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Merge branch 'release_16.01' into dev

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This commit is contained in:
Nate Coraor
2016-02-03 13:11:07 -05:00
parent b82efd9375 cd3f3b330d
commit 246870c459
13 changed files with 35 additions and 31 deletions
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client/galaxy/scripts/layout/page.js
+1 -1
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@@ -94,7 +94,7 @@ var PageLayoutView = Backbone.View.extend( BaseMVC.LoggableMixin ).extend({
page[ panelId ].setElement( '#' + panelId );
page[ panelId ].render();
} else if ( panelId !== 'center' ) {
page.center.$el( panelId, 0 );
page.center.$el.css( panelId, 0 );
}
});
return this;
lib/galaxy/datatypes/binary.py
+1 -1
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@@ -339,7 +339,7 @@ class Bam( Binary ):
os.unlink( stderr_name )
# Now use pysam with BAI index to determine additional metadata
try:
bam_file = pysam.AlignmentFile( filename=dataset.file_name, mode='rb', index_filename=index_file.file_name )
bam_file = pysam.AlignmentFile( dataset.file_name, mode='rb', index_filename=index_file.file_name )
dataset.metadata.reference_names = list( bam_file.references )
dataset.metadata.reference_lengths = list( bam_file.lengths )
dataset.metadata.bam_header = bam_file.header
lib/galaxy/dependencies/conda-environment.txt
+1 -1
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@@ -78,4 +78,4 @@ Fabric
#Whoosh==2.4.1+gx1
# Flexible BAM index naming
#pysam==0.8.3+gx1
#pysam==0.8.4+gx1
lib/galaxy/dependencies/pinned-hashed-requirements.txt
+20 -19
View File
@@ -150,22 +150,23 @@ ecdsa==0.13 --hash:sha256=89f149066e4a1e419892cef830fd0db85c227d5d427f7075422ace
Whoosh==2.4.1+gx1 --hash:sha256=98897e796c048810d71f7f4fc174914869f1b3b77f44e5a19a5e649b078d5e0e \
--hash:sha256=5ec3c22e782c86e981fab62a24ac9feea09e42c43b763a6493c78b82a3b6e3fd
# Flexible BAM index naming
pysam==0.8.3+gx1 --hash:sha256=020aa9101579ac1e82a194fdb08f49f517c634911409e9a2cda4d0a1c72a8c7c \
--hash:sha256=1a3d86849b9bd962979b65aaa9af236030dcc1db40296c88d2aa436a0c9df79b \
--hash:sha256=0fc55fb252eb0e7914679e9e22672fdc6a1e09804cbcc62769f004ebbed9b4c1 \
--hash:sha256=dde8f5037661d7be42e2c3f50c01566dcaedbf2f88133a3bb50c6ae3f75e6e13 \
--hash:sha256=7809fd926a071519c0a2b220346e45c094577877e5b2adba2903e7b52490c736 \
--hash:sha256=021070ed70a89e19eee6a989933d69d0bdb076c02342e2987bb5fab43f63ad17 \
--hash:sha256=374ea868bf64daa4665e8743db1be2e88712953a923020225f57a589b790537c \
--hash:sha256=9884b6904face1977649847261e7c984120adaa169a0d62e07820a44c71e18c5 \
--hash:sha256=873b81951e9d572b53ab4c7a0d3ef915f7d0e1db5f75603d8861cf1d3810491e \
--hash:sha256=37d0ba3880b5a517f354281159f6751f6f9f1c1074ea48bf5f4c424e6ec488dd \
--hash:sha256=db99cb20cb5e07998b2acfd29e34c367ef408a184a7b3150586212175a0719bf \
--hash:sha256=a1fcb2a6459b799bff7a046e190452b151c5985dea404eaee82bd645b1bfe34d \
--hash:sha256=306e4d900dfb582cf87bc21904e2193ef81db76173e976b74152c95ddd93bdc6 \
--hash:sha256=2341438d636b8e3cb51b219aab1cc909142d3af176042d12b128d4177682b1ab \
--hash:sha256=0f33df9eba7b079b7489ac3dd908a6e44b0e98d094e633b29035d33bfc990b9e \
