Mercurial > repos > iuc > data_manager_funannotate

annotate data_manager/funannotate.py @ 2:13018941c6a0 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 2c9bec50907576e22b02b8ea570073018c635475"
author iuc
date Fri, 19 Nov 2021 11:15:54 +0000
parents 8dff71edbce5
children
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ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
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diff changeset
1 #!/usr/bin/env python
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
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2
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
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3 import argparse
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
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4 import json
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
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5 import operator
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
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diff changeset
6 import os
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
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7 import subprocess
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
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8 import sys
1
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
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diff changeset
9 import tarfile
0
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
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diff changeset
10 from datetime import datetime
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
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11
1
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
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diff changeset
12 import requests
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
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13
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
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14 # Some additional busco/orthodb10 datasets that can be added to funannotate db
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
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15 # Will probably not be needed anymore in future versions of funannotate when it
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
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diff changeset
16 # will use a recent busco version
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
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17 BUSCO_10_DATASETS_URL = "https://busco-data.ezlab.org/v5/data/lineages/{dataset}"
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
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18 BUSCO_10_DATASETS = [
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
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diff changeset
19 "acidobacteria_odb10.2020-03-06.tar.gz",
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
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20 "aconoidasida_odb10.2020-08-05.tar.gz",
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iuc
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21 "actinobacteria_class_odb10.2021-02-23.tar.gz",
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
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22 "actinobacteria_phylum_odb10.2021-02-23.tar.gz",
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iuc
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23 "actinopterygii_odb10.2021-02-19.tar.gz",
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iuc
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24 "agaricales_odb10.2020-08-05.tar.gz",
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iuc
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25 "agaricomycetes_odb10.2020-08-05.tar.gz",
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26 "alphabaculovirus_odb10.2020-11-26.tar.gz",
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27 "alphaherpesvirinae_odb10.2020-11-26.tar.gz",
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28 "alphaproteobacteria_odb10.2021-02-23.tar.gz",
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29 "alteromonadales_odb10.2021-02-23.tar.gz",
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30 "alveolata_odb10.2020-09-10.tar.gz",
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31 "apicomplexa_odb10.2020-09-10.tar.gz",
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32 "aquificae_odb10.2021-02-23.tar.gz",
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33 "arachnida_odb10.2020-08-05.tar.gz",
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34 "archaea_odb10.2021-02-23.tar.gz",
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35 "arthropoda_odb10.2020-09-10.tar.gz",
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36 "ascomycota_odb10.2020-09-10.tar.gz",
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37 "aves_odb10.2021-02-19.tar.gz",
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38 "aviadenovirus_odb10.2020-11-26.tar.gz",
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39 "bacillales_odb10.2021-02-23.tar.gz",
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40 "bacilli_odb10.2021-02-23.tar.gz",
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41 "bacteria_odb10.2020-03-06.tar.gz",
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42 "bacteroidales_odb10.2021-02-23.tar.gz",
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43 "bacteroidetes-chlorobi_group_odb10.2021-02-23.tar.gz",
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44 "bacteroidetes_odb10.2021-02-23.tar.gz",
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45 "bacteroidia_odb10.2021-02-23.tar.gz",
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46 "baculoviridae_odb10.2020-11-26.tar.gz",
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47 "basidiomycota_odb10.2020-09-10.tar.gz",
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48 "bclasvirinae_odb10.2020-11-26.tar.gz",
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49 "betabaculovirus_odb10.2020-11-26.tar.gz",
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50 "betaherpesvirinae_odb10.2020-11-26.tar.gz",
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51 "betaproteobacteria_odb10.2021-02-23.tar.gz",
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52 "boletales_odb10.2020-08-05.tar.gz",
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53 "brassicales_odb10.2020-08-05.tar.gz",
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54 "burkholderiales_odb10.2021-02-23.tar.gz",
