From 8c33b219cc1e08bb375586934778f2b40e2cfb7f Mon Sep 17 00:00:00 2001
From: gpawel <gpawel>
Date: Wed, 27 Feb 2013 13:55:25 +0000
Subject: [PATCH] fixing paths to incoming directory

SVN: 28475
---
 .../1/dss/drop-boxes/create-flowcell-hiseq/plugin.properties    | 2 +-
 .../1/dss/drop-boxes/create-flowcell-miseq/plugin.properties    | 2 +-
 .../1/dss/drop-boxes/read-demultiplex-stats/plugin.properties   | 2 +-
 .../1/dss/drop-boxes/read-rta-timestamp/plugin.properties       | 2 +-
 .../1/dss/drop-boxes/register-basecall-stats/plugin.properties  | 2 +-
 .../1/dss/drop-boxes/register-bigwig/plugin.properties          | 2 +-
 .../1/dss/drop-boxes/register-bowtie/plugin.properties          | 2 +-
 .../1/dss/drop-boxes/register-fastqc/plugin.properties          | 2 +-
 .../1/dss/drop-boxes/register-flowcell-hiseq/plugin.properties  | 2 +-
 .../1/dss/drop-boxes/register-flowcell-miseq/plugin.properties  | 2 +-
 .../1/dss/drop-boxes/register-lane-hiseq/plugin.properties      | 2 +-
 .../1/dss/drop-boxes/register-lane-miseq/plugin.properties      | 2 +-
 .../1/dss/drop-boxes/register-macs/plugin.properties            | 2 +-
 .../1/dss/drop-boxes/register-runstatistics/plugin.properties   | 2 +-
 .../1/dss/drop-boxes/register-thumbnails/plugin.properties      | 2 +-
 .../1/dss/drop-boxes/register-unaligned/plugin.properties       | 2 +-
 16 files changed, 16 insertions(+), 16 deletions(-)

diff --git a/deep_sequencing_unit/source/core-plugins/illumina-ngs/1/dss/drop-boxes/create-flowcell-hiseq/plugin.properties b/deep_sequencing_unit/source/core-plugins/illumina-ngs/1/dss/drop-boxes/create-flowcell-hiseq/plugin.properties
index 5f63b57d7e1..5c56666b206 100644
--- a/deep_sequencing_unit/source/core-plugins/illumina-ngs/1/dss/drop-boxes/create-flowcell-hiseq/plugin.properties
+++ b/deep_sequencing_unit/source/core-plugins/illumina-ngs/1/dss/drop-boxes/create-flowcell-hiseq/plugin.properties
@@ -5,7 +5,7 @@
 # Variables:
 #   incoming-root-dir
 #     Path to the directory which contains incoming directories for drop boxes.
-incoming-dir = /links/shared/dsu/dss/create-flowcell-hiseq
+incoming-dir = ${incoming-root-dir}/create-flowcell-hiseq
 incoming-data-completeness-condition = marker-file
 top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.api.v2.JythonTopLevelDataSetHandlerV2
 script-path = create-flowcell-hiseq.py
diff --git a/deep_sequencing_unit/source/core-plugins/illumina-ngs/1/dss/drop-boxes/create-flowcell-miseq/plugin.properties b/deep_sequencing_unit/source/core-plugins/illumina-ngs/1/dss/drop-boxes/create-flowcell-miseq/plugin.properties
index 07d7e308bc8..1c15a550f60 100644
--- a/deep_sequencing_unit/source/core-plugins/illumina-ngs/1/dss/drop-boxes/create-flowcell-miseq/plugin.properties
+++ b/deep_sequencing_unit/source/core-plugins/illumina-ngs/1/dss/drop-boxes/create-flowcell-miseq/plugin.properties
