annotate README.rst @ 15:32f1f56bd970 draft

Updated for Trimmomatic 0.39 and adds quality score options.
author pjbriggs
date Thu, 02 Mar 2023 15:24:24 +0000
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1 Trimmomatic: flexible read trimming tool for Illumina NGS data
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2 ==============================================================
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3
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4 Galaxy tool wrapper for the Trimmomatic program, which provides various functions for
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5 manipluating Illumina FASTQ files (both single and paired-end).
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6
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7 Trimmomatic has been developed within Bjorn Usadel's group at RWTH Aachen university
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8 http://www.usadellab.org/cms/index.php?page=trimmomatic
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9
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10 The reference for Trimmomatic is:
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11
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12 - Bolger, A.M., Lohse, M., & Usadel, B. (2014). Trimmomatic: A flexible trimmer
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13 for Illumina Sequence Data. Bioinformatics, btu170.
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15 Automated installation
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16 ======================
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17
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18 Installation via the Galaxy Tool Shed will take care of installing the tool wrapper
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19 and the trimmomatic program and data, and setting the appropriate environment
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20 variables.
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21
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22 Controlling the available memory
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23 ================================
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25 The default amount of memory avilable to trimmomatic is set to 8GB.
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26 To change the default amount of memory you can set the environment variable
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27 ``_JAVA_OPTIONS`` to ``-Xmx<amount_of_memory_in_GB>G``. The recommended way to
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28 set this is in the job_conf.xml file. To change the available memory to 6GB, a
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29 line like the below should be added:
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31 ``<env id="_JAVA_OPTIONS">-Xmx6G</env>``
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33 This will set the environment variable ``_JAVA_OPTIONS`` to ``-Xmx6G``.
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34
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35 Manual Installation
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36 ===================
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37
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38 There are two files to install:
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39
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40 - ``trimmomatic.xml`` (the Galaxy tool definition)
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41 - ``trimmomatic.sh`` (the shell script wrapper)
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42
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43 The suggested location is in a ``tools/trimmomatic/`` folder. You will then
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44 need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool
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45 by adding the line:
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46
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47 <tool file="trimmomatic/trimmomatic.xml" />
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48
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49 You will also need to install trimmomatic 0.38:
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50
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51 - http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.38.zip
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52
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53 The tool wrapper uses the following environment variables in order to find the
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54 appropriate files:
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55
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56 - ``TRIMMOMATIC_DIR`` should point to the directory holding the
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57 ``trimmomatic-0.36.jar`` file
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58 - ``TRIMMOMATIC_ADAPTERS_DIR`` should point to the directory holding the adapter
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59 sequence files (used by the ``ILLUMINACLIP`` option).
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60
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61 If you want to run the functional tests, copy the sample test files under
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62 sample test files under Galaxy's ``test-data/`` directory. Then:
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63
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64 ./run_tests.sh -id trimmomatic
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65
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66 You will need to have set the environment variables above.
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67
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68 History
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69 =======
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70
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71 ========== ======================================================================
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72 Version Changes
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73 ---------- ----------------------------------------------------------------------
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74 0.39 - Update to Trimmomatic 0.39.
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75 0.38.1 - Bug fix: add dependency on ``coreutils`` so that ``readlink -e`` is
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76 supported across both Linux and MacOS platforms.
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77 0.38.0 - Update to Trimmomatic 0.38.
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78 0.36.6 - Added trimlog and log outputs; add support for ``fastqillumina``
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79 and ``fastqsolexa`` input types
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80 0.36.5 - Remove tool_dependencies.xml and always use conda to resolve tool
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81 dependencies
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82 0.36.4 - Add option to provide custom adapter sequences for ILLUMINACLIP
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83 - Add options ``minAdapterLength`` and ``keepBothReads`` for ILLUMINACLIP
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84 in palindrome mode
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85 0.36.3 - Fix naming of output collections. Instead of all outputs being called
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86 "Trimmomatic on collection NN" these will now be called "Trimmomatic
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87 on collection NN: paired" or "Trimmomatic on collection NN: unpaired".
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88 0.36.2 - Support fastqsanger.gz datatype. If fastqsanger.gz is used as input
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89 the output will also be fastqsanger.gz.
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90 - Use $_JAVA_OPTIONS to customize memory requirements.
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91 0.36.1 - Reimplement to work with bioconda Trimmomatic 0.36 (toolshed version
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92 is still supported for now).
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93 0.36.0 - Update to Trimmomatic 0.36.
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94 0.32.4 - Add support for ``AVGQUAL`` and ``MAXINFO`` operations.
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95 0.32.3 - Add support for FASTQ R1/R2 pairs using dataset collections (input
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96 can be dataset collection, in which case tool also outputs dataset
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97 collections) and improve order and naming of output files.
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98 0.32.2 - Use ``GALAXY_SLOTS`` to set the appropriate number of threads to use
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99 at runtime (default is 6).
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100 0.32.1 - Remove ``trimmomatic_adapters.loc.sample`` and hard-code adapter files
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101 into the XML wrapper.
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102 0.32.0 - Add tool_dependencies.xml to install Trimmomatic 0.32 automatically and
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103 set the environment.
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104 - Update tool versioning to use Trimmomatic version number (i.e. ``0.32``)
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105 with tool iteration appended (i.e. ``.1``).
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106 0.0.4 - Specify '-threads 6' in <command> section.
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107 0.0.3 - Added MINLEN, LEADING, TRAILING, CROP and HEADCROP options of trimmomatic.
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108 0.0.2 - Updated ILLUMINACLIP option to use standard adapter sequences (requires
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109 the trimmomatic_adapters.loc file; sample version is supplied) plus
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110 cosmetic updates to wording and help text for some options.
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111 0.0.1 - Initial version
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112 ========== ======================================================================
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113
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114
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115 Credits
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116 =======
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117
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118 This wrapper has been developed and is maintained by Peter Briggs (@pjbriggs).
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119 Peter van Heusden (@pvanheus) and Marius van den Beek (@mvdbeek) contributed
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120 support for gz compressed FastQ files. Charles Girardot (@cgirardot) and
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121 Jelle Scholtalbers (@scholtalbers) contributed additional options to ILLUMINACLIP.
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122 Matthias Bernt (@bernt-matthias) added log and trimlog output.
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123 Nicola Soranzo (@nsoranzo) suggested using coreutils to enable cross-platform
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124 support across Linux and MacOS.
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125 Cristóbal Gallardo (@gallardoalba) updated Trimmomatic up to version 0.39.
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126
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127 Developers
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128 ==========
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129
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130 This tool is developed on the following GitHub repository:
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131 https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/trimmomatic
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132
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133 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use
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134 the ``package_trimmomatic.sh`` script.
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135
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136
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137 Licence (MIT)
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138 =============
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139
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140 Permission is hereby granted, free of charge, to any person obtaining a copy
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141 of this software and associated documentation files (the "Software"), to deal
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142 in the Software without restriction, including without limitation the rights
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143 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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144 copies of the Software, and to permit persons to whom the Software is
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145 furnished to do so, subject to the following conditions:
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146
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147 The above copyright notice and this permission notice shall be included in
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148 all copies or substantial portions of the Software.
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149
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150 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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151 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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152 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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153 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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154 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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155 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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156 THE SOFTWARE.