1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/56cb3ab8b5ef/
changeset: 56cb3ab8b5ef
user: jgoecks
date: 2011-10-12 15:52:30
summary: Remove duplicate history links in copy datasets done message.
affected #: 1 file (-1 bytes)
--- a/lib/galaxy/web/controllers/dataset.py Tue Oct 11 16:53:21 2011 -0400
+++ b/lib/galaxy/web/controllers/dataset.py Wed Oct 12 09:52:30 2011 -0400
@@ -1141,9 +1141,6 @@
num_source = len( source_dataset_ids ) - invalid_datasets
num_target = len(target_histories)
done_msg = "%i %s copied to %i %s: %s." % (num_source, inflector.cond_plural(num_source, "dataset"), num_target, inflector.cond_plural(num_target, "history"), hist_names_str )
- if new_history is not None:
- done_msg += " <a href=\"%s\" target=\"_top\">Switch to the new history.</a>" % url_for(
- controller="history", action="switch_to_history", hist_id=trans.security.encode_id( new_history.id ) )
trans.sa_session.refresh( history )
source_datasets = history.visible_datasets
target_histories = [history]
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.
1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/1bc0b9fd0d08/
changeset: 1bc0b9fd0d08
user: jgoecks
date: 2011-10-11 22:53:21
summary: Handle scores with value '.' in data providers.
affected #: 1 file (-1 bytes)
--- a/lib/galaxy/visualization/tracks/data_providers.py Tue Oct 11 16:00:04 2011 -0400
+++ b/lib/galaxy/visualization/tracks/data_providers.py Tue Oct 11 16:53:21 2011 -0400
@@ -205,7 +205,10 @@
# Score (filter data)
if length >= 5 and filter_cols and filter_cols[0] == "Score":
- payload.append( float(feature[4]) )
+ try:
+ payload.append( float( feature[4] ) )
+ except:
+ payload.append( feature[4] )
rval.append( payload )
@@ -828,7 +831,10 @@
# Add filter data to payload.
for col in filter_cols:
if col == "Score":
- payload.append( float( feature.score ) )
+ try:
+ payload.append( float( feature.score ) )
+ except:
+ payload.append( feature.score )
elif col in feature.attributes:
try:
payload.append( float( feature.attributes[col] ) )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.
1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/b1355f513577/
changeset: b1355f513577
user: jgoecks
date: 2011-10-11 20:14:06
summary: Trackster: no need to parse floats because data providers now return floats rather than strings.
affected #: 1 file (-1 bytes)
--- a/static/scripts/trackster.js Tue Oct 11 14:05:08 2011 -0400
+++ b/static/scripts/trackster.js Tue Oct 11 14:14:06 2011 -0400
@@ -1638,7 +1638,7 @@
// No element to filter on.
return true;
}
- var val = parseFloat(element[this.index]);
+ var val = element[this.index];
return (isNaN(val) || (val >= this.low && val <= this.high));
},
/**
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.
1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/2766ff1b36c0/
changeset: 2766ff1b36c0
user: dan
date: 2011-10-11 16:09:32
summary: Add Secure Hash/Message Digest tool to tool_conf.xml.main.
affected #: 1 file (-1 bytes)
--- a/tool_conf.xml.main Mon Oct 10 18:42:31 2011 -0400
+++ b/tool_conf.xml.main Tue Oct 11 10:09:32 2011 -0400
@@ -45,6 +45,7 @@
<tool file="filters/tailWrapper.xml" /><tool file="filters/trimmer.xml" /><tool file="filters/wc_gnu.xml" />
+ <tool file="filters/secure_hash_message_digest.xml" /></section><section name="Convert Formats" id="convert"><tool file="filters/bed2gff.xml" />
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.
1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/d7614e783b2c/
changeset: d7614e783b2c
user: jen
date: 2011-10-11 00:42:31
summary: Other genome description: corrected typo.
affected #: 4 files (-1 bytes)
--- a/tools/sr_mapping/bowtie_color_wrapper.xml Mon Oct 10 18:33:48 2011 -0400
+++ b/tools/sr_mapping/bowtie_color_wrapper.xml Mon Oct 10 18:42:31 2011 -0400
@@ -566,7 +566,7 @@
**A Note on Built-in Reference Genomes**
-The default variant for all genomes is "Full", defined as all primary chromosomes (or scaffolds/contigs) including mitochondrial plus associated unmapped and other plasmid segments. When only one version of a genome is available in this tool, it represents the default "Full" variant. Some genomes will have more than one variant available. The "Canonical Male" or sometimes simply "Canonical" variant contains the primary chromosomes for a genome. For example a human "Canonical" variant contains chr1-chr22, chrX, chrY, and chrM. The "Canonical Female" variant contains the primary chromosomes excluding chrY.
+The default variant for all genomes is "Full", defined as all primary chromosomes (or scaffolds/contigs) including mitochondrial plus associated unmapped, plasmid, and other segments. When only one version of a genome is available in this tool, it represents the default "Full" variant. Some genomes will have more than one variant available. The "Canonical Male" or sometimes simply "Canonical" variant contains the primary chromosomes for a genome. For example a human "Canonical" variant contains chr1-chr22, chrX, chrY, and chrM. The "Canonical Female" variant contains the primary chromosomes excluding chrY.