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55 "campylobacterales_odb10.2020-03-06.tar.gz",
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56 "capnodiales_odb10.2020-08-05.tar.gz",
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57 "carnivora_odb10.2021-02-19.tar.gz",
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58 "cellvibrionales_odb10.2020-03-06.tar.gz",
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59 "cetartiodactyla_odb10.2021-02-19.tar.gz",
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60 "chaetothyriales_odb10.2020-08-05.tar.gz",
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61 "cheoctovirus_odb10.2020-11-26.tar.gz",
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62 "chlamydiae_odb10.2020-03-06.tar.gz",
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63 "chlorobi_odb10.2020-03-06.tar.gz",
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64 "chloroflexi_odb10.2020-03-06.tar.gz",
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65 "chlorophyta_odb10.2020-08-05.tar.gz",
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66 "chordopoxvirinae_odb10.2020-11-26.tar.gz",
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67 "chromatiales_odb10.2020-03-06.tar.gz",
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68 "chroococcales_odb10.2020-03-06.tar.gz",
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69 "clostridia_odb10.2020-03-06.tar.gz",
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70 "clostridiales_odb10.2020-03-06.tar.gz",
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71 "coccidia_odb10.2020-08-05.tar.gz",
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72 "coriobacteriales_odb10.2020-03-06.tar.gz",
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73 "coriobacteriia_odb10.2020-03-06.tar.gz",
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74 "corynebacteriales_odb10.2020-03-06.tar.gz",
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parents: 0
diff changeset
148 "oceanospirillales_odb10.2020-03-06.tar.gz",
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents: 0
diff changeset
149 "onygenales_odb10.2020-08-05.tar.gz",
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents: 0
diff changeset
150 "oscillatoriales_odb10.2021-02-23.tar.gz",
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents: 0
diff changeset
151 "pahexavirus_odb10.2020-11-26.tar.gz",
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents: 0
diff changeset
152 "passeriformes_odb10.2021-02-19.tar.gz",
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents: 0
diff changeset
153 "pasteurellales_odb10.2021-02-23.tar.gz",
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents: 0
diff changeset
154 "peduovirus_odb10.2021-02-23.tar.gz",
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents: 0
diff changeset
155 "planctomycetes_odb10.2020-03-06.tar.gz",
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents: 0
diff changeset
156 "plasmodium_odb10.2020-08-05.tar.gz",
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents: 0
diff changeset
157 "pleosporales_odb10.2020-08-05.tar.gz",
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents: 0
diff changeset
158 "poales_odb10.2020-08-05.tar.gz",
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents: 0
diff changeset
159 "polyporales_odb10.2020-08-05.tar.gz",
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents: 0
diff changeset
160 "poxviridae_odb10.2020-11-26.tar.gz",
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents: 0
diff changeset
161 "primates_odb10.2021-02-19.tar.gz",
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents: 0
diff changeset
162 "propionibacteriales_odb10.2020-03-06.tar.gz",
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents: 0
diff changeset
163 "proteobacteria_odb10.2021-02-23.tar.gz",
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents: 0
diff changeset
164 "pseudomonadales_odb10.2020-03-06.tar.gz",
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents: 0
diff changeset
165 "rhizobiales_odb10.2020-03-06.tar.gz",
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents: 0
diff changeset
166 "rhizobium-agrobacterium_group_odb10.2020-03-06.tar.gz",
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents: 0
diff changeset
167 "rhodobacterales_odb10.2021-02-23.tar.gz",
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents: 0
diff changeset
168 "rhodospirillales_odb10.2020-03-06.tar.gz",
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents: 0
diff changeset
169 "rickettsiales_odb10.2020-03-06.tar.gz",
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents: 0
diff changeset
170 "rudiviridae_odb10.2020-11-26.tar.gz",
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents: 0
diff changeset
171 "saccharomycetes_odb10.2020-08-05.tar.gz",
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents: 0
diff changeset
172 "sauropsida_odb10.2021-02-19.tar.gz",
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents: 0
diff changeset
173 "selenomonadales_odb10.2020-03-06.tar.gz",
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents: 0
diff changeset
174 "simplexvirus_odb10.2020-11-26.tar.gz",
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents: 0
diff changeset
175 "skunavirus_odb10.2020-11-26.tar.gz",
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents: 0
diff changeset
176 "solanales_odb10.2020-08-05.tar.gz",
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents: 0
diff changeset
177 "sordariomycetes_odb10.2020-08-05.tar.gz",
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents: 0
diff changeset
178 "sphingobacteriia_odb10.2020-03-06.tar.gz",
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents: 0
diff changeset
179 "sphingomonadales_odb10.2021-02-23.tar.gz",
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents: 0
diff changeset
180 "spirochaetales_odb10.2020-03-06.tar.gz",
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents: 0
diff changeset
181 "spirochaetes_odb10.2021-02-23.tar.gz",
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents: 0
diff changeset
182 "spirochaetia_odb10.2021-02-23.tar.gz",
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents: 0
diff changeset
183 "spounavirinae_odb10.2020-11-26.tar.gz",
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents: 0
diff changeset
184 "stramenopiles_odb10.2020-08-05.tar.gz",
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents: 0
diff changeset
185 "streptomycetales_odb10.2020-03-06.tar.gz",
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents: 0
diff changeset
186 "streptosporangiales_odb10.2020-03-06.tar.gz",
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents: 0
