1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/c0e7ba8bfd57/
changeset: r5558:c0e7ba8bfd57
user: kanwei
date: 2011-05-13 22:49:43
summary: trackster: tweak resolution, fix LineTrack data bug
affected #: 2 files (67 bytes)
--- a/lib/galaxy/visualization/tracks/data_providers.py Fri May 13 10:02:28 2011 -0400
+++ b/lib/galaxy/visualization/tracks/data_providers.py Fri May 13 16:49:43 2011 -0400
@@ -332,10 +332,11 @@
# The first zoom level for BBI files is 640. If too much is requested, it will look at each block instead
# of summaries. The calculation done is: zoom <> (end-start)/num_points/2.
# Thus, the optimal number of points is (end-start)/num_points/2 = 640
- # num_points = (end-start) / 1280
+ # num_points = (end-start) / 1280
num_points = (end-start) / 1280
- if (end - start) < num_points:
+ if num_points < 1:
num_points = end - start
+ num_points = max(num_points, 10)
data = bbi.query(chrom, start, end, num_points)
f.close()
--- a/static/scripts/trackster.js Fri May 13 10:02:28 2011 -0400
+++ b/static/scripts/trackster.js Fri May 13 16:49:43 2011 -0400
@@ -181,6 +181,7 @@
// Other constants.
DENSITY = 200,
+ RESOLUTION = 5,
FEATURE_LEVELS = 10,
DEFAULT_DATA_QUERY_WAIT = 5000,
// Maximum number of chromosomes that are selectable at any one time.
@@ -762,7 +763,7 @@
this.high = Math.ceil(high);
// 10^log10(range / DENSITY) Close approximation for browser window, assuming DENSITY = window width
- this.resolution = Math.pow( 10, Math.ceil( Math.log( (this.high - this.low) / DENSITY ) / Math.LN10 ) );
+ this.resolution = Math.pow( RESOLUTION, Math.ceil( Math.log( (this.high - this.low) / DENSITY ) / Math.log(RESOLUTION) ) );
this.zoom_res = Math.pow( FEATURE_LEVELS, Math.max(0,Math.ceil( Math.log( this.resolution, FEATURE_LEVELS ) / Math.log(FEATURE_LEVELS) )));
// Overview
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/c99af10d79a4/
changeset: r5549:c99af10d79a4
user: kellyv
date: 2011-05-12 19:38:00
summary: Updated help section of BWA wrappers to include tags for the RG header record type
affected #: 2 files (120 bytes)
--- a/tools/sr_mapping/bwa_color_wrapper.xml Thu May 12 12:20:52 2011 -0400
+++ b/tools/sr_mapping/bwa_color_wrapper.xml Thu May 12 13:38:00 2011 -0400
@@ -137,23 +137,23 @@
<option value="no">No</option></param><when value="yes">
- <param name="rgid" type="text" size="25" label="Read group identifier. Each @RG line must have a unique ID. The value of ID is used in the RG
+ <param name="rgid" type="text" size="25" label="Read group identifier (ID). Each @RG line must have a unique ID. The value of ID is used in the RG
tags of alignment records. Must be unique among all read groups in header section." help="Required if RG specified. Read group
IDs may be modified when merging SAM files in order to handle collisions." />
- <param name="rgcn" type="text" size="25" label="Sequencing center that produced the read" help="Optional" />
- <param name="rgds" type="text" size="25" label="Description" help="Optional" />
- <param name="rgdt" type="text" size="25" label="Date that run was produced (ISO8601 format date or date/time, like YYYY-MM-DD)" help="Optional" />
- <param name="rgfo" type="text" size="25" label="Flow order. The array of nucleotide bases that correspond to the nucleotides used for each
-flow of each read." help="Optional. Multi-base flows are encoded in IUPAC format, and non-nucleotide flows by
+ <param name="rgcn" type="text" size="25" label="Sequencing center that produced the read (CN)" help="Optional" />
+ <param name="rgds" type="text" size="25" label="Description (DS)" help="Optional" />
+ <param name="rgdt" type="text" size="25" label="Date that run was produced (DT)" help="Optional. ISO8601 format date or date/time, like YYYY-MM-DD" />
+ <param name="rgfo" type="text" size="25" label="Flow order (FO). The array of nucleotide bases that correspond to the nucleotides used for each
+flow of each read." help="Optional. Multi-base flows are encoded in IUPAC format, and non-nucleotide flows by