------
--- a/tools/sr_mapping/bowtie_wrapper.xml Mon Oct 10 18:33:48 2011 -0400
+++ b/tools/sr_mapping/bowtie_wrapper.xml Mon Oct 10 18:42:31 2011 -0400
@@ -687,7 +687,7 @@
**A Note on Built-in Reference Genomes**
-The default variant for all genomes is "Full", defined as all primary chromosomes (or scaffolds/contigs) including mitochondrial plus associated unmapped and other plasmid segments. When only one version of a genome is available in this tool, it represents the default "Full" variant. Some genomes will have more than one variant available. The "Canonical Male" or sometimes simply "Canonical" variant contains the primary chromosomes for a genome. For example a human "Canonical" variant contains chr1-chr22, chrX, chrY, and chrM. The "Canonical Female" variant contains the primary chromosomes excluding chrY.
+The default variant for all genomes is "Full", defined as all primary chromosomes (or scaffolds/contigs) including mitochondrial plus associated unmapped, plasmid, and other segments. When only one version of a genome is available in this tool, it represents the default "Full" variant. Some genomes will have more than one variant available. The "Canonical Male" or sometimes simply "Canonical" variant contains the primary chromosomes for a genome. For example a human "Canonical" variant contains chr1-chr22, chrX, chrY, and chrM. The "Canonical Female" variant contains the primary chromosomes excluding chrY.
------
--- a/tools/sr_mapping/bwa_color_wrapper.xml Mon Oct 10 18:33:48 2011 -0400
+++ b/tools/sr_mapping/bwa_color_wrapper.xml Mon Oct 10 18:42:31 2011 -0400
@@ -342,7 +342,7 @@
**A Note on Built-in Reference Genomes**
-The default variant for all genomes is "Full", defined as all primary chromosomes (or scaffolds/contigs) including mitochondrial plus associated unmapped and other plasmid segments. When only one version of a genome is available in this tool, it represents the default "Full" variant. Some genomes will have more than one variant available. The "Canonical Male" or sometimes simply "Canonical" variant contains the primary chromosomes for a genome. For example a human "Canonical" variant contains chr1-chr22, chrX, chrY, and chrM. The "Canonical Female" variant contains the primary chromosomes excluding chrY.
+The default variant for all genomes is "Full", defined as all primary chromosomes (or scaffolds/contigs) including mitochondrial plus associated unmapped, plasmid, and other segments. When only one version of a genome is available in this tool, it represents the default "Full" variant. Some genomes will have more than one variant available. The "Canonical Male" or sometimes simply "Canonical" variant contains the primary chromosomes for a genome. For example a human "Canonical" variant contains chr1-chr22, chrX, chrY, and chrM. The "Canonical Female" variant contains the primary chromosomes excluding chrY.
------
--- a/tools/sr_mapping/bwa_wrapper.xml Mon Oct 10 18:33:48 2011 -0400
+++ b/tools/sr_mapping/bwa_wrapper.xml Mon Oct 10 18:42:31 2011 -0400
@@ -334,7 +334,7 @@
**A Note on Built-in Reference Genomes**
-The default variant for all genomes is "Full", defined as all primary chromosomes (or scaffolds/contigs) including mitochondrial plus associated unmapped and other plasmid segments. When only one version of a genome is available in this tool, it represents the default "Full" variant. Some genomes will have more than one variant available. The "Canonical Male" or sometimes simply "Canonical" variant contains the primary chromosomes for a genome. For example a human "Canonical" variant contains chr1-chr22, chrX, chrY, and chrM. The "Canonical Female" variant contains the primary chromosomes excluding chrY.
+The default variant for all genomes is "Full", defined as all primary chromosomes (or scaffolds/contigs) including mitochondrial plus associated unmapped, plasmid, and other segments. When only one version of a genome is available in this tool, it represents the default "Full" variant. Some genomes will have more than one variant available. The "Canonical Male" or sometimes simply "Canonical" variant contains the primary chromosomes for a genome. For example a human "Canonical" variant contains chr1-chr22, chrX, chrY, and chrM. The "Canonical Female" variant contains the primary chromosomes excluding chrY.
------
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.
1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/173422ea8e01/
changeset: 173422ea8e01
user: jen
date: 2011-10-11 00:33:48
summary: Other genome description: revised all, corrected canonical male
affected #: 4 files (-1 bytes)
--- a/tools/sr_mapping/bowtie_color_wrapper.xml Mon Oct 10 15:51:43 2011 -0400
+++ b/tools/sr_mapping/bowtie_color_wrapper.xml Mon Oct 10 18:33:48 2011 -0400
@@ -566,7 +566,7 @@
**A Note on Built-in Reference Genomes**
-Some genomes have multiple variants. If only one "type" of genome is listed, it is the Full version, which means that everything that came in the original genome data download (possibly with mitochondrial and plasmid DNA added if it wasn't already included). The Full version is available for every genome. Some genomes also come in the Canonical variant, which contains only the "canonical" (well-defined) chromosomes or segments, such as chr1-chr22, chrX, chrY, and chrM for human. Other variations include gender. These will come in the canonical form only, so the general Canonical variant is actually Canonical Female and the other is Canonical Male (identical to female excluding chrX).
