| name |
  |
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| type |
  lib |
|
|
 lib appl |
|
| creDate |
|
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| description |
|
|
| www |
|
|
| citation |
|
|
| ftp |
|
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| fax |
|
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| ftpSite |
|
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| updDate |
|
|
| more |
|
|
| literature |
|
|
| example |
|
|
| email |
|
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| fields |
 |
|
| options |
|
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| date |
|
|
| signature |
|
|
| address |
|
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| contact |
|
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| updates |
|
|
| updMethod |
 none |
|
|
none mirror copy create createfromdatafiles createfromlinks sharedata createfromonline |
|
|
Method for updating a database
none: no updating
mirror: ftp/mirror
copy: copy from a directory/cdrom
create: generated from existing SRS indexes
createfromdatafiles: generated from existing data files
createfromlinks: generated from existing SRS link indexes
sharesdata: uses same datafiles as parent database eg. uniest
createfromonline: created AFTER parents are moved online
|
| mirrorTimeout |
120 |
|
|
timeout for an ftp connection (seconds)
|
| mirrorRetry |
3 |
|
|
numbers of retries before aborting a download
|
| mirrorChains |
1 |
|
|
number of simultaneous connections for a database
The download dependencies for databases with multiple
downloads will be chained in such a way that there
will be no more than this number of connections
|
| contentFile |
|
|
|
contents file on remote site
|
| localContentFile |
|
|
|
contents file on local site
|
| transferMode |
binary |
|
|
binary ascii |
|
|
ftp transfer mode
|
| userName |
anonymous |
|
|
username on remote site
|
| passWord |
 paolo.romano@hsanmartino.it |
|
|
password on remote site
|
| localSearchName |
* |
|
|
search pattern to find files on local site
|
| searchName |
|
|
|
search pattern to find files on remote site
|
| files |
 |
|
|
list of files to download (alternative to searchName)
|
| remoteNamePattern |
|
|
|
file name pattern on the remote site
|
| localNamePattern |
|
|
|
file name pattern locally, after downloading
|
| caseTranslation |
none |
|
|
none upper lower |
|
|
tranlate to lower or upper case, or not at all
|
| subDirectories |
no |
|
|
no yes flatten |
|
|
This option controls whether Prisma will descend into sub-directories
on the remote site. By default, Prisma will not do this.
If yes is chosen, all files corresponding to the search name beneath
the download directory will be transferred, and the directory structure
will be preserved. If flatten is chosen, all the matching files from
the subdirectory will be transferred to the same level in the offline
directory.
|
| downLoadDir |
|
|
|
remote directory, or directory to copy from
|
| remoteOptionalNamePattern |
|
|
|
second level of name translation, pattern at the remote site
|
| localOptionalNamePattern |
|
|
|
second level of name translation, pattern at the local site
|
| optionalCaseTranslation |
none |
|
|
none upper lower |
|
|
case conversion for second level translation
|
| dbDependOn |
|
|
|
list of database names on which the locally generated
database depends
|
| weekDay |
0123456 |
|
|
crontab like string specifying which day of the week
to check for a database (Sunday=0)
|
| unpackCommand |
Lists
|
|
|
system command(s) to use on data before indexing
like unzip/untar. Occurences of "%s"
will be replaced by the filename.
|
| reformatCommand |
Lists
|
|
|
command(s) to do additional reformatting after indexing
like fasta/blast file generation. Occurences of "%s"
will be replaced by the filename.
|
| installType |
move |
|
|
move switchlink command none |
|
|
type of installation:
move: moves data to the online directory<
switchlink: to switch links between (symbolic) online
data locations and their physical locations
command: use command specified by installCommand
none: do not install
|
| installFiles |
Lists
|
|
|
specification of additional files to move when
installing database files with mv (like fasta files)
|
| installCommand |
Lists
|
|
|
specifies command(s) to use for installation
(instead of the default mv)
|
| noSRS |
no |
|
|
no yes |
|
|
flag to specify that the database needs to be installed
but is not indexed for SRS
|
| doRemove |
delete |
|
|
delete rename move |
|
|
flag indicating what to do with old files (either
obsolete as indicated by mirror, or files in the
in the new offLine data directory after a "switchlink"
installation)
|
| removeDir |
|
|
|
directory to which to move old files for doRemove:move
|
| removeExt |
old |
|
|
extension to add to old files for doRemove:rename
|
| getReleaseCommand |
|
|
|
Command which will return the release number for a library which
can be added to the indices for display on the information page.
This command will be run after the database has been installed online.
%d is a placeholder for the online directory.
|
| forceOnline |
no |
|
|
no yes |
|
|
flag to indicate if database is to be moved online
even if a link index or dependant database failed
to be built correctly
|
| keepFileDates |
no |
|
|
no yes |
|
|
Flag to switch on and off preservation of file dates from
remote site during mirroring by dbSync.pl
|
| checkFileSizes |
yes |
|
|
no yes |
|
|
This flag controls whether dbSync compares the size of local
and remote files. By default, files will not be downloaded if
they are newer and have changed size.
This flag turns off this default behaviour so
that the date alone will be used for comparison.
|
| checkNoFiles |
yes |
|
|
no yes |
|
|
Flag to switch on and off "sanity checking" by prismacheck
If no files found on remote file, local checking will ensue
(avoids deletion of entire datasets) should be turned on for EMBLNEW etc.
|
| inheritFiles |
no |
|
|
no yes |
|
|
flag for dependent dbs to inherit file lists from parents
same number of files available to dependent as to parents
file name and size translation patterns can be specified
file list will be used for parallelisation and for default file installation
All normal parallelisation options are available
|
| inheritFilePatternFrom |
|
|
|
Perl file pattern list that works with inheritFilePatternTo when inheritFiles is selected to determine the names of files produced for a dependent database based on those used by the parent database. Uses same syntax as local and remote FilePattern
NOTE: Currently, ^ and $ cannot be used in expressions except to denote prepending and appending of strings
e.g. '[^,$]' -> '[em_,.dat]' will transform 'file' to 'em_file.dat' will work
'[^em,dat$]' -> '[embl,data]' will not work (will be fixed in future releases)
|
| inheritFilePatternTo |
|
|
|
See inheritFilePatternFrom
|
| inheritFileSize |
 1.000000 |
|
|
Multiplication factor relating size of original parent file to dependent database file
allows use of filesSize or chunkSize parallelisation. Used as a general guideline only!
|
| useFiles |
no |
|
|
no yes |
|
|
When selected for a dependent database, the $Library.files list will be used
to build a file list for use in files parallelisation (*size parallelisation cannot be used at present since no size information is generated).
These files MUST be present in the offline directory after pretrans.
The generated list will also be used for default file installation.
|
| testEntries |
|
|
|
Include a list of particularly good examples of entries that srsinspect can use to test
an SRS server. These should be supplied as a list of accession numbers or whatever is
the unique identifier for the library in database in question.
|
| applicationInput |
|
|
|
A concatenated string of application options and/or inputs that can be used by srsinspect
for testing this application.
|
| ignoredTokens |
|
|
|
A list of tokens that srsinspect should not attempt to access while it is testing the
contents of token tables.
|
| seeAlso |
|
|
|
Applications related
|