various other characters. Format : /\*|[ACMGRSVTWYHKDBN]+/" />
- <param name="rgks" type="text" size="25" label="The array of nucleotide bases that correspond to the key sequence of each read" help="Optional" />
- <param name="rglb" type="text" size="25" label="Library name" help="Required if RG specified" />
- <param name="rgpg" type="text" size="25" label="Programs used for processing the read group" help="Optional" />
- <param name="rgpi" type="text" size="25" label="Predicted median insert size" help="Optional" />
- <param name="rgpl" type="text" size="25" label="Platform/technology used to produce the reads. Valid values : CAPILLARY, LS454, ILLUMINA,
-SOLID, HELICOS, IONTORRENT and PACBIO" help="Required if RG specified" />
- <param name="rgpu" type="text" size="25" label="Platform unit (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD). Unique identifier." help="Optional" />
- <param name="rgsm" type="text" size="25" label="Sample. Use pool name where a pool is being sequenced" help="Required if RG specified" />
+ <param name="rgks" type="text" size="25" label="The array of nucleotide bases that correspond to the key sequence of each read (KS)" help="Optional" />
+ <param name="rglb" type="text" size="25" label="Library name (LB)" help="Required if RG specified" />
+ <param name="rgpg" type="text" size="25" label="Programs used for processing the read group (PG)" help="Optional" />
+ <param name="rgpi" type="text" size="25" label="Predicted median insert size (PI)" help="Optional" />
+ <param name="rgpl" type="text" size="25" label="Platform/technology used to produce the reads (PL)" help="Required if RG specified. Valid values : CAPILLARY, LS454, ILLUMINA,
+SOLID, HELICOS, IONTORRENT and PACBIO" />
+ <param name="rgpu" type="text" size="25" label="Platform unit (PU)" help="Optional. Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" />
+ <param name="rgsm" type="text" size="25" label="Sample (SM)" help="Required if RG specified. Use pool name where a pool is being sequenced" /></when><when value="no" /></conditional>
--- a/tools/sr_mapping/bwa_wrapper.xml Thu May 12 12:20:52 2011 -0400
+++ b/tools/sr_mapping/bwa_wrapper.xml Thu May 12 13:38:00 2011 -0400
@@ -130,23 +130,23 @@
<option value="no">No</option></param><when value="yes">
- <param name="rgid" type="text" size="25" label="Read group identifier. Each @RG line must have a unique ID. The value of ID is used in the RG
+ <param name="rgid" type="text" size="25" label="Read group identifier (ID). Each @RG line must have a unique ID. The value of ID is used in the RG
tags of alignment records. Must be unique among all read groups in header section." help="Required if RG specified. Read group
IDs may be modified when merging SAM files in order to handle collisions." />
- <param name="rgcn" type="text" size="25" label="Sequencing center that produced the read" help="Optional" />
- <param name="rgds" type="text" size="25" label="Description" help="Optional" />
- <param name="rgdt" type="text" size="25" label="Date that run was produced (ISO8601 format date or date/time, like YYYY-MM-DD)" help="Optional" />
- <param name="rgfo" type="text" size="25" label="Flow order. The array of nucleotide bases that correspond to the nucleotides used for each
+ <param name="rgcn" type="text" size="25" label="Sequencing center that produced the read (CN)" help="Optional" />
+ <param name="rgds" type="text" size="25" label="Description (DS)" help="Optional" />
+ <param name="rgdt" type="text" size="25" label="Date that run was produced (DT)" help="Optional. ISO8601 format date or date/time, like YYYY-MM-DD" />
+ <param name="rgfo" type="text" size="25" label="Flow order (FO). The array of nucleotide bases that correspond to the nucleotides used for each
flow of each read." help="Optional. Multi-base flows are encoded in IUPAC format, and non-nucleotide flows by
various other characters. Format : /\*|[ACMGRSVTWYHKDBN]+/" />