@@ -4,7 +4,7 @@
 # Variables:
 #   incoming-root-dir
 #     Path to the directory which contains incoming directories for drop boxes.
-incoming-dir = ${root}/dss/create-flowcell-miseq
+incoming-dir = ${incoming-root-dir}/dss/create-flowcell-miseq
 incoming-data-completeness-condition = marker-file
 top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.api.v2.JythonTopLevelDataSetHandlerV2
 script-path = create-flow-cell-miseq.py
diff --git a/deep_sequencing_unit/source/core-plugins/illumina-ngs/1/dss/drop-boxes/read-demultiplex-stats/plugin.properties b/deep_sequencing_unit/source/core-plugins/illumina-ngs/1/dss/drop-boxes/read-demultiplex-stats/plugin.properties
index 78ce865e67d..1337bde948b 100644
--- a/deep_sequencing_unit/source/core-plugins/illumina-ngs/1/dss/drop-boxes/read-demultiplex-stats/plugin.properties
+++ b/deep_sequencing_unit/source/core-plugins/illumina-ngs/1/dss/drop-boxes/read-demultiplex-stats/plugin.properties
@@ -2,7 +2,7 @@
 # Variables:
 #   incoming-root-dir
 #     Path to the directory which contains incoming directories for drop boxes.
-incoming-dir = ${root}/dss/read-demultiplex-stats
+incoming-dir = ${incoming-root-dir}/read-demultiplex-stats
 incoming-data-completeness-condition = marker-file
 top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.api.v2.JythonTopLevelDataSetHandlerV2
 script-path = read-demultiplex-stats.py
diff --git a/deep_sequencing_unit/source/core-plugins/illumina-ngs/1/dss/drop-boxes/read-rta-timestamp/plugin.properties b/deep_sequencing_unit/source/core-plugins/illumina-ngs/1/dss/drop-boxes/read-rta-timestamp/plugin.properties
index 6074eab9e6c..ef56111b768 100644
--- a/deep_sequencing_unit/source/core-plugins/illumina-ngs/1/dss/drop-boxes/read-rta-timestamp/plugin.properties
+++ b/deep_sequencing_unit/source/core-plugins/illumina-ngs/1/dss/drop-boxes/read-rta-timestamp/plugin.properties
@@ -4,7 +4,7 @@
 # Variables:
 #   incoming-root-dir
 #     Path to the directory which contains incoming directories for drop boxes.
-incoming-dir = ${root}/dss/read-rta-timestamp
+incoming-dir = ${incoming-root-dir}/read-rta-timestamp
 incoming-data-completeness-condition = marker-file
 top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.api.v2.JythonTopLevelDataSetHandlerV2
 script-path = read-rta-timestamp.py
diff --git a/deep_sequencing_unit/source/core-plugins/illumina-ngs/1/dss/drop-boxes/register-basecall-stats/plugin.properties b/deep_sequencing_unit/source/core-plugins/illumina-ngs/1/dss/drop-boxes/register-basecall-stats/plugin.properties
index 17aed1797bd..d6e67945db5 100644
--- a/deep_sequencing_unit/source/core-plugins/illumina-ngs/1/dss/drop-boxes/register-basecall-stats/plugin.properties
+++ b/deep_sequencing_unit/source/core-plugins/illumina-ngs/1/dss/drop-boxes/register-basecall-stats/plugin.properties
@@ -4,7 +4,7 @@
 # Variables:
 #   incoming-root-dir
 #     Path to the directory which contains incoming directories for drop boxes.
-incoming-dir = ${root}/dss/register-basecall-stats
+incoming-dir = ${incoming-root-dir}/register-basecall-stats
 incoming-data-completeness-condition = marker-file
 top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.api.v2.JythonTopLevelDataSetHandlerV2
 script-path = register-basecall-stats.py
diff --git a/deep_sequencing_unit/source/core-plugins/illumina-ngs/1/dss/drop-boxes/register-bigwig/plugin.properties b/deep_sequencing_unit/source/core-plugins/illumina-ngs/1/dss/drop-boxes/register-bigwig/plugin.properties
index c59f43ebe29..26d6bb1da8d 100644
--- a/deep_sequencing_unit/source/core-plugins/illumina-ngs/1/dss/drop-boxes/register-bigwig/plugin.properties
+++ b/deep_sequencing_unit/source/core-plugins/illumina-ngs/1/dss/drop-boxes/register-bigwig/plugin.properties
