1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/d39523d118fe/
changeset: d39523d118fe
user: dan
date: 2011-11-17 20:18:55
summary: Update tool_conf.xml.sample.
affected #: 1 file
diff -r 4e075c43e20fd8f2b8a8015b2830b4b9704b83ec -r d39523d118fe21d71c994d185c2a0d96196f09b0 tool_conf.xml.sample
--- a/tool_conf.xml.sample
+++ b/tool_conf.xml.sample
@@ -378,6 +378,8 @@
<tool file="samtools/samtools_rmdup.xml" /></section><section name="NGS: GATK Tools (beta)" id="gatk">
+ <label text="Alignment Utilities" id="gatk_bam_utilities"/>
+ <tool file="gatk/depth_of_coverage.xml" /><label text="Realignment" id="gatk_realignment" /><tool file="gatk/realigner_target_creator.xml" />
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/12ecc1ea2821/
changeset: 12ecc1ea2821
user: jgoecks
date: 2011-11-17 15:12:19
summary: When fetching BAM data for Trackster, use BAI from metadata when possible rather than waiting for converted dataset with duplicate BAI.
affected #: 1 file
diff -r 486196344e13fcf1d6826ce714bf05cca4e6f6a7 -r 12ecc1ea2821255e81e4fb6de402108e4f30e0ed lib/galaxy/web/controllers/tracks.py
--- a/lib/galaxy/web/controllers/tracks.py
+++ b/lib/galaxy/web/controllers/tracks.py
@@ -607,8 +607,16 @@
else:
tracks_dataset_type = data_sources['data']['name']
data_provider_class = get_data_provider( name=tracks_dataset_type, original_dataset=dataset )
- converted_dataset = dataset.get_converted_dataset( trans, tracks_dataset_type )
- deps = dataset.get_converted_dataset_deps( trans, tracks_dataset_type )
+ # HACK: Use bai from bam HDA's metadata if available. This saves
+ # the client from waiting a long time to generate a duplicate
+ # bam via a converted dataset.
+ if dataset.ext == "bam" and dataset.metadata.get( "bam_index", None ) is not None:
+ converted_dataset = dataset.metadata.bam_index
+ deps = None
+ else:
+ # Default behavior.
+ converted_dataset = dataset.get_converted_dataset( trans, tracks_dataset_type )
+ deps = dataset.get_converted_dataset_deps( trans, tracks_dataset_type )
data_provider = data_provider_class( converted_dataset=converted_dataset, original_dataset=dataset, dependencies=deps )
# Get and return data from data_provider.
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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3 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/f31e7076b885/
changeset: f31e7076b885
branch: updates-for-tophat-1.3.1+
user: jjohnson
date: 2011-11-03 16:30:36
summary: Tophat - update tool wrappers for Tophat version 1.3.1+
affected #: 3 files
diff -r 0cdd7bb67d95efd4a5cfc9219a36f4f6232a243a -r f31e7076b885b0a1b36969f6c293c075ddc4943a tools/ngs_rna/tophat_color_wrapper.xml
--- a/tools/ngs_rna/tophat_color_wrapper.xml
+++ b/tools/ngs_rna/tophat_color_wrapper.xml
@@ -40,15 +40,18 @@
-g $singlePaired.sParams.max_multihits
--min-segment-intron $singlePaired.sParams.min_segment_intron
--max-segment-intron $singlePaired.sParams.max_segment_intron
+ --initial-read-mismatches=$singlePaired.sParams.initial_read_mismatches
--seg-mismatches=$singlePaired.sParams.seg_mismatches
--seg-length=$singlePaired.sParams.seg_length
--library-type=$singlePaired.sParams.library_type
## Indel search.
#if $singlePaired.sParams.indel_search.allow_indel_search == "Yes":
- --allow-indels
+ ## --allow-indels
--max-insertion-length $singlePaired.sParams.indel_search.max_insertion_length
--max-deletion-length $singlePaired.sParams.indel_search.max_deletion_length
+ #else:
