Mercurial > repos > brinkmanlab > microbedb

annotate builds.sql @ 5:67447b96c3ff draft

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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/microbedb commit 5c194fba785b48181a68d413b2f70eaca23ff6db"
author brinkmanlab
date Mon, 09 Nov 2020 01:09:50 +0000
parents 258826db8291
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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40d14d5c8125 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/microbedb commit e63162a36457c0337c67e536a8a394beb06f4d70"
brinkmanlab
parents:
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1 DROP TABLE IF EXISTS builds_temp;
40d14d5c8125 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/microbedb commit e63162a36457c0337c67e536a8a394beb06f4d70"
brinkmanlab
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2 CREATE TEMP TABLE builds_temp(dbkey unique, label);
40d14d5c8125 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/microbedb commit e63162a36457c0337c67e536a8a394beb06f4d70"
brinkmanlab
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3 .mode csv
40d14d5c8125 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/microbedb commit e63162a36457c0337c67e536a8a394beb06f4d70"
brinkmanlab
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4 .separator ' '
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258826db8291 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/microbedb commit 668759e2fc5d53432092d7c1395b402385733171"
brinkmanlab
parents: 0
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5 .import '$__app__.config.builds_file_path' builds_temp
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40d14d5c8125 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/microbedb commit e63162a36457c0337c67e536a8a394beb06f4d70"
brinkmanlab
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6 INSERT OR REPLACE INTO builds_temp (dbkey, label)
40d14d5c8125 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/microbedb commit e63162a36457c0337c67e536a8a394beb06f4d70"
brinkmanlab
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7 SELECT (r.rep_accnum || '_' || r.rep_version) AS dbkey,
40d14d5c8125 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/microbedb commit e63162a36457c0337c67e536a8a394beb06f4d70"
brinkmanlab
parents:
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8 (REPLACE(r.definition, ', complete genome.', '') || ' [' || r.rep_accnum || '.' || r.rep_version ||
40d14d5c8125 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/microbedb commit e63162a36457c0337c67e536a8a394beb06f4d70"
brinkmanlab
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9 ']') AS label
40d14d5c8125 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/microbedb commit e63162a36457c0337c67e536a8a394beb06f4d70"
brinkmanlab
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10 FROM genomeproject
40d14d5c8125 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/microbedb commit e63162a36457c0337c67e536a8a394beb06f4d70"
brinkmanlab
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11 JOIN replicon r ON genomeproject.gpv_id = r.gpv_id AND r.rep_type = 'chromosome'
40d14d5c8125 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/microbedb commit e63162a36457c0337c67e536a8a394beb06f4d70"
brinkmanlab
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12 WHERE genomeproject.version_id = (SELECT MAX(version_id) FROM version)
40d14d5c8125 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/microbedb commit e63162a36457c0337c67e536a8a394beb06f4d70"
brinkmanlab
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13 AND genomeproject.file_types IS NOT NULL
40d14d5c8125 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/microbedb commit e63162a36457c0337c67e536a8a394beb06f4d70"
brinkmanlab
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14 AND genomeproject.file_types LIKE '%.fna%'
40d14d5c8125 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/microbedb commit e63162a36457c0337c67e536a8a394beb06f4d70"
brinkmanlab
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15 AND r.rep_type = 'chromosome';
40d14d5c8125 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/microbedb commit e63162a36457c0337c67e536a8a394beb06f4d70"
brinkmanlab
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16 .mode list
40d14d5c8125 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/microbedb commit e63162a36457c0337c67e536a8a394beb06f4d70"
brinkmanlab
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17 .separator ' '
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258826db8291 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/microbedb commit 668759e2fc5d53432092d7c1395b402385733171"
brinkmanlab
parents: 0
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18 .once '$__app__.config.builds_file_path'
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40d14d5c8125 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/microbedb commit e63162a36457c0337c67e536a8a394beb06f4d70"
brinkmanlab
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19 SELECT dbkey, label FROM builds_temp ORDER BY dbkey;