commit/galaxy-central: dan: Add samtools rmdup tool.
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1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/55f8f2d8ac18/
changeset: 55f8f2d8ac18
user: dan
date: 2011-08-31 22:50:58
summary: Add samtools rmdup tool.
affected #: 4 files (105 bytes)
--- a/tool_conf.xml.main Wed Aug 31 11:44:52 2011 -0400
+++ b/tool_conf.xml.main Wed Aug 31 16:50:58 2011 -0400
@@ -382,6 +382,7 @@
<tool file="samtools/pileup_parser.xml" /><tool file="samtools/pileup_interval.xml" /><tool file="samtools/samtools_flagstat.xml" />
+ <tool file="samtools/samtools_rmdup.xml" /></section><section name="NGS: Indel Analysis" id="indel_analysis"><tool file="indels/sam_indel_filter.xml" />
--- a/tool_conf.xml.sample Wed Aug 31 11:44:52 2011 -0400
+++ b/tool_conf.xml.sample Wed Aug 31 16:50:58 2011 -0400
@@ -352,8 +352,9 @@
<tool file="samtools/pileup_parser.xml" /><tool file="samtools/pileup_interval.xml" /><tool file="samtools/samtools_flagstat.xml" />
+ <tool file="samtools/samtools_rmdup.xml" /></section>
- <section name="NGS: GATK Tools" id="gatk">
+ <section name="NGS: GATK Tools (beta)" id="gatk"><label text="Realignment" id="gatk_realignment" /><tool file="gatk/realigner_target_creator.xml" /><tool file="gatk/indel_realigner.xml" />
--- a/tools/samtools/samtools_flagstat.xml Wed Aug 31 11:44:52 2011 -0400
+++ b/tools/samtools/samtools_flagstat.xml Wed Aug 31 16:50:58 2011 -0400
@@ -3,7 +3,7 @@
<requirement type="package">samtools</requirement></requirements><description>provides simple stats on BAM files</description>
- <command>samtools flagstat $input1 > $output1
+ <command>samtools flagstat "$input1" > "$output1"
</command><inputs><param name="input1" type="data" format="bam" label="BAM File to Convert" />
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: jgoecks: Trackster: add mode parameter to draw_tile and use to support better overview drawing.
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1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/52e6f9a13e34/
changeset: 52e6f9a13e34
user: jgoecks
date: 2011-08-31 17:44:52
summary: Trackster: add mode parameter to draw_tile and use to support better overview drawing.
affected #: 1 file (38 bytes)
--- a/static/scripts/trackster.js Tue Aug 30 16:56:52 2011 -0400
+++ b/static/scripts/trackster.js Wed Aug 31 11:44:52 2011 -0400
@@ -2240,7 +2240,7 @@
// Draw tile if necessary.
if (!tile) {
- tile = track.draw_tile(overview_data, resolution, 0, w_scale);
+ tile = track.draw_tile(overview_data, "Auto", resolution, 0, w_scale);
track.tile_cache.set(key, tile);
}
@@ -2395,7 +2395,7 @@
// If we can draw now, do so
if ( can_draw_now ) {
extend( tile_data, more_tile_data );
- var tile = track.draw_tile(tile_data, resolution, tile_index, w_scale, seq_data);
+ var tile = track.draw_tile(tile_data, track.mode, resolution, tile_index, w_scale, seq_data);
track.tile_cache.set(key, tile);
// Don't show if no tile
if (tile !== undefined) {
@@ -2558,7 +2558,7 @@
/**
* Draw ReferenceTrack tile.
*/
- draw_tile: function(seq, resolution, tile_index, w_scale) {
+ draw_tile: function(seq, mode, resolution, tile_index, w_scale) {
var track = this,
tile_length = DENSITY * resolution;
@@ -2696,7 +2696,7 @@
/**
* Draw LineTrack tile.