+ --no-novel-indels
#end if
## Supplying junctions parameters.
@@ -99,15 +102,18 @@
-g $singlePaired.pParams.max_multihits
--min-segment-intron $singlePaired.pParams.min_segment_intron
--max-segment-intron $singlePaired.pParams.max_segment_intron
+ --initial-read-mismatches=$singlePaired.pParams.initial_read_mismatches
--seg-mismatches=$singlePaired.pParams.seg_mismatches
--seg-length=$singlePaired.pParams.seg_length
--library-type=$singlePaired.pParams.library_type
## Indel search.
#if $singlePaired.pParams.indel_search.allow_indel_search == "Yes":
- --allow-indels
+ ## --allow-indels
--max-insertion-length $singlePaired.pParams.indel_search.max_insertion_length
--max-deletion-length $singlePaired.pParams.indel_search.max_deletion_length
+ #else:
+ --no-novel-indels
#end if
## Supplying junctions parameters.
@@ -203,6 +209,7 @@
<param name="max_multihits" type="integer" value="40" label="Maximum number of alignments to be allowed" /><param name="min_segment_intron" type="integer" value="50" label="Minimum intron length that may be found during split-segment (default) search" /><param name="max_segment_intron" type="integer" value="500000" label="Maximum intron length that may be found during split-segment (default) search" />
+ <param name="initial_read_mismatches" type="integer" min="0" max="3" value="2" label="Number of mismatches allowed in the initial read mapping" /><param name="seg_mismatches" type="integer" min="0" max="3" value="2" label="Number of mismatches allowed in each segment alignment for reads mapped independently" /><param name="seg_length" type="integer" value="25" label="Minimum length of read segments" />
@@ -309,6 +316,7 @@
<param name="max_multihits" type="integer" value="40" label="Maximum number of alignments to be allowed" /><param name="min_segment_intron" type="integer" value="50" label="Minimum intron length that may be found during split-segment (default) search" /><param name="max_segment_intron" type="integer" value="500000" label="Maximum intron length that may be found during split-segment (default) search" />
+ <param name="initial_read_mismatches" type="integer" min="0" max="3" value="2" label="Number of mismatches allowed in the initial read mapping" /><param name="seg_mismatches" type="integer" min="0" max="3" value="2" label="Number of mismatches allowed in each segment alignment for reads mapped independently" /><param name="seg_length" type="integer" value="25" label="Minimum length of read segments" /><!-- Options for supplying own junctions. -->
diff -r 0cdd7bb67d95efd4a5cfc9219a36f4f6232a243a -r f31e7076b885b0a1b36969f6c293c075ddc4943a tools/ngs_rna/tophat_wrapper.py
--- a/tools/ngs_rna/tophat_wrapper.py
+++ b/tools/ngs_rna/tophat_wrapper.py
@@ -29,10 +29,11 @@
help='The maximum intron length. When searching for junctions ab initio, TopHat will ignore donor/acceptor pairs farther than this many bases apart, except when such a pair is supported by a split segment alignment of a long read.' )
parser.add_option( '-F', '--junction_filter', dest='junction_filter', help='Filter out junctions supported by too few alignments (number of reads divided by average depth of coverage)' )
parser.add_option( '-g', '--max_multihits', dest='max_multihits', help='Maximum number of alignments to be allowed' )
+ parser.add_option( '', '--initial-read-mismatches', dest='initial_read_mismatches', help='Number of mismatches allowed in the initial read mapping' )
parser.add_option( '', '--seg-mismatches', dest='seg_mismatches', help='Number of mismatches allowed in each segment alignment for reads mapped independently' )
parser.add_option( '', '--seg-length', dest='seg_length', help='Minimum length of read segments' )
parser.add_option( '', '--library-type', dest='library_type', help='TopHat will treat the reads as strand specific. Every read alignment will have an XS attribute tag. Consider supplying library type options below to select the correct RNA-seq protocol.' )
- parser.add_option( '', '--allow-indels', action="store_true", help='Allow indel search. Indel search is disabled by default.' )
+ parser.add_option( '', '--allow-indels', action="store_true", help='Allow indel search. Indel search is disabled by default.(Not used since version 1.3.0)' )
parser.add_option( '', '--max-insertion-length', dest='max_insertion_length', help='The maximum insertion length. The default is 3.' )
parser.add_option( '', '--max-deletion-length', dest='max_deletion_length', help='The maximum deletion length. The default is 3.' )
@@ -50,6 +51,7 @@
sequence, inclusive.')
parser.add_option( '', '--no-novel-juncs', action="store_true", dest='no_novel_juncs', help="Only look for junctions indicated in the \
supplied GFF file. (ignored without -G)")
+ parser.add_option( '', '--no-novel-indels', action="store_true", dest='no_novel_indels', help="Skip indel search. Indel search is enabled by default.")
