assemblyseqload/ncbi_assocload.config at master · mgijax/assemblyseqload · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
#format: sh
###########################################################################
#
#  ncbi_assocload.config
#
#  This file sets up environment variables that are needed for the
#  NCBI Sequence/Marker data to be handled by the Association loader.
#
###########################################################################

###########################################################################
#
#  LOAD SPECIFIC SETTINGS
#
###########################################################################

#  Path name of the archive, logs, reports and output directories
FILEDIR=${DATALOADSOUTPUT}/assembly/ncbi_assocload
ARCHIVEDIR=${FILEDIR}/archive
LOGDIR=${FILEDIR}/logs
RPTDIR=${FILEDIR}/reports
OUTPUTDIR=${FILEDIR}/output

#  Complete path name of the input file
INFILE_NAME=${DATALOADSOUTPUT}/mgi/genemodelload/output/ncbi_assoc_load.txt

#  Set the size of the memory buffer used when reading an input file
INFILE_BUFFERSIZE=21000000

#  Complete path name of the log files
LOG_PROC=${LOGDIR}/assocload.proc.log
LOG_DIAG=${LOGDIR}/assocload.diag.log
LOG_CUR=${LOGDIR}/assocload.cur.log
LOG_VAL=${LOGDIR}/assocload.val.log

#  Send debug messages to the diagnostic log (true or false)
LOG_DEBUG=false

export FILEDIR ARCHIVEDIR LOGDIR RPTDIR OUTPUTDIR
export INFILE_NAME INFILE_BUFFERSIZE
export LOG_PROC LOG_DIAG LOG_CUR LOG_VAL LOG_DEBUG

#  The J-Number for the assocload
J_NUMBER=J:90438

#  The name of the job stream for the load
JOBSTREAM=ncbi_assocload

export J_NUMBER JOBSTREAM

#  Association Loader settings
ASSOCLOAD_FROM_FILE=true
ASSOCLOAD_TARGET_MGI_TYPE=Marker
ASSOCLOAD_DELETE_RELOAD=true

export ASSOCLOAD_FROM_FILE
export ASSOCLOAD_TARGET_MGI_TYPE ASSOCLOAD_DELETE_RELOAD

###########################################################################
#
#  BCP MANAGER SETTINGS BY DATABASE
#
###########################################################################

#  Settings used to create a BCP manager for the RADAR database
#  additional settings are in unists.config
RADAR_BCP_PATH=${OUTPUTDIR}
RADAR_BCP_OK_TO_OVERWRITE=true

export RADAR_BCP_PATH RADAR_BCP_OK_TO_OVERWRITE

#  Settings used to create a BCP manager for the MGD database
#  additional settings are in unists.config
MGD_BCP_PATH=${OUTPUTDIR}
MGD_BCP_OK_TO_OVERWRITE=true

export MGD_BCP_PATH MGD_BCP_OK_TO_OVERWRITE

###########################################################################
#
#  BCP SETTINGS BY TABLE (OVERRIDE BCP MANAGER SETTINGS)
#
###########################################################################

#  RADAR database table settings
#
MGI_ASSOCIATION_BCP_PRESQL="delete from MGI_Association where _JobStream_key in (select _JobStream_key from APP_JobStream where jobStreamName = '${JOBSTREAM}')"

export MGI_ASSOCIATION_BCP_PRESQL

###########################################################################
#
#  MISCELLANEOUS SETTINGS
#
###########################################################################

#  The name of the load for the subject of an email notification
MAIL_LOADNAME="NCBI Gene Model Sequence/Marker Association Load"

export MAIL_LOADNAME