Genbank configuration file
The file $gbRoot/etc/genbank.conf
contains options control the alignment and loading of
GenBank and RefSeq data. The file is in the same format as
.hg.conf
:
- blank lines or lines where the first non-blank character is a "#" are ignored.
- records are lines of:
name=value
Global configuration parameters
-
cluster.iservers
- space-separated list of iservers to use
to serve sequence fasta files. Empty no
or empty
for a global filesystem.
-
cluster.rootDir
- root directory on cluster filesystems,
either iserver or local file systems.
-
cluster.paraHub
- Host where parasol hub is running.
per-database configuration parameters
Per-database configuration parameters start with the database name,
represented here by $db
. Default values are set with a
database name of default
-
$db.genome
- glob pattern for genome
sequences, which can be NIB or FASTA files.
-
$db.lift
- path to lift file for genome,
or no
if none.
-
$db.genbank.mrna.native.pslReps
- Arguments
for pslReps
for GenBank native mRNAs, or no
to skip pslReps.
-
$db.genbank.mrna.xeno.pslReps
-
$db.genbank.est.native.pslReps
-
$db.genbank.est.xeno.pslReps
-
$db.refseq.mrna.name.pslReps
- Arguments
for pslReps
for RefSeq native mRNAs, or no
to skip pslReps.
-
$db.refseq.mrna.xeno.pslReps
-
$db.mgcTables.$host
- indicates which
MGC tables to create when loading database on $host
.
Values are no
, all
, full
.
$host
is the value returned by uname -n
.
-
$db.mgcTables.default
- indicates which
MGC tables to create when the is no host-specific setting.
-
$db.perChromTables
- Set to no
if per-chromosome alignment tables should not be created.
-
$db.genbank.mrna.native.load
- Load native
GenBank mMRNAs, yes
or no
.
Also for type of est
and organism category
of xeno
.
-
$db.refseq.mrna.native.load
- Load native
GenBank mMRNAs, yes
or no
.
Also for organism category of xeno
.
-
$db.genbank.mrna.native.loadDesc
- Load description table for native mRNAs, yes
or no
.
Also for type of est
and organism category
of xeno
.
-
$db.refseq.mrna.native.loadDesc
- Load description table for native mRNAs, yes
or no
.
Also for type of est
and organism category
of xeno
.
of xeno
.
-
$db.downloadDir
- directory relative to goldenPath/
where download files are stored.
-
$db.iservers
- List of iservers to use for
alignment. Normally the default
entry is used,