# Types of search.
parser.add_option( '', '--microexon-search', action="store_true", dest='microexon_search', help='With this option, the pipeline will attempt to find alignments incident to microexons. Works only for reads 50bp or longer.')
parser.add_option( '', '--closure-search', action="store_true", dest='closure_search', help='Enables the mate pair closure-based search for junctions. Closure-based search should only be used when the expected inner distance between mates is small (<= 50bp)')
@@ -160,12 +162,16 @@
opts += ' --no-novel-juncs'
if options.library_type:
opts += ' --library-type %s' % options.library_type
- if options.allow_indels:
- # Max options do not work for Tophat v1.2.0, despite documentation to the contrary.
- opts += ' --allow-indels'
- #opts += ' --max-insertion-length %i --max-deletion-length %i' % ( int( options.max_insertion_length ), int( options.max_deletion_length ) )
+ if options.no_novel_indels:
+ opts += ' --no-novel-indels'
+ else:
+ if options.max_insertion_length:
+ opts += ' --max-insertion-length %i' % int( options.max_insertion_length )
+ if options..max_deletion_length:
+ opts += ' --max-deletion-length %i' % int( options.max_deletion_length )
+ # Max options do not work for Tophat v1.2.0, despite documentation to the contrary. (Fixed in version 1.3.1)
# need to warn user of this fact
- sys.stdout.write( "Max insertion length and max deletion length options don't work in Tophat v1.2.0\n" )
+ #sys.stdout.write( "Max insertion length and max deletion length options don't work in Tophat v1.2.0\n" )
# Search type options.
if options.coverage_search:
@@ -180,6 +186,8 @@
opts += ' --microexon-search'
if options.single_paired == 'paired':
opts += ' --mate-std-dev %s' % options.mate_std_dev
+ if options.initial_read_mismatches:
+ opts += ' --initial-read-mismatches %d' % int( options.initial_read_mismatches )
if options.seg_mismatches:
opts += ' --segment-mismatches %d' % int( options.seg_mismatches )
if options.seg_length:
diff -r 0cdd7bb67d95efd4a5cfc9219a36f4f6232a243a -r f31e7076b885b0a1b36969f6c293c075ddc4943a tools/ngs_rna/tophat_wrapper.xml
--- a/tools/ngs_rna/tophat_wrapper.xml
+++ b/tools/ngs_rna/tophat_wrapper.xml
@@ -38,15 +38,18 @@
-g $singlePaired.sParams.max_multihits
--min-segment-intron $singlePaired.sParams.min_segment_intron
--max-segment-intron $singlePaired.sParams.max_segment_intron
+ --initial-read-mismatches=$singlePaired.sParams.initial_read_mismatches
--seg-mismatches=$singlePaired.sParams.seg_mismatches
--seg-length=$singlePaired.sParams.seg_length
--library-type=$singlePaired.sParams.library_type
## Indel search.
#if $singlePaired.sParams.indel_search.allow_indel_search == "Yes":
- --allow-indels
+ ## --allow-indels
--max-insertion-length $singlePaired.sParams.indel_search.max_insertion_length
--max-deletion-length $singlePaired.sParams.indel_search.max_deletion_length
+ #else:
