1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/dd656a54171b/
changeset: dd656a54171b
user: jgoecks
date: 2011-06-15 19:22:18
summary: Improve filtering tool's stdout reporting of lines filtered; fixes #536
affected #: 1 file (36 bytes)
--- a/tools/stats/filtering.py Wed Jun 15 11:37:21 2011 -0400
+++ b/tools/stats/filtering.py Wed Jun 15 13:22:18 2011 -0400
@@ -130,7 +130,7 @@
valid_lines = total_lines - skipped_lines
print 'Filtering with %s, ' % cond_text
if valid_lines > 0:
- print 'kept %4.2f%% of %d lines.' % ( 100.0*lines_kept/valid_lines, total_lines )
+ print 'kept %4.2f%% of %d valid lines (%d total lines).' % ( 100.0*lines_kept/valid_lines, valid_lines, total_lines )
else:
print 'Possible invalid filter condition "%s" or non-existent column referenced. See tool tips, syntax and examples.' % cond_text
if invalid_lines:
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/0ffa5a6d8215/
changeset: 0ffa5a6d8215
user: greg
date: 2011-06-15 17:37:21
summary: Do not assume that a library_dataset has a library_dataset_dataset_association when checking to see if a folder is public.
affected #: 1 file (51 bytes)
--- a/lib/galaxy/security/__init__.py Tue Jun 14 16:42:11 2011 -0400
+++ b/lib/galaxy/security/__init__.py Wed Jun 15 11:37:21 2011 -0400
@@ -649,7 +649,8 @@
if not self.folder_is_public( sub_folder ):
return False
for library_dataset in folder.datasets:
- if not self.dataset_is_public( library_dataset.library_dataset_dataset_association.dataset ):
+ ldda = library_dataset.library_dataset_dataset_association
+ if ldda and ldda.dataset and not self.dataset_is_public( ldda.dataset ):
return False
return True
def make_folder_public( self, folder ):
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/f6bbb5ee934d/
changeset: f6bbb5ee934d
user: greg
date: 2011-06-14 22:42:11
summary: Add Pacific Biosciences tools.
affected #: 14 files (417 bytes)
--- a/tool_conf.xml.sample Tue Jun 14 13:48:17 2011 -0400
+++ b/tool_conf.xml.sample Tue Jun 14 16:42:11 2011 -0400
@@ -433,7 +433,17 @@
<tool file="vcf_tools/filter.xml" /><tool file="vcf_tools/extract.xml" /></section>
-
+ <section name="PacBio/Illumina Assembly" id="hybrid">
+ <tool file="ilmn_pacbio/quake.xml"/>
+ <tool file="ilmn_pacbio/quake_pe.xml"/>
+ <tool file="ilmn_pacbio/soap_denovo.xml"/>
+<!--
+ Uncomment this tool when we support the HDF5 format
+ <tool file="ilmn_pacbio/smrtpipe_filter.xml"/>
+-->
+ <tool file="ilmn_pacbio/smrtpipe_hybrid.xml"/>
+ <tool file="ilmn_pacbio/assembly_stats.xml"/>
+ </section><!--
TODO: uncomment the following EMBOSS section whenever
moving to test, but comment it in .sample to eliminate
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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