@@ -2,7 +2,7 @@
 # Variables:
 #   incoming-root-dir
 #     Path to the directory which contains incoming directories for drop boxes.
-incoming-dir = ${root}/dss/register-bigwig/
+incoming-dir = ${incoming-root-dir}/register-bigwig/
 incoming-data-completeness-condition = marker-file
 top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.api.v2.JythonTopLevelDataSetHandlerV2
 script-path = register-bigwig.py
diff --git a/deep_sequencing_unit/source/core-plugins/illumina-ngs/1/dss/drop-boxes/register-bowtie/plugin.properties b/deep_sequencing_unit/source/core-plugins/illumina-ngs/1/dss/drop-boxes/register-bowtie/plugin.properties
index 79d85834f49..f0fac2c142a 100644
--- a/deep_sequencing_unit/source/core-plugins/illumina-ngs/1/dss/drop-boxes/register-bowtie/plugin.properties
+++ b/deep_sequencing_unit/source/core-plugins/illumina-ngs/1/dss/drop-boxes/register-bowtie/plugin.properties
@@ -4,7 +4,7 @@
 # Variables:
 #   incoming-root-dir
 #     Path to the directory which contains incoming directories for drop boxes.
-incoming-dir = ${root}/dss/register-bowtie
+incoming-dir = ${incoming-root-dir}/register-bowtie
 incoming-data-completeness-condition = marker-file
 top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.api.v2.JythonTopLevelDataSetHandlerV2
 script-path = register-bowtie.py
diff --git a/deep_sequencing_unit/source/core-plugins/illumina-ngs/1/dss/drop-boxes/register-fastqc/plugin.properties b/deep_sequencing_unit/source/core-plugins/illumina-ngs/1/dss/drop-boxes/register-fastqc/plugin.properties
index f6c0d69fdb1..353a2b7aa8a 100644
--- a/deep_sequencing_unit/source/core-plugins/illumina-ngs/1/dss/drop-boxes/register-fastqc/plugin.properties
+++ b/deep_sequencing_unit/source/core-plugins/illumina-ngs/1/dss/drop-boxes/register-fastqc/plugin.properties
@@ -4,7 +4,7 @@
 # Variables:
 #   incoming-root-dir
 #     Path to the directory which contains incoming directories for drop boxes.
-incoming-dir = ${root}/dss/register-fastqc
+incoming-dir = ${incoming-root-dir}/register-fastqc
 incoming-data-completeness-condition = marker-file
 top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.api.v2.JythonTopLevelDataSetHandlerV2
 script-path = register-fastqc.py
diff --git a/deep_sequencing_unit/source/core-plugins/illumina-ngs/1/dss/drop-boxes/register-flowcell-hiseq/plugin.properties b/deep_sequencing_unit/source/core-plugins/illumina-ngs/1/dss/drop-boxes/register-flowcell-hiseq/plugin.properties
index 427cd80979a..8730e628162 100644
--- a/deep_sequencing_unit/source/core-plugins/illumina-ngs/1/dss/drop-boxes/register-flowcell-hiseq/plugin.properties
+++ b/deep_sequencing_unit/source/core-plugins/illumina-ngs/1/dss/drop-boxes/register-flowcell-hiseq/plugin.properties