diff changeset
187 "sulfolobales_odb10.2021-02-23.tar.gz",
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents: 0
diff changeset
188 "synechococcales_odb10.2020-03-06.tar.gz",
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents: 0
diff changeset
189 "synergistetes_odb10.2020-03-06.tar.gz",
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents: 0
diff changeset
190 "tenericutes_odb10.2020-03-06.tar.gz",
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents: 0
diff changeset
191 "tequatrovirus_odb10.2020-11-26.tar.gz",
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents: 0
diff changeset
192 "teseptimavirus_odb10.2020-11-26.tar.gz",
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents: 0
diff changeset
193 "tetrapoda_odb10.2021-02-19.tar.gz",
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents: 0
diff changeset
194 "tevenvirinae_odb10.2021-02-23.tar.gz",
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents: 0
diff changeset
195 "thaumarchaeota_odb10.2021-02-23.tar.gz",
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents: 0
diff changeset
196 "thermoanaerobacterales_odb10.2020-03-06.tar.gz",
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents: 0
diff changeset
197 "thermoplasmata_odb10.2021-02-23.tar.gz",
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents: 0
diff changeset
198 "thermoproteales_odb10.2021-02-23.tar.gz",
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents: 0
diff changeset
199 "thermoprotei_odb10.2021-02-23.tar.gz",
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents: 0
diff changeset
200 "thermotogae_odb10.2020-03-06.tar.gz",
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents: 0
diff changeset
201 "thiotrichales_odb10.2020-03-06.tar.gz",
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents: 0
diff changeset
202 "tissierellales_odb10.2020-03-06.tar.gz",
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents: 0
diff changeset
203 "tissierellia_odb10.2020-03-06.tar.gz",
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents: 0
diff changeset
204 "tremellomycetes_odb10.2020-08-05.tar.gz",
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents: 0
diff changeset
205 "tunavirinae_odb10.2020-11-26.tar.gz",
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents: 0
diff changeset
206 "varicellovirus_odb10.2020-11-26.tar.gz",
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents: 0
diff changeset
207 "verrucomicrobia_odb10.2020-03-06.tar.gz",
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents: 0
diff changeset
208 "vertebrata_odb10.2021-02-19.tar.gz",
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents: 0
diff changeset
209 "vibrionales_odb10.2020-03-06.tar.gz",
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents: 0
diff changeset
210 "viridiplantae_odb10.2020-09-10.tar.gz",
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents: 0
diff changeset
211 "xanthomonadales_odb10.2020-03-06.tar.gz",
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents: 0
diff changeset
212 ]
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents: 0
diff changeset
213
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents: 0
diff changeset
214
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents: 0
diff changeset
215 def download_file(url, dest):
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents: 0
diff changeset
216 with requests.get(url, stream=True) as r:
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents: 0
diff changeset
217 r.raise_for_status()
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents: 0
diff changeset
218 with open(dest, 'wb') as f:
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents: 0
diff changeset
219 for chunk in r.iter_content(chunk_size=8192):
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents: 0
diff changeset
220 f.write(chunk)
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents: 0
diff changeset
221
0
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
222
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
223 if __name__ == "__main__":
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
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224
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
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225 parser = argparse.ArgumentParser()
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
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226 parser.add_argument('--partial', dest='partial', action='store_true', help='Only download a small subset of data (for testing)')
2
13018941c6a0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 2c9bec50907576e22b02b8ea570073018c635475"
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227 parser.add_argument('--wget', dest='wget', action='store_true', help='Download using wget (instead of urllib)')
0
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
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228 parser.add_argument("version_id")
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
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229 parser.add_argument("datatable_name")
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
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230 parser.add_argument("galaxy_datamanager_filename")
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
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231 args = parser.parse_args()
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
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232
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
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233 with open(args.galaxy_datamanager_filename) as fh:
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
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234 config = json.load(fh)
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
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235
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
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236 output_directory = config.get("output_data", [{}])[0].get("extra_files_path", None)
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
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237 data_manager_dict = {}
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
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238 data_manager_dict["data_tables"] = config.get("data_tables", {})
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
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239 data_manager_dict["data_tables"][args.datatable_name] = data_manager_dict[
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
