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Merge pull request #1297 from deeptools/ESS_docs
version boost, and include GRCm39 in ESS docs
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‎docs/content/feature/effectiveGenomeSize.rst

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@@ -23,6 +23,8 @@ The effective genome size for a number of genomes using this method is given bel
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+---------------+------------------+
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|GRCm38 | 2652783500 |
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+---------------+------------------+
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|GRCm39 | 2654621783 |
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+---------------+------------------+
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|dm3 | 162367812 |
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+---------------+------------------+
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|dm6 | 142573017 |
@@ -44,18 +46,18 @@ These are then based on the read length.
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We can approximate these values for various read lengths using the `khmer program <https://khmer.readthedocs.io/en/latest/>`__ program and ``unique-kmers.py`` in particular.
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A table of effective genome sizes given a read length using this method is provided below:
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+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+
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|Read length | GRCh37 | GRCh38 | T2T/CHM13CAT_v2 | GRCm37 | GRCm38 | dm3 | dm6 | GRCz10 | GRCz11 | WBcel235 | TAIR10 |
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+=================+=================+=================+=================+=================+=================+=================+=================+=================+=================+=================+=================+
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|50 | 2685511454 | 2701495711 | 2725240337 | 2304947876 | 2308125299 | 130428510 | 125464678 | 1195445541 | 1197575653 | 95159402 | 114339094 |
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+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+
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|75 | 2736124898 | 2747877702 | 2786136059 | 2404646149 | 2407883243 | 135004387 | 127324557 | 1251132611 | 1250812288 | 96945370 | 115317469 |
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+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+
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|100 | 2776919708 | 2805636231 | 2814334875 | 2462480910 | 2467481008 | 139647132 | 129789773 | 1280188944 | 1280354977 | 98259898 | 118459858 |
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+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+
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|150 | 2827436883 | 2862010428 | 2931551487 | 2489384085 | 2494787038 | 144307658 | 129940985 | 1312207019 | 1311832909 | 98721103 | 118504138 |
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+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+
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|200 | 2855463800 | 2887553103 | 2936403235 | 2513019076 | 2520868989 | 148523810 | 132508963 | 1321355041 | 1322366338 | 98672558 | 117723393 |
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+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+
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|250 | 2855044784 | 2898802627 | 2960856300 | 2528988583 | 2538590322 | 151901455 | 132900923 | 1339205109 | 1342093482 | 101271756 | 119585546 |
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+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+
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+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+
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|Read length | GRCh37 | GRCh38 | T2T/CHM13CAT_v2 | GRCm37 | GRCm38 | GRCm39 | dm3 | dm6 | GRCz10 | GRCz11 | WBcel235 | TAIR10 |
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+=================+=================+=================+=================+=================+=================+=================+=================+=================+=================+=================+=================+=================+
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|50 | 2685511454 | 2701495711 | 2725240337 | 2304947876 | 2308125299 | 2309746861 | 130428510 | 125464678 | 1195445541 | 1197575653 | 95159402 | 114339094 |
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+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+
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|75 | 2736124898 | 2747877702 | 2786136059 | 2404646149 | 2407883243 | 2410055689 | 135004387 | 127324557 | 1251132611 | 1250812288 | 96945370 | 115317469 |
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+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+
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|100 | 2776919708 | 2805636231 | 2814334875 | 2462480910 | 2467481008 | 2468088461 | 139647132 | 129789773 | 1280188944 | 1280354977 | 98259898 | 118459858 |
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+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+
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|150 | 2827436883 | 2862010428 | 2931551487 | 2489384085 | 2494787038 | 2495461690 | 144307658 | 129940985 | 1312207019 | 1311832909 | 98721103 | 118504138 |
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+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+
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|200 | 2855463800 | 2887553103 | 2936403235 | 2513019076 | 2520868989 | 2521902382 | 148523810 | 132508963 | 1321355041 | 1322366338 | 98672558 | 117723393 |
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+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+
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|250 | 2855044784 | 2898802627 | 2960856300 | 2528988583 | 2538590322 | 2538633971 | 151901455 | 132900923 | 1339205109 | 1342093482 | 101271756 | 119585546 |
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+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+

‎galaxy/wrapper/deepTools_macros.xml

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<macros>
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<token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
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<token name="@TOOL_VERSION@">3.5.5</token>
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<token name="@TOOL_VERSION@">3.5.6</token>
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<token name="@GALAXY_VERSION@">22.05</token>
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<xml name="requirements">
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<requirements>

‎pyproject.toml

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[project]
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name = "deepTools"
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version = "3.5.5"
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version = "3.5.6"
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authors = [
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{name="Fidel Ramirez"},
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{name="Devon P Ryan"},

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