1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/de06e2e6cc7f/
changeset: de06e2e6cc7f
user: dan
date: 2011-08-30 22:56:52
summary: Add basic VCF4.1 support.
affected #: 1 file (78 bytes)
--- a/lib/galaxy_utils/sequence/vcf.py Tue Aug 30 15:52:10 2011 -0400
+++ b/lib/galaxy_utils/sequence/vcf.py Tue Aug 30 16:56:52 2011 -0400
@@ -55,9 +55,12 @@
def __init__( self, vcf_line, metadata, sample_names ):
VariantCall33.__init__( self, vcf_line, metadata, sample_names)
+class VariantCall41( VariantCall40 ):
+ version = 'VCFv4.1'
+
#VCF Format version lookup dict
VCF_FORMATS = {}
-for format in [ VariantCall33, VariantCall40 ]:
+for format in [ VariantCall33, VariantCall40, VariantCall41 ]:
VCF_FORMATS[format.version] = format
class Reader( object ):
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/5d2a2ac4710f/
changeset: 5d2a2ac4710f
user: dan
date: 2011-08-30 16:02:17
summary: Add SICER to tool_conf.xml.main.
affected #: 1 file (50 bytes)
--- a/tool_conf.xml.main Tue Aug 30 09:33:10 2011 -0400
+++ b/tool_conf.xml.main Tue Aug 30 10:02:17 2011 -0400
@@ -390,6 +390,7 @@
</section><section name="NGS: Peak Calling" id="peak_calling"><tool file="peak_calling/macs_wrapper.xml" />
+ <tool file="peak_calling/sicer_wrapper.xml" /><tool file="genetrack/genetrack_indexer.xml" /><tool file="genetrack/genetrack_peak_prediction.xml" /></section>
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/cddcdadea10d/
changeset: cddcdadea10d
user: dan
date: 2011-08-30 15:33:10
summary: Update for wavelet variance tool contributed by Erika Kvikstad.
affected #: 1 file (72 bytes)
--- a/tools/discreteWavelet/execute_dwt_var_perFeature.pl Mon Aug 29 14:42:04 2011 -0400
+++ b/tools/discreteWavelet/execute_dwt_var_perFeature.pl Tue Aug 30 09:33:10 2011 -0400
@@ -41,10 +41,10 @@
#library(\"wavethresh\");
#library(\"waveslim\");
# turn off diagnostics for de-bugging only, turn back on for functional tests on test
- require(\"Rwave\",quietly=TRUE,warn.conflicts = FALSE);
- require(\"wavethresh\",quietly=TRUE,warn.conflicts = FALSE);
- require(\"waveslim\",quietly=TRUE,warn.conflicts = FALSE);
- require(\"bitops\",quietly=TRUE,warn.conflicts = FALSE);
+ suppressMessages(require(\"Rwave\",quietly=TRUE,warn.conflicts = FALSE));
+ suppressMessages(require(\"wavethresh\",quietly=TRUE,warn.conflicts = FALSE));
+ suppressMessages(require(\"waveslim\",quietly=TRUE,warn.conflicts = FALSE));
+ suppressMessages(require(\"bitops\",quietly=TRUE,warn.conflicts = FALSE));
# to determine if data is properly formatted 2^N observations
is.power2<- function(x){x && !(bitAnd(x,x - 1));}
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/949e4f5fa03a/
changeset: 949e4f5fa03a
user: natefoo
date: 2011-08-29 20:42:04
summary: Missing import in library_contents.py
affected #: 2 files (77 bytes)
--- a/lib/galaxy/web/api/library_contents.py Mon Aug 29 11:29:31 2011 -0400
+++ b/lib/galaxy/web/api/library_contents.py Mon Aug 29 14:42:04 2011 -0400
@@ -7,6 +7,7 @@
from galaxy.web.base.controller import *
from galaxy.util.sanitize_html import sanitize_html
from galaxy.model.orm import *
+from galaxy.web.api.util import *
log = logging.getLogger( __name__ )
--- a/scripts/api/common.py Mon Aug 29 11:29:31 2011 -0400
+++ b/scripts/api/common.py Mon Aug 29 14:42:04 2011 -0400
@@ -88,6 +88,8 @@
print '------------------'
for k, v in r.items():
print '%s: %s' % ( k, v )
+ elif type( r ) == str:
+ print r
else:
print 'response is unknown type: %s' % type( r )
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/c8d224f51d7e/
changeset: c8d224f51d7e
user: dan
date: 2011-08-29 17:22:54
summary: Add wavelet variance tool contributed by Erika Kvikstad.
affected #: 6 files (80 bytes)
--- a/tool_conf.xml.sample Mon Aug 29 10:57:08 2011 -0400
+++ b/tool_conf.xml.sample Mon Aug 29 11:22:54 2011 -0400
@@ -146,15 +146,16 @@
<label text="GFF" id="gff" /><tool file="stats/count_gff_features.xml" /></section>
- <!--
- Keep this section commented until all of the tools have functional tests
<section name="Wavelet Analysis" id="dwt">
+ <tool file="discreteWavelet/execute_dwt_var_perFeature.xml" />
+ <!--
+ Keep this section/tools commented until all of the tools have functional tests
<tool file="discreteWavelet/execute_dwt_IvC_all.xml" /><tool file="discreteWavelet/execute_dwt_cor_aVa_perClass.xml" /><tool file="discreteWavelet/execute_dwt_cor_aVb_all.xml" /><tool file="discreteWavelet/execute_dwt_var_perClass.xml" />
+ --></section>
- --><section name="Graph/Display Data" id="plots"><tool file="plotting/histogram2.xml" /><tool file="plotting/scatterplot.xml" />
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/832538ba7258/
changeset: 832538ba7258
user: natefoo
date: 2011-08-29 16:57:08
summary: Properly handle error conditions in library_common.upload_dataset when uploading via the API.
affected #: 1 file (152 bytes)
--- a/lib/galaxy/web/controllers/library_common.py Mon Aug 29 09:32:26 2011 -0400
+++ b/lib/galaxy/web/controllers/library_common.py Mon Aug 29 10:57:08 2011 -0400
@@ -852,6 +852,8 @@
# created_outputs_dict can be a string only if cntrller == 'api'
if type( created_outputs_dict ) == str:
return 400, created_outputs_dict
+ elif type( created_outputs_dict ) == tuple:
+ return created_outputs_dict[0], created_outputs_dict[1]
return 200, created_outputs_dict
total_added = len( created_outputs_dict.keys() )
ldda_id_list = [ str( v.id ) for k, v in created_outputs_dict.items() ]
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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