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Fix bad database pathnames in yeast configuration file examples

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1 parent 29e4a44 commit f50dc9dcc60d1942f560a746954b1361663922f5 Lincoln Stein committed Nov 29, 2011
Showing with 13 additions and 12 deletions.
  1. +3 −2 Changes
  2. +1 −1 conf/pop_demo.conf
  3. +2 −2 conf/slave_preload.conf
  4. +1 −1 conf/volvox.conf
  5. +2 −2 conf/yeast_chr1+2.conf
  6. +2 −2 conf/yeast_renderfarm.conf
  7. +2 −2 conf/yeast_simple.conf
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5 Changes
@@ -10,8 +10,9 @@
or individual track definitions.
* Can now close tracks from main view even when corresponding track checkbox not showing
in the track listing.
- * Default to flock locking instead of NFS locking due to apparent race conditions
- discovered in File::NFSLock code.
+ * Default to flock locking instead of NFS locking; the former seems to be faster.
+ * Enable shared session locking to improve performance.
+ * Fix bad database pathnames in yeast configuration file examples.
* mod_perl is no longer supported due to unfixable issues with zombie processes.
2.43
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2 conf/pop_demo.conf
@@ -2,7 +2,7 @@
description = Population Demo
db_adaptor = Bio::DB::SeqFeature::Store
db_args = -adaptor memory
- -dir /var/lib/gbrowse2/databases/pop_demo
+ -dir $PERSISTENT/databases/pop_demo
html1=<h2>This is a demo of GBrowse and PhyloGeoViz working together to display population data on a Google Map.</h2>
<h3>This demo uses the public PhyloGeoViz. To fully take advantage of all the features, PhyloGeoViz will also need to be installed locally. Please see the gbrowse_gmap documentation for further details by running "perldoc /path/to/gbrowse_gmap". </h3>
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4 conf/slave_preload.conf
@@ -1,9 +1,9 @@
[yeast12]
db_adaptor = Bio::DB::SeqFeature::Store
db_args = -adaptor memory
- -dir /var/lib/gbrowse2/databases/yeast_chr1+2
+ -dir $PERSISTENT/databases/yeast_chr1+2
[scaffolds]
db_adaptor = Bio::DB::SeqFeature::Store
db_args = -adaptor memory
- -dir /var/lib/gbrowse2/databases/yeast_scaffolds
+ -dir $PERSISTENT/databases/yeast_scaffolds
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2 conf/volvox.conf
@@ -1,7 +1,7 @@
[GENERAL]
db_adaptor = Bio::DB::SeqFeature::Store
db_args = -adaptor memory
- -dir '/home/aelnaiem/GBrowse/htdocs/databases/volvox'
+ -dir $PERSISTENT/databases/volvox
# just the basic track dumper plugin
plugins = TrackDumper
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4 conf/yeast_chr1+2.conf
@@ -36,13 +36,13 @@ automatic classes = Symbol Gene Clone
[scaffolds:database]
db_adaptor = Bio::DB::SeqFeature::Store
db_args = -adaptor memory
- -dir /var/lib/gbrowse2/databases/yeast_scaffolds
+ -dir $PERSISTENT/databases/yeast_scaffolds
search options = default +autocomplete
[annotations:database]
db_adaptor = Bio::DB::SeqFeature::Store
db_args = -adaptor memory
- -dir /var/lib/gbrowse2/databases/yeast_chr1+2
+ -dir $PERSISTENT/databases/yeast_chr1+2
search options = default +autocomplete
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4 conf/yeast_renderfarm.conf
@@ -36,13 +36,13 @@ automatic classes = Symbol Gene Clone
[scaffolds:database]
db_adaptor = Bio::DB::SeqFeature::Store
db_args = -adaptor memory
- -dir /var/lib/gbrowse2/databases/yeast_scaffolds
+ -dir $PERSISTENT/databases/yeast_scaffolds
search options = default +autocomplete
[annotations:database]
db_adaptor = Bio::DB::SeqFeature::Store
db_args = -adaptor memory
- -dir /var/lib/gbrowse2/databases/yeast_chr1+2
+ -dir $PERSISTENT/databases/yeast_chr1+2
search options = default +autocomplete
# Advanced feature: custom balloons
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4 conf/yeast_simple.conf
@@ -32,13 +32,13 @@ automatic classes = Symbol Gene Clone
[scaffolds:database]
db_adaptor = Bio::DB::SeqFeature::Store
db_args = -adaptor memory
- -dir /var/lib/gbrowse2/databases/yeast_scaffolds
+ -dir $PERSISTENT/databases/yeast_scaffolds
search options = default +autocomplete
[annotations:database]
db_adaptor = Bio::DB::SeqFeature::Store
db_args = -adaptor memory
- -dir /var/lib/gbrowse2/databases/yeast_chr1+2
+ -dir $PERSISTENT/databases/yeast_chr1+2
search options = default +autocomplete
# Default glyph settings

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