--hash:sha256=faa8aae3f8f105c5c823a7d570dd3caba31ece69b8f3325106435b9f1fcb68d2 \
--hash:sha256=2db995758d666c51fecf11cbee1afda357477e01077aacf68ae0c00304c7bc51 \
--hash:sha256=2de7a2098f64672d0396ac727633285f3562f804e7845e105ee19da544d7da8a
# Flexible BAM/tabix index naming
pysam==0.8.4+gx1 --hash:sha256=9a548c88dbc928b64292ffa4a7697a4ee8c6653f998ef75c717c6dd37c8f67d3 \
--hash:sha256=bc2ba93bdf9228aaf479eae953a2d9012c9f69ee753446eec3edbdd5c55e8bd4 \
--hash:sha256=55e06fa6ce2df2e2bdb0705a14eefc6ad433effc79ab53d30642d8d0b33a98ff \
--hash:sha256=dd8600bee61cca3005c0e95b29aefa3611c452d980055799c3999e1c3cc044bb \
--hash:sha256=e4cc2b4b24d84b71c82f3194815b986e4f450ab62b96d7f28a453f5a47afdc24 \
--hash:sha256=f4eb92138ac871fe4db2e5a70ddbc2d6ffcf0c77314b4866b013b7a4d3a52aa6 \
--hash:sha256=c388728ec37d979c84980f662e9329452f90acf5e2e34c3afb1f66403e063b3f \
--hash:sha256=001620b7ea051fd2c868ef4f83a07838177a28c42839d76a86f653e124f9830b \
--hash:sha256=c27e705259d74dba190a2d729c326384ee9949e73478d7dca8e9e2aa593b54c1 \
--hash:sha256=4c3dae36124646a3bed6bc7e6fd2c979a4430aa290b61da1a611d3cf7e9b38e5 \
--hash:sha256=73124bec6d2699a30396c6eb63584230c8fdc0dce563391c217b9b57777d0d14 \
--hash:sha256=8db6bde296f6a34b584dddaeac1dc53f5819d0f63b0cded014a143366c64307f \
--hash:sha256=a40617160ba503ba31c297de24007e189cbb54325ea11265fa1b96e7d3f32625 \
--hash:sha256=2045ceb8f733dc787b5fa23293330d8f669a42952be14014d91b2d1d4db99c9e \
--hash:sha256=f140cd6c2c7b78be20f207e86be79772496a770c0d132604db0f632d54564ff8 \
--hash:sha256=d35cb62c382bda70552878069d7cc0321b41ec6095838332a15c44a14736b8aa \
--hash:sha256=2fae280fecfa6547b7c8291bc3966a940ce80400d79cdbc612cefb2bc399f5fd \
--hash:sha256=a85c470c3ae9d77f13b9fd57fcfdddf26b176d69840eb6654112fd711c86c243 \
--hash:sha256=9028099e40c45a3959add2c091b8817454b41c8aaa192e72d9c3ee9a5a1c5f8b
lib/galaxy/dependencies/pinned-requirements.txt
+1 -1
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@@ -66,4 +66,4 @@ ecdsa==0.13
Whoosh==2.4.1+gx1
# Flexible BAM index naming
pysam==0.8.3+gx1
pysam==0.8.4+gx1
lib/galaxy/dependencies/requirements.txt
+1 -1
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@@ -60,4 +60,4 @@ Fabric
Whoosh==2.4.1+gx1
# Flexible BAM index naming
pysam==0.8.3+gx1
pysam==0.8.4+gx1
lib/galaxy/tools/__init__.py
+3
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@@ -866,6 +866,9 @@ class Tool( object, Dictifiable ):
# Should have one child "input" which determines the case
test_param_input_source = input_source.parse_test_input_source()
group.test_param = self.parse_param_elem( test_param_input_source, enctypes, context )
if group.test_param.optional:
log.warning("Tool with id %s declares a conditional test parameter as optional, this is invalid and will be ignored." % self.id)
group.test_param.optional = False
possible_cases = list( group.test_param.legal_values ) # store possible cases, undefined whens will have no inputs
# Must refresh when test_param changes
group.test_param.refresh_on_change = True
lib/galaxy/visualization/data_providers/genome.py
+3 -3
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@@ -847,11 +847,11 @@ class BamDataProvider( GenomeDataProvider, FilterableMixin ):
"""