+ --no-novel-indels
#end if
## Supplying junctions parameters.
@@ -97,15 +100,18 @@
-g $singlePaired.pParams.max_multihits
--min-segment-intron $singlePaired.pParams.min_segment_intron
--max-segment-intron $singlePaired.pParams.max_segment_intron
+ --initial-read-mismatches=$singlePaired.pParams.initial_read_mismatches
--seg-mismatches=$singlePaired.pParams.seg_mismatches
--seg-length=$singlePaired.pParams.seg_length
--library-type=$singlePaired.pParams.library_type
## Indel search.
#if $singlePaired.pParams.indel_search.allow_indel_search == "Yes":
- --allow-indels
+ ## --allow-indels
--max-insertion-length $singlePaired.pParams.indel_search.max_insertion_length
--max-deletion-length $singlePaired.pParams.indel_search.max_deletion_length
+ #else:
+ --no-novel-indels
#end if
## Supplying junctions parameters.
@@ -201,6 +207,7 @@
<param name="max_multihits" type="integer" value="40" label="Maximum number of alignments to be allowed" /><param name="min_segment_intron" type="integer" value="50" label="Minimum intron length that may be found during split-segment (default) search" /><param name="max_segment_intron" type="integer" value="500000" label="Maximum intron length that may be found during split-segment (default) search" />
+ <param name="initial_read_mismatches" type="integer" min="0" max="3" value="2" label="Number of mismatches allowed in the initial read mapping" /><param name="seg_mismatches" type="integer" min="0" max="3" value="2" label="Number of mismatches allowed in each segment alignment for reads mapped independently" /><param name="seg_length" type="integer" value="25" label="Minimum length of read segments" />
@@ -307,6 +314,7 @@
<param name="max_multihits" type="integer" value="40" label="Maximum number of alignments to be allowed" /><param name="min_segment_intron" type="integer" value="50" label="Minimum intron length that may be found during split-segment (default) search" /><param name="max_segment_intron" type="integer" value="500000" label="Maximum intron length that may be found during split-segment (default) search" />
+ <param name="initial_read_mismatches" type="integer" min="0" max="3" value="2" label="Number of mismatches allowed in the initial read mapping" /><param name="seg_mismatches" type="integer" min="0" max="3" value="2" label="Number of mismatches allowed in each segment alignment for reads mapped independently" /><param name="seg_length" type="integer" value="25" label="Minimum length of read segments" /><!-- Options for supplying own junctions. -->
https://bitbucket.org/galaxy/galaxy-central/changeset/3b176f04a8b8/
changeset: 3b176f04a8b8
branch: updates-for-tophat-1.3.1+
user: jjohnson
date: 2011-11-03 16:40:49
summary: Tophat - Indel search should be default option
affected #: 2 files
diff -r f31e7076b885b0a1b36969f6c293c075ddc4943a -r 3b176f04a8b852a6af12e7bf017d44019874ca62 tools/ngs_rna/tophat_color_wrapper.xml
--- a/tools/ngs_rna/tophat_color_wrapper.xml
+++ b/tools/ngs_rna/tophat_color_wrapper.xml
@@ -196,8 +196,8 @@
<param name="max_intron_length" type="integer" value="500000" label="The maximum intron length" help="When searching for junctions ab initio, TopHat will ignore donor/acceptor pairs farther than this many bases apart, except when such a pair is supported by a split segment alignment of a long read." /><conditional name="indel_search"><param name="allow_indel_search" type="select" label="Allow indel search">
+ <option value="Yes">Yes</option><option value="No">No</option>
- <option value="Yes">Yes</option></param><when value="No"/><when value="Yes">
@@ -303,8 +303,8 @@
<param name="max_intron_length" type="integer" value="500000" label="The maximum intron length" help="When searching for junctions ab initio, TopHat will ignore donor/acceptor pairs farther than this many bases apart, except when such a pair is supported by a split segment alignment of a long read." /><conditional name="indel_search"><param name="allow_indel_search" type="select" label="Allow indel search">
+ <option value="Yes">Yes</option><option value="No">No</option>
- <option value="Yes">Yes</option></param><when value="No"/><when value="Yes">
diff -r f31e7076b885b0a1b36969f6c293c075ddc4943a -r 3b176f04a8b852a6af12e7bf017d44019874ca62 tools/ngs_rna/tophat_wrapper.xml
--- a/tools/ngs_rna/tophat_wrapper.xml
+++ b/tools/ngs_rna/tophat_wrapper.xml
@@ -194,8 +194,8 @@
<param name="max_intron_length" type="integer" value="500000" label="The maximum intron length" help="When searching for junctions ab initio, TopHat will ignore donor/acceptor pairs farther than this many bases apart, except when such a pair is supported by a split segment alignment of a long read." /><conditional name="indel_search"><param name="allow_indel_search" type="select" label="Allow indel search">
+ <option value="Yes">Yes</option><option value="No">No</option>
- <option value="Yes">Yes</option></param><when value="No"/><when value="Yes">
@@ -301,8 +301,8 @@
<param name="max_intron_length" type="integer" value="500000" label="The maximum intron length" help="When searching for junctions ab initio, TopHat will ignore donor/acceptor pairs farther than this many bases apart, except when such a pair is supported by a split segment alignment of a long read." /><conditional name="indel_search"><param name="allow_indel_search" type="select" label="Allow indel search">
+ <option value="Yes">Yes</option><option value="No">No</option>
- <option value="Yes">Yes</option></param><when value="No"/><when value="Yes">
https://bitbucket.org/galaxy/galaxy-central/changeset/6483b3fbf1d6/
changeset: 6483b3fbf1d6
branch: updates-for-tophat-1.3.1+
user: jjohnson
date: 2011-11-03 17:09:35
summary: Tophat - fix typo in code.