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240 "data_tables"
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
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241 ].get(args.datatable_name, [])
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
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242
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
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243 os.mkdir(output_directory)
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
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244 cmd_args = ['funannotate', 'setup', '-d', output_directory, '-b', 'all']
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
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245 if args.partial:
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
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246 cmd_args += ['-i', 'merops', '-b', 'eukaryota']
2
13018941c6a0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 2c9bec50907576e22b02b8ea570073018c635475"
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247 if args.wget:
13018941c6a0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 2c9bec50907576e22b02b8ea570073018c635475"
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248 cmd_args += ['--wget']
0
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
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249 proc = subprocess.Popen(args=cmd_args, shell=False, cwd=output_directory)
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
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250 return_code = proc.wait()
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
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251 if return_code:
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
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252 print("Error downloading Funannotate database.", file=sys.stderr)
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
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253 sys.exit(return_code)
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
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254
1
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
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255 # Download newer busco datasets from orthodb 10
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
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256 if args.partial:
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
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257 BUSCO_10_DATASETS = BUSCO_10_DATASETS[:1]
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
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258
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
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259 for busco_dataset in BUSCO_10_DATASETS:
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
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260 print("Downloading additional busco orthodb10 dataset %s" % busco_dataset)
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
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261 dest_tar = os.path.join(output_directory, busco_dataset)
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
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262 download_file(BUSCO_10_DATASETS_URL.format(dataset=busco_dataset), dest_tar)
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
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263 print("Extracting %s" % busco_dataset)
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
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264 tar = tarfile.open(dest_tar, "r:gz")
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
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265 tar.extractall(output_directory)
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
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266 tar.close()
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
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267 os.remove(dest_tar)
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
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268
0
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
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269 version_id = datetime.today().strftime('%Y-%m-%d-%H%M%S')
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
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270
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
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271 version = '1.0'
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
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272
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
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273 data_manager_dict["data_tables"][args.datatable_name].append(
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
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274 dict(
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
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275 value=version_id,
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
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276 description="Funannotate database %s" % version_id,
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
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277 format_version=version,
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
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278 path=output_directory,
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
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279 )
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
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280 )
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
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281
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
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282 data_manager_dict["data_tables"][args.datatable_name].sort(
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
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283 key=operator.itemgetter("value"), reverse=True
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
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284 )
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
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285 with open(args.galaxy_datamanager_filename, "w") as fh:
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
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286 json.dump(data_manager_dict, fh, indent=2, sort_keys=True)