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Add support for the new test/data repository and a fix for the bowtie tests.

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This commit is contained in:
Nate Coraor
2010-11-22 10:54:31 -05:00
parent 9a0205cfe4
commit 246ea04cc7
2 changed files with 6 additions and 4 deletions
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scripts/functional_tests.py
+4
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@@ -55,6 +55,9 @@ def main():
start_server = 'GALAXY_TEST_EXTERNAL' not in os.environ
tool_path = os.environ.get( 'GALAXY_TEST_TOOL_PATH', 'tools' )
tool_config_file = os.environ.get( 'GALAXY_TEST_TOOL_CONF', 'tool_conf.xml.sample' )
tool_data_table_config_path = 'tool_data_table_conf.xml'
if os.path.exists( 'tool_data_table_conf.test.xml' ):
tool_data_table_config_path = 'tool_data_table_conf.test.xml'
if start_server:
psu_production = False
galaxy_test_proxy_port = None
@@ -148,6 +151,7 @@ def main():
datatype_converters_config_file = "datatype_converters_conf.xml.sample",
tool_parse_help = False,
test_conf = "test.conf",
tool_data_table_config_path = tool_data_table_config_path,
log_destination = "stdout",
use_heartbeat = False,
allow_user_creation = True,
tools/sr_mapping/bowtie_wrapper.xml
+2 -4
View File
@@ -327,8 +327,7 @@
chrM_base needs to be the base location/name of the index files.
-->
<param name="genomeSource" value="indexed" />
<!-- this is the backwards-compatible "unique value" for this index, not an actual path -->
<param name="index" value="/galaxy/data/equCab2_chrM/bowtie_index/chrM" />
<param name="index" value="equCab2chrM" />
<param name="sPaired" value="single" />
<param name="sInput1" ftype="fastqsanger" value="bowtie_in2.fastqsanger" />
<param name="sSettingsType" value="preSet" />
@@ -385,8 +384,7 @@
chrM_base is the index files' location/base name.
-->
<param name="genomeSource" value="indexed" />
<!-- this is the backwards-compatible "unique value" for this index, not an actual path -->
<param name="index" value="/galaxy/data/equCab2_chrM/bowtie_index/chrM" />
<param name="index" value="equCab2chrM" />
<param name="sPaired" value="single" />
<param name="sInput1" ftype="fastqsanger" value="bowtie_in2.fastqsanger" />
<param name="sSettingsType" value="full" />