+The default variant for all genomes is "Full", defined as all primary chromosomes (or scaffolds/contigs) including mitochondrial plus associated unmapped and other plasmid segments. When only one version of a genome is available in this tool, it represents the default "Full" variant. Some genomes will have more than one variant available. The "Canonical Male" or sometimes simply "Canonical" variant contains the primary chromosomes for a genome. For example a human "Canonical" variant contains chr1-chr22, chrX, chrY, and chrM. The "Canonical Female" variant contains the primary chromosomes excluding chrY.
------
--- a/tools/sr_mapping/bowtie_wrapper.xml Mon Oct 10 15:51:43 2011 -0400
+++ b/tools/sr_mapping/bowtie_wrapper.xml Mon Oct 10 18:33:48 2011 -0400
@@ -687,7 +687,7 @@
**A Note on Built-in Reference Genomes**
-Some genomes have multiple variants. If only one "type" of genome is listed, it is the Full version, which means that everything that came in the original genome data download (possibly with mitochondrial and plasmid DNA added if it wasn't already included). The Full version is available for every genome. Some genomes also come in the Canonical variant, which contains only the "canonical" (well-defined) chromosomes or segments, such as chr1-chr22, chrX, chrY, and chrM for human. Other variations include gender. These will come in the canonical form only, so the general Canonical variant is actually Canonical Female and the other is Canonical Male (identical to female excluding chrX).
+The default variant for all genomes is "Full", defined as all primary chromosomes (or scaffolds/contigs) including mitochondrial plus associated unmapped and other plasmid segments. When only one version of a genome is available in this tool, it represents the default "Full" variant. Some genomes will have more than one variant available. The "Canonical Male" or sometimes simply "Canonical" variant contains the primary chromosomes for a genome. For example a human "Canonical" variant contains chr1-chr22, chrX, chrY, and chrM. The "Canonical Female" variant contains the primary chromosomes excluding chrY.
------
--- a/tools/sr_mapping/bwa_color_wrapper.xml Mon Oct 10 15:51:43 2011 -0400
+++ b/tools/sr_mapping/bwa_color_wrapper.xml Mon Oct 10 18:33:48 2011 -0400
@@ -342,7 +342,7 @@
**A Note on Built-in Reference Genomes**
-Some genomes have multiple variants. If only one "type" of genome is listed, it is the Full version, which means that everything that came in the original genome data download (possibly with mitochondrial and plasmid DNA added if it wasn't already included). The Full version is available for every genome. Some genomes also come in the Canonical variant, which contains only the "canonical" (well-defined) chromosomes or segments, such as chr1-chr22, chrX, chrY, and chrM for human. Other variations include gender. These will come in the canonical form only, so the general Canonical variant is actually Canonical Female and the other is Canonical Male (identical to female excluding chrX).
+The default variant for all genomes is "Full", defined as all primary chromosomes (or scaffolds/contigs) including mitochondrial plus associated unmapped and other plasmid segments. When only one version of a genome is available in this tool, it represents the default "Full" variant. Some genomes will have more than one variant available. The "Canonical Male" or sometimes simply "Canonical" variant contains the primary chromosomes for a genome. For example a human "Canonical" variant contains chr1-chr22, chrX, chrY, and chrM. The "Canonical Female" variant contains the primary chromosomes excluding chrY.
------
--- a/tools/sr_mapping/bwa_wrapper.xml Mon Oct 10 15:51:43 2011 -0400
+++ b/tools/sr_mapping/bwa_wrapper.xml Mon Oct 10 18:33:48 2011 -0400
@@ -334,7 +334,7 @@
**A Note on Built-in Reference Genomes**
-Some genomes have multiple variants. If only one "type" of genome is listed, it is the Full version, which means that everything that came in the original genome data download (possibly with mitochondrial and plasmid DNA added if it wasn't already included). The Full version is available for every genome. Some genomes also come in the Canonical variant, which contains only the "canonical" (well-defined) chromosomes or segments, such as chr1-chr22, chrX, chrY, and chrM for human. Other variations include gender. These will come in the canonical form only, so the general Canonical variant is actually Canonical Female and the other is Canonical Male (identical to female excluding chrX).
+The default variant for all genomes is "Full", defined as all primary chromosomes (or scaffolds/contigs) including mitochondrial plus associated unmapped and other plasmid segments. When only one version of a genome is available in this tool, it represents the default "Full" variant. Some genomes will have more than one variant available. The "Canonical Male" or sometimes simply "Canonical" variant contains the primary chromosomes for a genome. For example a human "Canonical" variant contains chr1-chr22, chrX, chrY, and chrM. The "Canonical Female" variant contains the primary chromosomes excluding chrY.
------
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.