| Previous changeset 3:0cadd0a04412 (2021-11-19) Next changeset 5:5459ec34767a (2025-03-07) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4 |
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modified:
data_manager/funannotate.xml test-data/funannotate.loc |
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removed:
data_manager/funannotate.py |
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| diff -r 0cadd0a04412 -r 1c81a82b5b8e data_manager/funannotate.py --- a/data_manager/funannotate.py Fri Nov 19 15:43:06 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,286 +0,0 @@\n-#!/usr/bin/env python\n-\n-import argparse\n-import json\n-import operator\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- '..b'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- parser = argparse.ArgumentParser()\n- parser.add_argument(\'--partial\', dest=\'partial\', action=\'store_true\', help=\'Only download a small subset of data (for testing)\')\n- parser.add_argument(\'--wget\', dest=\'wget\', action=\'store_true\', help=\'Download using wget (instead of urllib)\')\n- parser.add_argument("version_id")\n- parser.add_argument("datatable_name")\n- parser.add_argument("galaxy_datamanager_filename")\n- args = parser.parse_args()\n-\n- with open(args.galaxy_datamanager_filename) as fh:\n- config = json.load(fh)\n-\n- output_directory = config.get("output_data", [{}])[0].get("extra_files_path", None)\n- data_manager_dict = {}\n- data_manager_dict["data_tables"] = config.get("data_tables", {})\n- data_manager_dict["data_tables"][args.datatable_name] = data_manager_dict[\n- "data_tables"\n- ].get(args.datatable_name, [])\n-\n- os.mkdir(output_directory)\n- cmd_args = [\'funannotate\', \'setup\', \'-d\', output_directory, \'-b\', \'all\']\n- if args.partial:\n- cmd_args += [\'-i\', \'merops\', \'-b\', \'eukaryota\']\n- if args.wget:\n- cmd_args += [\'--wget\']\n- proc = subprocess.Popen(args=cmd_args, shell=False, cwd=output_directory)\n- return_code = proc.wait()\n- if return_code:\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-\n- data_manager_dict["data_tables"][args.datatable_name].append(\n- dict(\n- value=version_id,\n- description="Funannotate database %s" % version_id,\n- format_version=version,\n- path=output_directory,\n- )\n- )\n-\n- data_manager_dict["data_tables"][args.datatable_name].sort(\n- key=operator.itemgetter("value"), reverse=True\n- )\n- with open(args.galaxy_datamanager_filename, "w") as fh:\n- json.dump(data_manager_dict, fh, indent=2, sort_keys=True)\n' |
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| diff -r 0cadd0a04412 -r 1c81a82b5b8e data_manager/funannotate.xml --- a/data_manager/funannotate.xml Fri Nov 19 15:43:06 2021 +0000 +++ b/data_manager/funannotate.xml Fri Mar 07 22:33:21 2025 +0000 |
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| @@ -1,23 +1,47 @@ -<tool id="data_manager_funannotate" name="Funannotate data manager" version="0.0.3" tool_type="manage_data" profile="20.01"> +<tool id="data_manager_funannotate" name="Funannotate data manager" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="20.01"> + <macros> + <token name="@TOOL_VERSION@">1.8.15</token> + <token name="@VERSION_SUFFIX@">0</token> + </macros> <requirements> - <requirement type="package" version="1.8.9">funannotate</requirement> - <requirement type="package" version="2.26.0">requests</requirement> + <requirement type="package" version="@TOOL_VERSION@">funannotate</requirement> </requirements> <version_command>funannotate check --show-versions</version_command> <command detect_errors="exit_code"><![CDATA[ -#if $wget: - ## Asked for wget, we assume there's a certificate problem on (at least) one - ## of the many requested servers, force disable of all checks - echo "check_certificate = off" > \$HOME/.wgetrc && -#end if + #if $wget: + ## Asked for wget, we assume there's a certificate problem on (at least) one + ## of the many requested servers, force disable of all checks + echo "check_certificate = off" > \$HOME/.wgetrc && + #end if -python -u '$__tool_directory__/funannotate.py' -$partial_data -$wget -\$(date +'%Y-%m-%d-%H%M%S') -'funannotate' -'${output_file}' + funannotate setup + -d '$output_file.extra_files_path' + #if $partial_data + -i merops -b eukaryota + #else + -b all + #end if + $wget + && + cp '$dmjson' '$output_file' ]]></command> + <configfiles> + <configfile name="dmjson"><![CDATA[ +#from datetime import datetime +#set version_id=datetime.now().strftime("%Y-%m-%d-%H%M%S") + { + "data_tables":{ + "funannotate":[ + { + "value":"$version_id", + "description":"Funannotate database $version_id", + "format_version":"1.0", + "path":"$output_file.extra_files_path" + } + ] + } + }]]></configfile> + </configfiles> <inputs> <param name="partial_data" type="hidden" value="" help="Used for testing"/> <param name="wget" type="boolean" truevalue="--wget" falsevalue="" checked="False" label="Download using wget" help="Try this if you get certificate errors"/> @@ -31,7 +55,7 @@ <output name="output_file"> <assert_contents> <has_text text="Funannotate database "/> - <has_text text='"format_version": "1.0"'/> + <has_text text='"format_version":"1.0"'/> </assert_contents> </output> </test> @@ -41,7 +65,7 @@ <output name="output_file"> <assert_contents> <has_text text="Funannotate database "/> - <has_text text='"format_version": "1.0"'/> + <has_text text='"format_version":"1.0"'/> </assert_contents> </output> </test> |
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| diff -r 0cadd0a04412 -r 1c81a82b5b8e test-data/funannotate.loc --- a/test-data/funannotate.loc Fri Nov 19 15:43:06 2021 +0000 +++ b/test-data/funannotate.loc Fri Mar 07 22:33:21 2025 +0000 |
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| @@ -7,3 +7,10 @@ # for example # 2021-07-20-120000 Funannotate database 2021-07-20-120000 1.0 /tmp/database/funannotate/2021-07-20-120000 # 2021-05-27-120000 Funannotate database 2021-05-27-120000 3.0 /tmp/database/funannotate/2021-05-27-120000 +2025-02-17-000000 Funannotate database 2025-02-17-000000 /tmp/tmpm1ezjinx/galaxy-dev/tool-data/funannotate/2025-02-17-000000 +2025-02-17-210445 Funannotate database 2025-02-17-210445 /tmp/tmpg0tuguj6/galaxy-dev/tool-data/funannotate/2025-02-17-210445 +2025-02-17-210504 Funannotate database 2025-02-17-210504 /tmp/tmpg0tuguj6/galaxy-dev/tool-data/funannotate/2025-02-17-210504 +2025-02-17-210714 Funannotate database 2025-02-17-210714 1.0 /tmp/tmpdtjxf3c7/galaxy-dev/tool-data/funannotate/2025-02-17-210714 +2025-02-17-210732 Funannotate database 2025-02-17-210732 1.0 /tmp/tmpdtjxf3c7/galaxy-dev/tool-data/funannotate/2025-02-17-210732 +2025-02-17-211010 Funannotate database 2025-02-17-211010 1.0 /tmp/tmp07fm9fgh/galaxy-dev/tool-data/funannotate/2025-02-17-211010 +2025-02-17-211028 Funannotate database 2025-02-17-211028 1.0 /tmp/tmp07fm9fgh/galaxy-dev/tool-data/funannotate/2025-02-17-211028 |