Mercurial > repos > iuc > data_manager_mapseq

comparison data_manager_fetch_mapseq_db.py @ 2:23511530b8fd draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 960c1f69ec78943dfe72eff0a0992a2ce15d2555
author iuc
date Mon, 30 Sep 2024 10:08:03 +0000
parents 4cd97cc67061
children a0d77af1d226
comparison
equal deleted inserted replaced
1:4cd97cc67061 2:23511530b8fd
8 from datetime import datetime 8 from datetime import datetime
9 9
10 import wget 10 import wget
11 11
12 DB_paths = { 12 DB_paths = {
13 "mgnify_lsu": "ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/pipeline-5.0/ref-dbs/silva_lsu-20200130.tar.gz", 13 "mgnify_v5_lsu": "ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/pipeline-5.0/ref-dbs/silva_lsu-20200130.tar.gz",
14 "mgnify_ssu": "ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/pipeline-5.0/ref-dbs/silva_ssu-20200130.tar.gz", 14 "mgnify_v5_ssu": "ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/pipeline-5.0/ref-dbs/silva_ssu-20200130.tar.gz",
15 "mgnify_its_unite": "ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/pipeline-5.0/ref-dbs/UNITE-20200214.tar.gz", 15 "mgnify_v5_its_unite": "ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/pipeline-5.0/ref-dbs/UNITE-20200214.tar.gz",
16 "mgnify_its_itsonedb": "ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/pipeline-5.0/ref-dbs/ITSoneDB-20200214.tar.gz", 16 "mgnify_v5_its_itsonedb": "ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/pipeline-5.0/ref-dbs/ITSoneDB-20200214.tar.gz",
17 "mgnify_v6_lsu": "ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/pipelines/tool-dbs/silva-lsu/silva-lsu_138.1.tar.gz",
18 "mgnify_v6_ssu": "ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/pipelines/tool-dbs/silva-ssu/silva-ssu_138.1.tar.gz",
19 "mgnify_v6_its_unite": "ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/pipelines/tool-dbs/unite/unite_9.0.tar.gz",
20 "mgnify_v6_its_itsonedb": "ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/pipelines/tool-dbs/itsonedb/itsonedb_1.141.tar.gz",
21 "mgnify_v6_pr2": "ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/pipelines/tool-dbs/pr2/pr2_5.0.0.tar.gz",
17 "test_lsu": "https://zenodo.org/record/8205348/files/test_lsu.tar.gz", 22 "test_lsu": "https://zenodo.org/record/8205348/files/test_lsu.tar.gz",
18 } 23 }
19 24
20 DB_names = { 25 DB_names = {
21 "mgnify_lsu": "MGnify LSU (v5.0.7) - silva_lsu-20200130", 26 "mgnify_v5_lsu": "MGnify LSU (v5.0.7) - silva_lsu-20200130",
22 "mgnify_ssu": "MGnify SSU (v5.0.7) - silva_ssu-20200130", 27 "mgnify_v5_ssu": "MGnify SSU (v5.0.7) - silva_ssu-20200130",
23 "mgnify_its_unite": "MGnify ITS UNITE (v5.0.7) - UNITE-20200214", 28 "mgnify_v5_its_unite": "MGnify ITS UNITE (v5.0.7) - UNITE-20200214",
24 "mgnify_its_itsonedb": "MGnify ITS ITSonedb (v5.0.7) - ITSoneDB-20200214", 29 "mgnify_v5_its_itsonedb": "MGnify ITS ITSonedb (v5.0.7) - ITSoneDB-20200214",
30 "mgnify_v6_lsu": "MGnify LSU (v6.0) - silva_lsu-20240702",
31 "mgnify_v6_ssu": "MGnify SSU (v6.0) - silva_ssu-20240701",
32 "mgnify_v6_its_unite": "MGnify ITS UNITE (v6.0) - UNITE-20240702",
33 "mgnify_v6_its_itsonedb": "MGnify ITS ITSonedb (v6.0) - ITSoneDB-20240702",
34 "mgnify_v6_pr2": "MGnify PR2 (v6.0) - PR2-20240702",
25 "test_lsu": "Trimmed LSU Test DB", 35 "test_lsu": "Trimmed LSU Test DB",
26 } 36 }
27 37
28 38
29 def download_untar_store(url, tmp_path, dest_path): 39 def download_untar_store(url, tmp_path, dest_path):