# Open current BAM file using index.
bamfile = pysam.AlignmentFile( filename=self.original_dataset.file_name, mode='rb',
bamfile = pysam.AlignmentFile( self.original_dataset.file_name, mode='rb',
index_filename=self.converted_dataset.file_name )
# TODO: write headers as well?
new_bamfile = pysam.AlignmentFile( template=bamfile, filename=filename, mode='wb' )
new_bamfile = pysam.AlignmentFile( filename, template=bamfile, mode='wb' )
for region in regions:
# Write data from region.
@@ -879,7 +879,7 @@ class BamDataProvider( GenomeDataProvider, FilterableMixin ):
def open_data_file( self ):
# Attempt to open the BAM file with index
return pysam.AlignmentFile( filename=self.original_dataset.file_name, mode='rb',
return pysam.AlignmentFile( self.original_dataset.file_name, mode='rb',
index_filename=self.converted_dataset.file_name )
def get_iterator( self, data_file, chrom, start, end, **kwargs ):
static/maps/layout/page.js.map
+1 -1
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@@ -1 +1 @@
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static/scripts/bundled/libs.bundled.js
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static/scripts/bundled/libs.bundled.js.map
+1 -1
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static/scripts/layout/page.js
+1 -1
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@@ -1,2 +1,2 @@
define(["layout/masthead","layout/panel","mvc/ui/ui-modal","mvc/base-mvc"],function(a,b,c,d){var e=Backbone.View.extend(d.LoggableMixin).extend({_logNamespace:"layout",el:"body",className:"full-content",_panelIds:["left","center","right"],defaultOptions:{message_box_visible:!1,message_box_content:"",message_box_class:"info",show_inactivity_warning:!1,inactivity_box_content:""},initialize:function(b){this.log(this+".initialize:",b),_.extend(this,_.pick(b,this._panelIds)),this.options=_.defaults(_.omit(b,this._panelIds),this.defaultOptions),Galaxy.modal=this.modal=new c.View,this.masthead=new a.View(this.options.config),this.$el.attr("scroll","no"),this.$el.append(this._template()),this.$el.append(this.masthead.$el),this.$el.append(this.modal.$el),this.$messagebox=this.$("#messagebox"),this.$inactivebox=this.$("#inactivebox")},render:function(){return $(".select2-hidden-accessible").remove(),this.log(this+".render:"),this.masthead.render(),this.renderMessageBox(),this.renderInactivityBox(),this.renderPanels(),this},renderMessageBox:function(){if(this.options.message_box_visible){var a=this.options.message_box_content||"",b=this.options.message_box_class||"info";this.$el.addClass("has-message-box"),this.$messagebox.attr("class","panel-"+b+"-message").html(a).toggle(!!a).show()}else this.$el.removeClass("has-message-box"),this.$messagebox.hide();return this},renderInactivityBox:function(){if(this.options.show_inactivity_warning){var a=this.options.inactivity_box_content||"",b=$("<a/>").attr("href",Galaxy.root+"user/resend_verification").html("Resend verification.");this.$el.addClass("has-inactivity-box"),this.$inactivebox.html(a).append(" "+b).toggle(!!a).show()}else this.$el.removeClass("has-inactivity-box"),this.$inactivebox.hide();return this},renderPanels:function(){var a=this;return this._panelIds.forEach(function(b){_.has(a,b)?(a[b].setElement("#"+b),a[b].render()):"center"!==b&&a.center.