@@ -4,7 +4,7 @@
 # Variables:
 #   incoming-root-dir
 #     Path to the directory which contains incoming directories for drop boxes.
-incoming-dir = ${root}/dss/register-flowcell-hiseq
+incoming-dir = ${incoming-root-dir}/register-flowcell-hiseq
 #incoming-dir = /links/sonas/cisd/store/incoming-flowCell
 incoming-data-completeness-condition = marker-file
 top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.api.v2.JythonTopLevelDataSetHandlerV2
diff --git a/deep_sequencing_unit/source/core-plugins/illumina-ngs/1/dss/drop-boxes/register-flowcell-miseq/plugin.properties b/deep_sequencing_unit/source/core-plugins/illumina-ngs/1/dss/drop-boxes/register-flowcell-miseq/plugin.properties
index 20949c407e2..7f274a70db5 100644
--- a/deep_sequencing_unit/source/core-plugins/illumina-ngs/1/dss/drop-boxes/register-flowcell-miseq/plugin.properties
+++ b/deep_sequencing_unit/source/core-plugins/illumina-ngs/1/dss/drop-boxes/register-flowcell-miseq/plugin.properties
@@ -4,7 +4,7 @@
 # Variables:
 #   incoming-root-dir
 #     Path to the directory which contains incoming directories for drop boxes.
-incoming-dir = ${root}/dss/register-flowcell-miseq
+incoming-dir = ${incoming-root-dir}/register-flowcell-miseq
 incoming-data-completeness-condition = marker-file
 top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.api.v2.JythonTopLevelDataSetHandlerV2
 script-path = register-flowcell-miseq.py
diff --git a/deep_sequencing_unit/source/core-plugins/illumina-ngs/1/dss/drop-boxes/register-lane-hiseq/plugin.properties b/deep_sequencing_unit/source/core-plugins/illumina-ngs/1/dss/drop-boxes/register-lane-hiseq/plugin.properties
index 51e92f579bf..f7523f7cdec 100644
--- a/deep_sequencing_unit/source/core-plugins/illumina-ngs/1/dss/drop-boxes/register-lane-hiseq/plugin.properties
+++ b/deep_sequencing_unit/source/core-plugins/illumina-ngs/1/dss/drop-boxes/register-lane-hiseq/plugin.properties
@@ -4,7 +4,7 @@
 # Variables:
 #   incoming-root-dir
 #     Path to the directory which contains incoming directories for drop boxes.
-incoming-dir = ${root}/dss/register-lane-hiseq
+incoming-dir = ${incoming-root-dir}/register-lane-hiseq
 incoming-data-completeness-condition = marker-file
 top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.api.v2.JythonTopLevelDataSetHandlerV2
 script-path = register-lane-hiseq.py
diff --git a/deep_sequencing_unit/source/core-plugins/illumina-ngs/1/dss/drop-boxes/register-lane-miseq/plugin.properties b/deep_sequencing_unit/source/core-plugins/illumina-ngs/1/dss/drop-boxes/register-lane-miseq/plugin.properties
index 881421e7899..51c2eec3813 100644
--- a/deep_sequencing_unit/source/core-plugins/illumina-ngs/1/dss/drop-boxes/register-lane-miseq/plugin.properties
+++ b/deep_sequencing_unit/source/core-plugins/illumina-ngs/1/dss/drop-boxes/register-lane-miseq/plugin.properties
@@ -4,7 +4,7 @@
 # Variables:
 #   incoming-root-dir
 #     Path to the directory which contains incoming directories for drop boxes.
-incoming-dir = ${root}/dss/register-lane-miseq
+incoming-dir = ${incoming-root-dir}/register-lane-miseq
 incoming-data-completeness-condition = marker-file
 top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.api.v2.JythonTopLevelDataSetHandlerV2
 script-path = register-lane-miseq.py
diff --git a/deep_sequencing_unit/source/core-plugins/illumina-ngs/1/dss/drop-boxes/register-macs/plugin.properties b/deep_sequencing_unit/source/core-plugins/illumina-ngs/1/dss/drop-boxes/register-macs/plugin.properties
index b9d3428f09b..9d5511bd58c 100644
--- a/deep_sequencing_unit/source/core-plugins/illumina-ngs/1/dss/drop-boxes/register-macs/plugin.properties
+++ b/deep_sequencing_unit/source/core-plugins/illumina-ngs/1/dss/drop-boxes/register-macs/plugin.properties