*/
- draw_tile: function(result, resolution, tile_index, w_scale) {
+ draw_tile: function(result, mode, resolution, tile_index, w_scale) {
if (this.vertical_range === undefined) {
return;
}
@@ -2713,7 +2713,7 @@
// Paint line onto full canvas
var ctx = canvas.getContext("2d");
- var painter = new painters.LinePainter(result.data, tile_low, tile_low + tile_length, this.prefs, this.mode);
+ var painter = new painters.LinePainter(result.data, tile_low, tile_low + tile_length, this.prefs, mode);
painter.draw(ctx, width, height);
return new Tile(tile_index, resolution, canvas, result.data);
@@ -2968,18 +2968,18 @@
/**
* Draw FeatureTrack tile.
* @param result result from server
+ * @param mode mode to draw in
* @param resolution view resolution
* @param tile_index index of tile to be drawn
* @param w_scale base pairs per pixel
* @param ref_seq reference sequence data
*/
- draw_tile: function(result, resolution, tile_index, w_scale, ref_seq) {
+ draw_tile: function(result, mode, resolution, tile_index, w_scale, ref_seq) {
var track = this,
tile_low = tile_index * DENSITY * resolution,
tile_high = (tile_index + 1) * DENSITY * resolution,
tile_span = tile_high - tile_low,
width = Math.ceil(tile_span * w_scale),
- mode = this.mode,
min_height = 25,
left_offset = this.left_offset,
slots,
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: dan: Add basic VCF4.1 support.
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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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commit/galaxy-central: dan: Add SICER to tool_conf.xml.main.
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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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commit/galaxy-central: dan: Update for wavelet variance tool contributed by Erika Kvikstad.
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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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commit/galaxy-central: natefoo: Missing import in library_contents.py
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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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commit/galaxy-central: greg: Add a guid to tool shed repository tool metadata and add some fixes for previewing tool shed repository tools.
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1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/e08716dfa2d5/
changeset: e08716dfa2d5
user: greg
date: 2011-08-29 17:29:31
summary: Add a guid to tool shed repository tool metadata and add some fixes for previewing tool shed repository tools.
affected #: 5 files (1.6 KB)
--- a/lib/galaxy/webapps/community/app.py Mon Aug 29 11:22:54 2011 -0400
+++ b/lib/galaxy/webapps/community/app.py Mon Aug 29 11:29:31 2011 -0400
@@ -13,6 +13,8 @@
self.config = config.Configuration( **kwargs )
self.config.check()
config.configure_logging( self.config )
+ # Set up datatypes registry
+ self.datatypes_registry = galaxy.datatypes.registry.Registry( self.config.root, self.config.datatypes_config )
# Determine the database url
if self.config.database_connection:
db_url = self.config.database_connection
--- a/lib/galaxy/webapps/community/config.py Mon Aug 29 11:22:54 2011 -0400
+++ b/lib/galaxy/webapps/community/config.py Mon Aug 29 11:29:31 2011 -0400
@@ -39,11 +39,21 @@
self.file_path = resolve_path( kwargs.get( "file_path", "database/files" ), self.root )
self.new_file_path = resolve_path( kwargs.get( "new_file_path", "database/tmp" ), self.root )
self.cookie_path = kwargs.get( "cookie_path", "/" )
+ self.datatypes_config = kwargs.get( 'datatypes_config_file', 'datatypes_conf.xml' )
self.test_conf = resolve_path( kwargs.get( "test_conf", "" ), self.root )
self.id_secret = kwargs.get( "id_secret", "USING THE DEFAULT IS NOT SECURE!" )
+ # Tool stuff
self.tool_secret = kwargs.get( "tool_secret", "" )
self.tool_data_path = resolve_path( kwargs.get( "tool_data_path", "tool-data" ), os.getcwd() )
self.tool_data_table_config_path = resolve_path( kwargs.get( 'tool_data_table_config_path', 'tool_data_table_conf.xml' ), self.root )
+ self.ftp_upload_dir = kwargs.get( 'ftp_upload_dir', None )
+ # Location for dependencies
+ if 'tool_dependency_dir' in kwargs:
+ self.tool_dependency_dir = resolve_path( kwargs.get( "tool_dependency_dir" ), self.root )
+ self.use_tool_dependencies = True
+ else:
+ self.tool_dependency_dir = None
+ self.use_tool_dependencies = False
self.use_remote_user = string_as_bool( kwargs.get( "use_remote_user", "False" ) )
self.remote_user_maildomain = kwargs.get( "remote_user_maildomain", None )
self.remote_user_logout_href = kwargs.get( "remote_user_logout_href", None )
--- a/lib/galaxy/webapps/community/controllers/common.py Mon Aug 29 11:22:54 2011 -0400
+++ b/lib/galaxy/webapps/community/controllers/common.py Mon Aug 29 11:29:31 2011 -0400
