fixing paths to incoming directory

SVN: 28475

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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