@@ -4,7 +4,7 @@
 # Variables:
 #   incoming-root-dir
 #     Path to the directory which contains incoming directories for drop boxes.
-incoming-dir = ${root}/dss/register-macs
+incoming-dir = ${incoming-root-dir}/register-macs
 incoming-data-completeness-condition = marker-file
 top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.api.v2.JythonTopLevelDataSetHandlerV2
 script-path = register-macs.py
diff --git a/deep_sequencing_unit/source/core-plugins/illumina-ngs/1/dss/drop-boxes/register-runstatistics/plugin.properties b/deep_sequencing_unit/source/core-plugins/illumina-ngs/1/dss/drop-boxes/register-runstatistics/plugin.properties
index 40f3884ecfc..8572688f224 100644
--- a/deep_sequencing_unit/source/core-plugins/illumina-ngs/1/dss/drop-boxes/register-runstatistics/plugin.properties
+++ b/deep_sequencing_unit/source/core-plugins/illumina-ngs/1/dss/drop-boxes/register-runstatistics/plugin.properties
@@ -4,7 +4,7 @@
 # Variables:
 #   incoming-root-dir
 #     Path to the directory which contains incoming directories for drop boxes.
-incoming-dir = ${root}/dss/register-runstatistics
+incoming-dir = ${incoming-root-dir}/register-runstatistics
 incoming-data-completeness-condition = marker-file
 top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.api.v2.JythonTopLevelDataSetHandlerV2
 script-path = register-runstatistics.py
diff --git a/deep_sequencing_unit/source/core-plugins/illumina-ngs/1/dss/drop-boxes/register-thumbnails/plugin.properties b/deep_sequencing_unit/source/core-plugins/illumina-ngs/1/dss/drop-boxes/register-thumbnails/plugin.properties
index 5d976b5624c..5b89e279f2f 100644
--- a/deep_sequencing_unit/source/core-plugins/illumina-ngs/1/dss/drop-boxes/register-thumbnails/plugin.properties
+++ b/deep_sequencing_unit/source/core-plugins/illumina-ngs/1/dss/drop-boxes/register-thumbnails/plugin.properties
@@ -4,7 +4,7 @@
 # Variables:
 #   incoming-root-dir
 #     Path to the directory which contains incoming directories for drop boxes.
-incoming-dir = ${root}/dss/register-thumbnails
+incoming-dir = ${incoming-root-dir}/register-thumbnails
 #incoming-dir = /links/sonas/cisd/store/incoming-flowCell
 incoming-data-completeness-condition = marker-file
 top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.api.v2.JythonTopLevelDataSetHandlerV2
diff --git a/deep_sequencing_unit/source/core-plugins/illumina-ngs/1/dss/drop-boxes/register-unaligned/plugin.properties b/deep_sequencing_unit/source/core-plugins/illumina-ngs/1/dss/drop-boxes/register-unaligned/plugin.properties
index ca004d09705..9c8c317b60d 100644
--- a/deep_sequencing_unit/source/core-plugins/illumina-ngs/1/dss/drop-boxes/register-unaligned/plugin.properties
+++ b/deep_sequencing_unit/source/core-plugins/illumina-ngs/1/dss/drop-boxes/register-unaligned/plugin.properties
@@ -4,7 +4,7 @@
 # Variables:
 #   incoming-root-dir
 #     Path to the directory which contains incoming directories for drop boxes.
-incoming-dir = ${root}/dss/register-unaligned
+incoming-dir = ${incoming-root-dir}/register-unaligned
 incoming-data-completeness-condition = marker-file
 top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.api.v2.JythonTopLevelDataSetHandlerV2
 script-path = register-unaligned.py
-- 
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