@@ -145,11 +145,22 @@
# The received metadata_dict includes no metadata for workflows, so a new repository_metadata table
# record is not needed.
return False
+def generate_tool_guid( trans, repository, tool ):
+ """
+ Generate a guid for the received tool. The form of the guid is
+ <tool shed host>/repos/<tool shed username>/<tool shed repo name>/<tool id>/<tool version>
+ """
+ return '%s/repos/%s/%s/%s/%s' % ( trans.request.host,
+ repository.user.username,
+ repository.name,
+ tool.id,
+ tool.version )
def generate_tool_metadata( trans, id, changeset_revision, root, name, tool, metadata_dict ):
"""
Update the received metadata_dict with changes that have been
applied to the received tool.
"""
+ repository = get_repository( trans, id )
tool_requirements = []
for tr in tool.requirements:
requirement_dict = dict( name=tr.name,
@@ -165,6 +176,7 @@
outputs=ttb.outputs )
tool_tests.append( test_dict )
tool_dict = dict( id=tool.id,
+ guid = generate_tool_guid( trans, repository, tool ),
name=tool.name,
version=tool.version,
description=tool.description,
--- a/templates/webapps/community/repository/tool_form.mako Mon Aug 29 11:22:54 2011 -0400
+++ b/templates/webapps/community/repository/tool_form.mako Mon Aug 29 11:29:31 2011 -0400
@@ -4,7 +4,7 @@
<%
from galaxy.util.expressions import ExpressionContext
from galaxy import util
- from galaxy.tools.parameters.basic import DataToolParameter, ColumnListParameter, SelectToolParameter
+ from galaxy.tools.parameters.basic import DataToolParameter, ColumnListParameter, GenomeBuildParameter, SelectToolParameter
from galaxy.web.form_builder import SelectField
is_admin = trans.user_is_admin()
@@ -60,8 +60,8 @@
%endif
%elif input.type == "upload_dataset":
%if input.get_datatype( trans, other_values ).composite_type is None:
- # Have non-composite upload appear as before
- ${do_inputs( input.inputs, tool_state[input.name][0], prefix + input.name + "_" + str( 0 ) + "|", other_values )}
+ ## Have non-composite upload appear as before
+ ${do_inputs( input.inputs, 'files', prefix + input.name + "_" + str( 0 ) + "|", other_values )}
%else:
<div class="repeat-group"><div class="form-title-row">
@@ -82,7 +82,7 @@
<%def name="row_for_param( prefix, param, parent_state, other_values )"><%
label = param.get_label()
- if isinstance( param, DataToolParameter ) or isinstance( param, ColumnListParameter ):
+ if isinstance( param, DataToolParameter ) or isinstance( param, ColumnListParameter ) or isinstance( param, GenomeBuildParameter ):
field = SelectField( param.name )
field.add_option( param.name, param.name )
field_html = field.get_html()
--- a/templates/webapps/community/repository/view_tool_metadata.mako Mon Aug 29 11:22:54 2011 -0400
+++ b/templates/webapps/community/repository/view_tool_metadata.mako Mon Aug 29 11:29:31 2011 -0400
@@ -137,6 +137,13 @@
<div style="clear: both"></div></div>
%endif
+ %if 'guid' in metadata:
+ <div class="form-row">
+ <label>Guid:</label>
+ ${metadata[ 'guid' ]}
+ <div style="clear: both"></div>
+ </div>
+ %endif
%if 'version' in metadata:
<div class="form-row"><label>Version:</label>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: dan: Add wavelet variance tool contributed by Erika Kvikstad.
by Bitbucket
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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