1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/4a33c32fe1a5/
Changeset: 4a33c32fe1a5
User: Dave Bouvier
Date: 2013-06-27 16:17:04
Summary: Fix path issue that was introduced with the refactoring of common_util.url_download.
Affected #: 1 file
diff -r 3fa9df444b4b81f94b1c42a033c685a6e23827be -r 4a33c32fe1a5b33f98fd1b5d9292588cbe82b6be lib/tool_shed/galaxy_install/tool_dependencies/common_util.py
--- a/lib/tool_shed/galaxy_install/tool_dependencies/common_util.py
+++ b/lib/tool_shed/galaxy_install/tool_dependencies/common_util.py
@@ -248,9 +248,9 @@
zip_archive_extracted = extract_zip( file_path, install_dir )
dir = zip_extraction_directory( install_dir, downloaded_file_name )
else:
- dir = install_dir
+ dir = os.path.abspath( install_dir )
else:
- dir = install_dir
+ dir = os.path.abspath( install_dir )
return dir
def zip_extraction_directory( file_path, file_name ):
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/4ddc245c2004/
Changeset: 4ddc245c2004
User: jgoecks
Date: 2013-06-26 22:26:13
Summary: Update standard IO parsing level to recognized level.
Affected #: 1 file
diff -r 47446977285f4a8ec634b1b8a6d78ddc9d73b243 -r 4ddc245c20043ee648b9568a70f5b8b8632212fe tools/ngs_rna/tophat2_wrapper.xml
--- a/tools/ngs_rna/tophat2_wrapper.xml
+++ b/tools/ngs_rna/tophat2_wrapper.xml
@@ -268,7 +268,7 @@
</inputs><stdio>
- <regex match="Exception" source="both" level="error" description="Tool exception"/>
+ <regex match="Exception" source="both" level="fatal" description="Tool exception"/><regex match=".*" source="both" level="log" description="tool progress"/></stdio>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/47446977285f/
Changeset: 47446977285f
User: jgoecks
Date: 2013-06-26 22:22:53
Summary: Add tool id to error message when parsing standard IO level.
Affected #: 1 file
diff -r 4440f4de1828f11439a88d1417ea914d1e6fec8f -r 47446977285f4a8ec634b1b8a6d78ddc9d73b243 lib/galaxy/tools/__init__.py
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -1528,7 +1528,8 @@
elif ( re.search( "fatal", err_level, re.IGNORECASE ) ):
return_level = StdioErrorLevel.FATAL
else:
- log.debug( "Error level %s did not match warning/fatal" % err_level )
+ log.debug( "Tool %s: error level %s did not match log/warning/fatal" %
+ ( self.id, err_level ) )
except Exception:
log.error( "Exception in parse_error_level "
+ str(sys.exc_info() ) )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/9a4e6dd2d863/
Changeset: 9a4e6dd2d863
User: dan
Date: 2013-06-26 17:57:51
Summary: Change EBI SRA tool to use auto detect for format determination now that they are providing additional formats. Fixes issue seen when sending SFF files.
Affected #: 1 file
diff -r 5a09adb8c39363a32aa373658635cf20ae2cc718 -r 9a4e6dd2d863e3e233f7e54382989d95810dbe9e tools/data_source/ebi_sra.xml
--- a/tools/data_source/ebi_sra.xml
+++ b/tools/data_source/ebi_sra.xml
@@ -9,7 +9,7 @@
</inputs><uihints minwidth="800"/><outputs>
- <data name="output" format="fastq"/>
+ <data name="output" format="auto"/></outputs><options sanitize="False" refresh="True"/></tool>
https://bitbucket.org/galaxy/galaxy-central/commits/53f9bc7009f4/
Changeset: 53f9bc7009f4
Branch: stable
User: dan
Date: 2013-06-26 17:57:51
Summary: Change EBI SRA tool to use auto detect for format determination now that they are providing additional formats. Fixes issue seen when sending SFF files.
Affected #: 1 file
diff -r f35d85e4b4d582cd50aee062bb1c2eaf89b131c2 -r 53f9bc7009f4c7c93177eb1f71d014e822b43640 tools/data_source/ebi_sra.xml
--- a/tools/data_source/ebi_sra.xml
+++ b/tools/data_source/ebi_sra.xml
@@ -9,7 +9,7 @@
</inputs><uihints minwidth="800"/><outputs>
- <data name="output" format="fastq"/>
+ <data name="output" format="auto"/></outputs><options sanitize="False" refresh="True"/></tool>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/5a09adb8c393/
Changeset: 5a09adb8c393
User: dan
Date: 2013-06-26 17:44:09
Summary: Fix for sniff.handle_uploaded_dataset_file broken in 7605:8bccff9db86973c924b17a4251573e25af7618a4 affects handling of data_source binary files.
Affected #: 1 file
diff -r d4372175b7fcf2b61a1e6c8caeb1a1b5dc891e60 -r 5a09adb8c39363a32aa373658635cf20ae2cc718 lib/galaxy/datatypes/sniff.py
--- a/lib/galaxy/datatypes/sniff.py
+++ b/lib/galaxy/datatypes/sniff.py
@@ -6,6 +6,7 @@
from galaxy import util
from galaxy.datatypes.checkers import *
from encodings import search_function as encodings_search_function
+from binary import Binary
log = logging.getLogger(__name__)
https://bitbucket.org/galaxy/galaxy-central/commits/f35d85e4b4d5/
Changeset: f35d85e4b4d5
Branch: stable
User: dan
Date: 2013-06-26 17:44:09
Summary: Fix for sniff.handle_uploaded_dataset_file broken in 7605:8bccff9db86973c924b17a4251573e25af7618a4 affects handling of data_source binary files.
Affected #: 1 file
diff -r 5a8069419967cfdb2157482ad239f75624354b78 -r f35d85e4b4d582cd50aee062bb1c2eaf89b131c2 lib/galaxy/datatypes/sniff.py
--- a/lib/galaxy/datatypes/sniff.py
+++ b/lib/galaxy/datatypes/sniff.py
@@ -6,6 +6,7 @@
from galaxy import util
from galaxy.datatypes.checkers import *
from encodings import search_function as encodings_search_function
+from binary import Binary
log = logging.getLogger(__name__)
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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