c56387ff06a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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8 More informations are available at:
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9
5c56387ff06a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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10 * https://github.com/OpenMS/OpenMS
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11 * https://www.openms.de/
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12
fdc984e79f40 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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13 The wrappers for these tools and most of their tests are automatically
fdc984e79f40 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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14 generated using the `generate.sh` script. The generation of the tools is
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15 based on the CTDConverter (https://github.com/WorkflowConversion/CTDConverter)
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16 which can be fine tuned via the `hardcoded_params.json` file. This file allows
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17 to blacklist and hardcode parameters and to modify or set arbitrary
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18 CTD/XML attributes.
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20 Note that, due to its size, the test data is excluded from this repository. In
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21 order to generate the test data on call `test-data.sh`.
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23 Manual updates should only be done to
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25 - the `@GALAXY_VERSION@"` token in `macros.xml`
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26 - and the manually contributed tests in `macros_test.xml` (The goal is that all
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27 tools that do not have an automatically generated test are covered here)
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28 - the `hardcoded_params.json` files
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29
fdc984e79f40 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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30 In a few cases patches may be acceptable.
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32 Installation
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33 ============
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34
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35 The Galaxy OpenMS tools can be installed from the toolshed. While most tools
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36 will work out of the box some need attention since requirements can not be
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37 fulfilled via Conda:
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39 Not yet in Conda are:
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fdc984e79f40 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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41 - SpectraST (http://tools.proteomecenter.org/wiki/index.php?title=SpectraST)
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42 - MaRaCluster (https://github.com/statisticalbiotechnology/maracluster)
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44 Binaries for these tools can easily be obtained via:
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46 ```
fdc984e79f40 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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47 VERSION=....
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48 git git clone -b release/$VERSION.0 https://github.com/OpenMS/OpenMS.git OpenMS$VERSION.0-git
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49 git submodule init OpenMS$VERSION.0-git
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50 git submodule update OpenMS$VERSION.0-git
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51 ```
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52
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53 They are located in `OpenMS$VERSION-git/THIRDPARTY/`.
0
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54
13
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55 Not in Conda due to licencing restrictions:
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57 - Mascot http://www.matrixscience.com/
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58 - MSFragger https://github.com/Nesvilab/MSFragger
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59 - Novor http://www.rapidnovor.org/novor
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60
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61 There are multiple ways to enable the Galaxy tools to use these binaries.
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62
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63 - Just copy them to the `bin` path within Galaxy's conda environment
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64 - Put them in any other path that that is included in PATH
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65 - Edit the corresponding tools: In the command line part search for the parameters `-executable`, `-maracluster_executable`, or `-mascot_directory` and edit them appropriately.
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66
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67 Working
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68 =======
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70 The tools work by:
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72 Preprocessing:
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74 - For each input / output data set parameter a directory is crated (named by
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75 the parameter)
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76 - For input data set parameters the links to the actual location of the data
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77 sets are created
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79 Main:
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80
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81 - The galaxy wrapper create two json config files: one containing the
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82 parameters and the values chosen by the user and the other the values of
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83 hardcoded parameters.
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84 - With `OpenMSTool -write_ctd ./` a CTD (names OpenMSTool.ctd) file is
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85 generated that contains the default values.
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86 - A call to `fill_ctd.py` fills in the values from the json config files into
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87 the CTD file
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88 - The actual tool is called `OpenMSTool -ini OpenMSTool.ctd` and also all input
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89 and output parameters are given on the command line.
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90
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91 Postprocessing:
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92
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93 - output data sets are moved to the final locations
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94
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95 Note: The reason for handling data sets on the command line (and not specifying
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96 them in the CTD file) is mainly that all files in Galaxy have the extension
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97 `.dat` and OpenMS tools require an appropriate extension. But this may change
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98 in the future.
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99
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100 Generating OpenMS wrappers
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101 ==========================
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102
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103 1. remove old test data: `rm -rf $(ls -d test-data/* | egrep -v "random|\.loc")`
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104 2. `./generate.sh`
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105
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106 Whats happening:
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107
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108 1. The binaries of the OpenMS package can generate a CTD file that describes
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109 the parameters. These CTD files are converted to xml Galaxy tool descriptions
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110 using the `CTDConverter`.
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111
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112 2. The CI testing framework of OpenMS contains command lines and test data
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113 (https://github.com/OpenMS/OpenMS/tree/develop/src/tests/topp). These tests
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114 are described in two CMake files.
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115
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116 - From these CMake files Galaxy tests are auto generated and stored in `macros_autotest.xml`
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117 - The command lines are stored in `prepare_test_data.sh` for regeneration of test data
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118
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119 More details can be found in the comments of the shell script.
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120
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121 Open problems
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122 =============
0
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123
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124 Some tools stall in CI testing using `--biocontainers` which is why the OpenMS
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125 tools are currently listed in `.tt_biocontainer_skip`. This is
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126
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127 - AssayGeneratorMetabo and SiriusAdapter (both depend on sirius)
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128 - OMSSAAdapter
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129
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130 Using `docker -t` seems to solve the problem (see
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131 https://github.com/galaxyproject/galaxy/issues/10153).
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132
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133 Licence (MIT)
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134 =============
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135
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136 Permission is hereby granted, free of charge, to any person obtaining a copy
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137 of this software and associated documentation files (the "Software"), to deal
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138 in the Software without restriction, including without limitation the rights
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139 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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140 copies of the Software, and to permit persons to whom the Software is
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141 furnished to do so, subject to the following conditions:
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142
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143 The above copyright notice and this permission notice shall be included in
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144 all copies or substantial portions of the Software.
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145
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146 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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147 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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148 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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149 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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150 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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151 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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152 THE SOFTWARE.
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153