$el(b,0)}),this},_template:function(){return['<div id="everything">','<div id="background"/>','<div id="messagebox"/>','<div id="inactivebox" class="panel-warning-message"/>','<div id="left"/>','<div id="center" class="inbound"/>','<div id="right"/>',"</div>",'<div id="dd-helper"/>',"<noscript>",'<div class="overlay overlay-background noscript-overlay">',"<div>",'<h3 class="title">Javascript Required for Galaxy</h3>',"<div>","The Galaxy analysis interface requires a browser with Javascript enabled.<br>","Please enable Javascript and refresh this page","</div>","</div>","</div>","</noscript>"].join("")},toString:function(){return"PageLayoutView"}});return{PageLayoutView:e}});
define(["layout/masthead","layout/panel","mvc/ui/ui-modal","mvc/base-mvc"],function(a,b,c,d){var e=Backbone.View.extend(d.LoggableMixin).extend({_logNamespace:"layout",el:"body",className:"full-content",_panelIds:["left","center","right"],defaultOptions:{message_box_visible:!1,message_box_content:"",message_box_class:"info",show_inactivity_warning:!1,inactivity_box_content:""},initialize:function(b){this.log(this+".initialize:",b),_.extend(this,_.pick(b,this._panelIds)),this.options=_.defaults(_.omit(b,this._panelIds),this.defaultOptions),Galaxy.modal=this.modal=new c.View,this.masthead=new a.View(this.options.config),this.$el.attr("scroll","no"),this.$el.append(this._template()),this.$el.append(this.masthead.$el),this.$el.append(this.modal.$el),this.$messagebox=this.$("#messagebox"),this.$inactivebox=this.$("#inactivebox")},render:function(){return $(".select2-hidden-accessible").remove(),this.log(this+".render:"),this.masthead.render(),this.renderMessageBox(),this.renderInactivityBox(),this.renderPanels(),this},renderMessageBox:function(){if(this.options.message_box_visible){var a=this.options.message_box_content||"",b=this.options.message_box_class||"info";this.$el.addClass("has-message-box"),this.$messagebox.attr("class","panel-"+b+"-message").html(a).toggle(!!a).show()}else this.$el.removeClass("has-message-box"),this.$messagebox.hide();return this},renderInactivityBox:function(){if(this.options.show_inactivity_warning){var a=this.options.inactivity_box_content||"",b=$("<a/>").attr("href",Galaxy.root+"user/resend_verification").html("Resend verification.");this.$el.addClass("has-inactivity-box"),this.$inactivebox.html(a).append(" "+b).toggle(!!a).show()}else this.$el.removeClass("has-inactivity-box"),this.$inactivebox.hide();return this},renderPanels:function(){var a=this;return this._panelIds.forEach(function(b){_.has(a,b)?(a[b].setElement("#"+b),a[b].render()):"center"!==b&&a.center.$el.css(b,0)}),this},_template:function(){return['<div id="everything">','<div id="background"/>','<div id="messagebox"/>','<div id="inactivebox" class="panel-warning-message"/>','<div id="left"/>','<div id="center" class="inbound"/>','<div id="right"/>',"</div>",'<div id="dd-helper"/>',"<noscript>",'<div class="overlay overlay-background noscript-overlay">',"<div>",'<h3 class="title">Javascript Required for Galaxy</h3>',"<div>","The Galaxy analysis interface requires a browser with Javascript enabled.<br>","Please enable Javascript and refresh this page","</div>","</div>","</div>","</noscript>"].join("")},toString:function(){return"PageLayoutView"}});return{PageLayoutView:e}});
//# sourceMappingURL=../../maps/layout/page.js.map
test-data/3.bam
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