- <param name="rgks" type="text" size="25" label="The array of nucleotide bases that correspond to the key sequence of each read" help="Optional" />
- <param name="rglb" type="text" size="25" label="Library name" help="Required if RG specified" />
- <param name="rgpg" type="text" size="25" label="Programs used for processing the read group" help="Optional" />
- <param name="rgpi" type="text" size="25" label="Predicted median insert size" help="Optional" />
- <param name="rgpl" type="text" size="25" label="Platform/technology used to produce the reads. Valid values : CAPILLARY, LS454, ILLUMINA,
-SOLID, HELICOS, IONTORRENT and PACBIO" help="Required if RG specified" />
- <param name="rgpu" type="text" size="25" label="Platform unit (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD). Unique identifier." help="Optional" />
- <param name="rgsm" type="text" size="25" label="Sample. Use pool name where a pool is being sequenced" help="Required if RG specified" />
+ <param name="rgks" type="text" size="25" label="The array of nucleotide bases that correspond to the key sequence of each read (KS)" help="Optional" />
+ <param name="rglb" type="text" size="25" label="Library name (LB)" help="Required if RG specified" />
+ <param name="rgpg" type="text" size="25" label="Programs used for processing the read group (PG)" help="Optional" />
+ <param name="rgpi" type="text" size="25" label="Predicted median insert size (PI)" help="Optional" />
+ <param name="rgpl" type="text" size="25" label="Platform/technology used to produce the reads (PL)" help="Required if RG specified. Valid values : CAPILLARY, LS454, ILLUMINA,
+SOLID, HELICOS, IONTORRENT and PACBIO" />
+ <param name="rgpu" type="text" size="25" label="Platform unit (PU)" help="Optional. Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" />
+ <param name="rgsm" type="text" size="25" label="Sample (SM)" help="Required if RG specified. Use pool name where a pool is being sequenced" /></when><when value="no" /></conditional>
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/41371f0f6f3d/
changeset: r5548:41371f0f6f3d
user: dan
date: 2011-05-12 18:20:52
summary: Add GATK tool-data to buildbot_setup.sh links.
affected #: 1 file (32 bytes)
--- a/buildbot_setup.sh Thu May 12 12:13:18 2011 -0400
+++ b/buildbot_setup.sh Thu May 12 12:20:52 2011 -0400
@@ -61,6 +61,7 @@
/galaxy/data/location/srma_index.loc
/galaxy/data/taxonomy
/galaxy/data/location/twobit.loc
+/galaxy/software/tool-data/gatk
"
SAMPLES="
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/e6ba910e0220/
changeset: r5546:e6ba910e0220
user: natefoo
date: 2011-05-12 17:55:32
summary: Fix test output for picard_ARRG.
affected #: 1 file (1 byte)
--- a/tools/picard/picard_AddOrReplaceReadGroups.xml Thu May 12 11:53:32 2011 -0400
+++ b/tools/picard/picard_AddOrReplaceReadGroups.xml Thu May 12 11:55:32 2011 -0400
@@ -63,7 +63,7 @@
<param name="rgsm" value="sam1" /><param name="rgOpts" value="preSet" /><param name="outputFormat" value="sam" />
- <output name="outFileSam" ftype="picard_ARRG_output1.sam" />
+ <output name="outFileSam" file="picard_ARRG_output1.sam" /></test><!-- Functional tests with Picard bam outputs currently aren't working
<test>
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/2650328b4321/
changeset: r5545:2650328b4321
user: natefoo
date: 2011-05-12 17:53:32
summary: Add a method to add manual builds to buildbot runs.
affected #: 2 files (178 bytes)
--- a/buildbot_setup.sh Wed May 11 16:02:06 2011 -0400
+++ b/buildbot_setup.sh Thu May 12 11:53:32 2011 -0400
@@ -135,4 +135,7 @@
echo "Setting up test data location files"
python test-data-repo/location/make_location.py
+echo "Appending tool-data/shared/ucsc/builds.txt.buildbot to tool-data/shared/ucsc/builds.txt"
+cat tool-data/shared/ucsc/builds.txt.buildbot >> tool-data/shared/ucsc/builds.txt
+
python ./scripts/fetch_eggs.py all
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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