| Previous changeset 0:ef7f9e2f32f2 (2021-08-26) Next changeset 2:13018941c6a0 (2021-11-19) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad" |
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modified:
data_manager/funannotate.py data_manager/funannotate.xml |
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| diff -r ef7f9e2f32f2 -r 8dff71edbce5 data_manager/funannotate.py --- a/data_manager/funannotate.py Thu Aug 26 06:54:45 2021 +0000 +++ b/data_manager/funannotate.py Thu Nov 18 21:55:43 2021 +0000 |
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| b'@@ -6,8 +6,219 @@\n import os\n import subprocess\n import sys\n+import tarfile\n from datetime import datetime\n \n+import requests\n+\n+# Some additional busco/orthodb10 datasets that can be added to funannotate db\n+# Will probably not be needed anymore in future versions of funannotate when it\n+# will use a recent busco version\n+BUSCO_10_DATASETS_URL = "https://busco-data.ezlab.org/v5/data/lineages/{dataset}"\n+BUSCO_10_DATASETS = [\n+ "acidobacteria_odb10.2020-03-06.tar.gz",\n+ "aconoidasida_odb10.2020-08-05.tar.gz",\n+ "actinobacteria_class_odb10.2021-02-23.tar.gz",\n+ "actinobacteria_phylum_odb10.2021-02-23.tar.gz",\n+ "actinopterygii_odb10.2021-02-19.tar.gz",\n+ "agaricales_odb10.2020-08-05.tar.gz",\n+ "agaricomycetes_odb10.2020-08-05.tar.gz",\n+ "alphabaculovirus_odb10.2020-11-26.tar.gz",\n+ "alphaherpesvirinae_odb10.2020-11-26.tar.gz",\n+ "alphaproteobacteria_odb10.2021-02-23.tar.gz",\n+ "alteromonadales_odb10.2021-02-23.tar.gz",\n+ "alveolata_odb10.2020-09-10.tar.gz",\n+ "apicomplexa_odb10.2020-09-10.tar.gz",\n+ "aquificae_odb10.2021-02-23.tar.gz",\n+ "arachnida_odb10.2020-08-05.tar.gz",\n+ "archaea_odb10.2021-02-23.tar.gz",\n+ "arthropoda_odb10.2020-09-10.tar.gz",\n+ "ascomycota_odb10.2020-09-10.tar.gz",\n+ "aves_odb10.2021-02-19.tar.gz",\n+ "aviadenovirus_odb10.2020-11-26.tar.gz",\n+ "bacillales_odb10.2021-02-23.tar.gz",\n+ "bacilli_odb10.2021-02-23.tar.gz",\n+ "bacteria_odb10.2020-03-06.tar.gz",\n+ "bacteroidales_odb10.2021-02-23.tar.gz",\n+ "bacteroidetes-chlorobi_group_odb10.2021-02-23.tar.gz",\n+ "bacteroidetes_odb10.2021-02-23.tar.gz",\n+ "bacteroidia_odb10.2021-02-23.tar.gz",\n+ "baculoviridae_odb10.2020-11-26.tar.gz",\n+ "basidiomycota_odb10.2020-09-10.tar.gz",\n+ "bclasvirinae_odb10.2020-11-26.tar.gz",\n+ "betabaculovirus_odb10.2020-11-26.tar.gz",\n+ "betaherpesvirinae_odb10.2020-11-26.tar.gz",\n+ "betaproteobacteria_odb10.2021-02-23.tar.gz",\n+ "boletales_odb10.2020-08-05.tar.gz",\n+ "brassicales_odb10.2020-08-05.tar.gz",\n+ "burkholderiales_odb10.2021-02-23.tar.gz",\n+ "campylobacterales_odb10.2020-03-06.tar.gz",\n+ "capnodiales_odb10.2020-08-05.tar.gz",\n+ "carnivora_odb10.2021-02-19.tar.gz",\n+ "cellvibrionales_odb10.2020-03-06.tar.gz",\n+ "cetartiodactyla_odb10.2021-02-19.tar.gz",\n+ "chaetothyriales_odb10.2020-08-05.tar.gz",\n+ "cheoctovirus_odb10.2020-11-26.tar.gz",\n+ "chlamydiae_odb10.2020-03-06.tar.gz",\n+ "chlorobi_odb10.2020-03-06.tar.gz",\n+ "chloroflexi_odb10.2020-03-06.tar.gz",\n+ "chlorophyta_odb10.2020-08-05.tar.gz",\n+ "chordopoxvirinae_odb10.2020-11-26.tar.gz",\n+ "chromatiales_odb10.2020-03-06.tar.gz",\n+ "chroococcales_odb10.2020-03-06.tar.gz",\n+ "clostridia_odb10.2020-03-06.tar.gz",\n+ "clostridiales_odb10.2020-03-06.tar.gz",\n+ "coccidia_odb10.2020-08-05.tar.gz",\n+ "coriobacteriales_odb10.2020-03-06.tar.gz",\n+ "coriobacteriia_odb10.2020-03-06.tar.gz",\n+ "corynebacteriales_odb10.2020-03-06.tar.gz",\n+ "cyanobacteria_odb10.2021-02-23.tar.gz",\n+ "cyprinodontiformes_odb10.2021-02-19.tar.gz",\n+ "cytophagales_odb10.2021-02-23.tar.gz",\n+ "cytophagia_odb10.2021-02-23.tar.gz",\n+ "delta-epsilon-subdivisions_odb10.2021-02-23.tar.gz",\n+ "deltaproteobacteria_odb10.2021-02-23.tar.gz",\n+ "desulfobacterales_odb10.2020-03-06.tar.gz",\n+ "desulfovibrionales_odb10.2021-02-23.tar.gz",\n+ "desulfurococcales_odb10.2021-02-23.tar.gz",\n+ "desulfuromonadales_odb10.2020-03-06.tar.gz",\n+ "diptera_odb10.2020-08-05.tar.gz",\n+ "dothideomycetes_odb10.2020-08-05.tar.gz",\n+ "embryophyta_odb10.2020-09-10.tar.gz",\n+ "endopterygota_odb10.2020-09-10.tar.gz",\n+ "enquatrovirus_odb10.2021-05-05.tar.gz",\n+ "enterobacterales_odb10.2021-02-23.tar.gz",\n+ "entomoplasmatales_odb10.2020-03-06.tar.gz",\n+ "epsilonproteobacteria_odb10.2020-03-06.tar.gz",\n+ "euarchontoglires_odb10.2021-02-19.tar.gz",\n+ "eudicots_odb10.2020-09-10.tar.gz",\n+ "euglenozoa_odb10.2020-08-05.ta'..b' "onygenales_odb10.2020-08-05.tar.gz",\n+ "oscillatoriales_odb10.2021-02-23.tar.gz",\n+ "pahexavirus_odb10.2020-11-26.tar.gz",\n+ "passeriformes_odb10.2021-02-19.tar.gz",\n+ "pasteurellales_odb10.2021-02-23.tar.gz",\n+ "peduovirus_odb10.2021-02-23.tar.gz",\n+ "planctomycetes_odb10.2020-03-06.tar.gz",\n+ "plasmodium_odb10.2020-08-05.tar.gz",\n+ "pleosporales_odb10.2020-08-05.tar.gz",\n+ "poales_odb10.2020-08-05.tar.gz",\n+ "polyporales_odb10.2020-08-05.tar.gz",\n+ "poxviridae_odb10.2020-11-26.tar.gz",\n+ "primates_odb10.2021-02-19.tar.gz",\n+ "propionibacteriales_odb10.2020-03-06.tar.gz",\n+ "proteobacteria_odb10.2021-02-23.tar.gz",\n+ "pseudomonadales_odb10.2020-03-06.tar.gz",\n+ "rhizobiales_odb10.2020-03-06.tar.gz",\n+ "rhizobium-agrobacterium_group_odb10.2020-03-06.tar.gz",\n+ "rhodobacterales_odb10.2021-02-23.tar.gz",\n+ "rhodospirillales_odb10.2020-03-06.tar.gz",\n+ "rickettsiales_odb10.2020-03-06.tar.gz",\n+ "rudiviridae_odb10.2020-11-26.tar.gz",\n+ "saccharomycetes_odb10.2020-08-05.tar.gz",\n+ "sauropsida_odb10.2021-02-19.tar.gz",\n+ "selenomonadales_odb10.2020-03-06.tar.gz",\n+ "simplexvirus_odb10.2020-11-26.tar.gz",\n+ "skunavirus_odb10.2020-11-26.tar.gz",\n+ "solanales_odb10.2020-08-05.tar.gz",\n+ "sordariomycetes_odb10.2020-08-05.tar.gz",\n+ "sphingobacteriia_odb10.2020-03-06.tar.gz",\n+ "sphingomonadales_odb10.2021-02-23.tar.gz",\n+ "spirochaetales_odb10.2020-03-06.tar.gz",\n+ "spirochaetes_odb10.2021-02-23.tar.gz",\n+ "spirochaetia_odb10.2021-02-23.tar.gz",\n+ "spounavirinae_odb10.2020-11-26.tar.gz",\n+ "stramenopiles_odb10.2020-08-05.tar.gz",\n+ "streptomycetales_odb10.2020-03-06.tar.gz",\n+ "streptosporangiales_odb10.2020-03-06.tar.gz",\n+ "sulfolobales_odb10.2021-02-23.tar.gz",\n+ "synechococcales_odb10.2020-03-06.tar.gz",\n+ "synergistetes_odb10.2020-03-06.tar.gz",\n+ "tenericutes_odb10.2020-03-06.tar.gz",\n+ "tequatrovirus_odb10.2020-11-26.tar.gz",\n+ "teseptimavirus_odb10.2020-11-26.tar.gz",\n+ "tetrapoda_odb10.2021-02-19.tar.gz",\n+ "tevenvirinae_odb10.2021-02-23.tar.gz",\n+ "thaumarchaeota_odb10.2021-02-23.tar.gz",\n+ "thermoanaerobacterales_odb10.2020-03-06.tar.gz",\n+ "thermoplasmata_odb10.2021-02-23.tar.gz",\n+ "thermoproteales_odb10.2021-02-23.tar.gz",\n+ "thermoprotei_odb10.2021-02-23.tar.gz",\n+ "thermotogae_odb10.2020-03-06.tar.gz",\n+ "thiotrichales_odb10.2020-03-06.tar.gz",\n+ "tissierellales_odb10.2020-03-06.tar.gz",\n+ "tissierellia_odb10.2020-03-06.tar.gz",\n+ "tremellomycetes_odb10.2020-08-05.tar.gz",\n+ "tunavirinae_odb10.2020-11-26.tar.gz",\n+ "varicellovirus_odb10.2020-11-26.tar.gz",\n+ "verrucomicrobia_odb10.2020-03-06.tar.gz",\n+ "vertebrata_odb10.2021-02-19.tar.gz",\n+ "vibrionales_odb10.2020-03-06.tar.gz",\n+ "viridiplantae_odb10.2020-09-10.tar.gz",\n+ "xanthomonadales_odb10.2020-03-06.tar.gz",\n+]\n+\n+\n+def download_file(url, dest):\n+ with requests.get(url, stream=True) as r:\n+ r.raise_for_status()\n+ with open(dest, \'wb\') as f:\n+ for chunk in r.iter_content(chunk_size=8192):\n+ f.write(chunk)\n+\n \n if __name__ == "__main__":\n \n@@ -38,6 +249,20 @@\n print("Error downloading Funannotate database.", file=sys.stderr)\n sys.exit(return_code)\n \n+ # Download newer busco datasets from orthodb 10\n+ if args.partial:\n+ BUSCO_10_DATASETS = BUSCO_10_DATASETS[:1]\n+\n+ for busco_dataset in BUSCO_10_DATASETS:\n+ print("Downloading additional busco orthodb10 dataset %s" % busco_dataset)\n+ dest_tar = os.path.join(output_directory, busco_dataset)\n+ download_file(BUSCO_10_DATASETS_URL.format(dataset=busco_dataset), dest_tar)\n+ print("Extracting %s" % busco_dataset)\n+ tar = tarfile.open(dest_tar, "r:gz")\n+ tar.extractall(output_directory)\n+ tar.close()\n+ os.remove(dest_tar)\n+\n version_id = datetime.today().strftime(\'%Y-%m-%d-%H%M%S\')\n \n version = \'1.0\'\n' |
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| diff -r ef7f9e2f32f2 -r 8dff71edbce5 data_manager/funannotate.xml --- a/data_manager/funannotate.xml Thu Aug 26 06:54:45 2021 +0000 +++ b/data_manager/funannotate.xml Thu Nov 18 21:55:43 2021 +0000 |
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| @@ -1,10 +1,11 @@ -<tool id="data_manager_funannotate" name="Funannotate data manager" version="0.0.1" tool_type="manage_data" profile="20.01"> +<tool id="data_manager_funannotate" name="Funannotate data manager" version="0.0.2" tool_type="manage_data" profile="20.01"> <requirements> - <requirement type="package" version="1.8.7">funannotate</requirement> + <requirement type="package" version="1.8.9">funannotate</requirement> + <requirement type="package" version="2.26.0">requests</requirement> </requirements> <version_command>funannotate check --show-versions</version_command> <command detect_errors="exit_code"><![CDATA[ -python '$__tool_directory__/funannotate.py' +python -u '$__tool_directory__/funannotate.py' $partial_data \$(date +'%Y-%m-%d-%H%M%S') 'funannotate' |