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annotate readme.md @ 5:34dda034b019 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:20:30 +0000
parents 031adfb7fce0
children fa544e12732f
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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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8 More informations are available at:
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10 * https://github.com/OpenMS/OpenMS
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11 * https://www.openms.de/
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13 The wrappers for these tools and most of their tests are automatically
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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 - and the manually contributed tests in `macros_test.xml` (The goal is that all
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26 tools that do not have an automatically generated test are covered here)
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27 - the `hardcoded_params.json` files
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28
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29 Wrapper versions are managed in `bump.json`. For tools listed in the file
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30 the wrapper version will be set accordingly and otherwise `0` is used.
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31 For a major update of the tool version the bump file should be reset (to `{}`).
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33 In a few cases patches may be acceptable.
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35 Installation
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36 ============
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37
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38 The Galaxy OpenMS tools can be installed from the toolshed. While most tools
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39 will work out of the box some need attention since requirements can not be
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40 fulfilled via Conda:
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42 Not yet in Conda are:
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44 - SpectraST (http://tools.proteomecenter.org/wiki/index.php?title=SpectraST)
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45 - MaRaCluster (https://github.com/statisticalbiotechnology/maracluster)
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47 Binaries for these tools can easily be obtained via:
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49 ```
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50 VERSION=....
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51 git git clone -b release/$VERSION.0 https://github.com/OpenMS/OpenMS.git OpenMS$VERSION.0-git
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52 git submodule init OpenMS$VERSION.0-git
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53 git submodule update OpenMS$VERSION.0-git
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54 ```
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56 They are located in `OpenMS$VERSION-git/THIRDPARTY/`.
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58 Not in Conda due to licencing restrictions:
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60 - Mascot http://www.matrixscience.com/
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61 - MSFragger https://github.com/Nesvilab/MSFragger
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62 - Novor http://www.rapidnovor.org/novor
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64 There are multiple ways to enable the Galaxy tools to use these binaries.
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65
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66 - Just copy them to the `bin` path within Galaxy's conda environment
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67 - Put them in any other path that that is included in PATH
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68 - 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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70 Working
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71 =======
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73 The tools work by:
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75 Preprocessing:
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77 - For input data set parameters the links to the actual location of the data
5
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78 sets are created, the link names are `element_identifier`.`EXT`, where `EXT`
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79 is an extension that is known by OpenMS
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80 - In order to avoid name collisions for the created links each is placed in a
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81 unique directory: `PARAM_NAME/DATASET_ID`, where `PARAM_NAME` is the name
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82 of the parameter and `DATASET_ID` is the id of the Galaxy dataset
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83 - the same happens for output parameters that are in 1:1 correspondence with
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84 an input parameter
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85
0
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86
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
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87 Main:
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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88
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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89 - The galaxy wrapper create two json config files: one containing the
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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90 parameters and the values chosen by the user and the other the values of
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
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91 hardcoded parameters.
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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92 - With `OpenMSTool -write_ctd ./` a CTD (names OpenMSTool.ctd) file is
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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93 generated that contains the default values.
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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94 - A call to `fill_ctd.py` fills in the values from the json config files into
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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95 the CTD file
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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96 - The actual tool is called `OpenMSTool -ini OpenMSTool.ctd` and also all input
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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97 and output parameters are given on the command line.
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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98
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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99 Postprocessing:
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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100
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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101 - output data sets are moved to the final locations
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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102
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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103 Note: The reason for handling data sets on the command line (and not specifying
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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104 them in the CTD file) is mainly that all files in Galaxy have the extension
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
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105 `.dat` and OpenMS tools require an appropriate extension. But this may change
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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106 in the future.
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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107
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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108 Generating OpenMS wrappers
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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109 ==========================
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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110
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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111 1. remove old test data: `rm -rf $(ls -d test-data/* | egrep -v "random|\.loc")`
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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112 2. `./generate.sh`
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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113
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
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114 Whats happening:
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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115
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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116 1. The binaries of the OpenMS package can generate a CTD file that describes
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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117 the parameters. These CTD files are converted to xml Galaxy tool descriptions
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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118 using the `CTDConverter`.
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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119
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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120 2. The CI testing framework of OpenMS contains command lines and test data
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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121 (https://github.com/OpenMS/OpenMS/tree/develop/src/tests/topp). These tests
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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122 are described in two CMake files.
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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123
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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124 - From these CMake files Galaxy tests are auto generated and stored in `macros_autotest.xml`
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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125 - The command lines are stored in `prepare_test_data.sh` for regeneration of test data
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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126
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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127 More details can be found in the comments of the shell script.
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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128
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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129 Open problems
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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130 =============
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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131
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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132 Some tools stall in CI testing using `--biocontainers` which is why the OpenMS
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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133 tools are currently listed in `.tt_biocontainer_skip`. This is
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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134
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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135 - AssayGeneratorMetabo and SiriusAdapter (both depend on sirius)
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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136 - OMSSAAdapter
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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137
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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138 Using `docker -t` seems to solve the problem (see
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
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139 https://github.com/galaxyproject/galaxy/issues/10153).
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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140
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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141 Licence (MIT)
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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142 =============
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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143
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
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144 Permission is hereby granted, free of charge, to any person obtaining a copy
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
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145 of this software and associated documentation files (the "Software"), to deal
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
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146 in the Software without restriction, including without limitation the rights
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
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147 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
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148 copies of the Software, and to permit persons to whom the Software is
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
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149 furnished to do so, subject to the following conditions:
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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150
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
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151 The above copyright notice and this permission notice shall be included in
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
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152 all copies or substantial portions of the Software.
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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153
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
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154 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
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155 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
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156 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
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157 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
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158 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
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159 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
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160 THE SOFTWARE.
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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161