affected #: 1 file
diff -r 3b176f04a8b852a6af12e7bf017d44019874ca62 -r 6483b3fbf1d689ae02e9eff2ee8cfaa38412fcbc tools/ngs_rna/tophat_wrapper.py
--- a/tools/ngs_rna/tophat_wrapper.py
+++ b/tools/ngs_rna/tophat_wrapper.py
@@ -167,7 +167,7 @@
else:
if options.max_insertion_length:
opts += ' --max-insertion-length %i' % int( options.max_insertion_length )
- if options..max_deletion_length:
+ if options.max_deletion_length:
opts += ' --max-deletion-length %i' % int( options.max_deletion_length )
# Max options do not work for Tophat v1.2.0, despite documentation to the contrary. (Fixed in version 1.3.1)
# need to warn user of this fact
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/72cbac1ff125/
changeset: 72cbac1ff125
user: natefoo
date: 2011-11-16 19:38:24
summary: Make linking data in a library upload a job parameter so it can be checked
during job finish to ensure the linked files are not overwritten when using
outputs_to_working_directory. This special-case fix is a temporary solution
that should be removed as soon as we have a smarter way to handle "immutable
outputs."
affected #: 4 files
diff -r 537a42e5d26578413f20b369643110404502b7c3 -r 72cbac1ff125c8133f4ba4e6c2607d816dcd8e56 lib/galaxy/jobs/__init__.py
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -541,7 +541,7 @@
self.version_string = open(version_filename).read()
os.unlink(version_filename)
- if self.app.config.outputs_to_working_directory:
+ if self.app.config.outputs_to_working_directory and not self.__link_file_check():
for dataset_path in self.get_output_fnames():
try:
shutil.move( dataset_path.false_path, dataset_path.real_path )
@@ -879,6 +879,15 @@
else:
return 'anonymous@unknown'
+ def __link_file_check( self ):
+ """ outputs_to_working_directory breaks library uploads where data is
+ linked. This method is a hack that solves that problem, but is
+ specific to the upload tool and relies on an injected job param. This
+ method should be removed ASAP and replaced with some properly generic
+ and stateful way of determining link-only datasets. -nate
+ """
+ return self.tool.id == 'upload1' and self.param_dict.get( 'link_data_only', None ) == 'link_to_files'
+
class TaskWrapper(JobWrapper):
"""
Extension of JobWrapper intended for running tasks.
diff -r 537a42e5d26578413f20b369643110404502b7c3 -r 72cbac1ff125c8133f4ba4e6c2607d816dcd8e56 lib/galaxy/tools/actions/upload.py
--- a/lib/galaxy/tools/actions/upload.py
+++ b/lib/galaxy/tools/actions/upload.py
@@ -25,4 +25,4 @@
json_file_path = upload_common.create_paramfile( trans, uploaded_datasets )
data_list = [ ud.data for ud in uploaded_datasets ]
- return upload_common.create_job( trans, incoming, tool, json_file_path, data_list, return_job=True )
+ return upload_common.create_job( trans, incoming, tool, json_file_path, data_list )
diff -r 537a42e5d26578413f20b369643110404502b7c3 -r 72cbac1ff125c8133f4ba4e6c2607d816dcd8e56 lib/galaxy/tools/actions/upload_common.py
--- a/lib/galaxy/tools/actions/upload_common.py
+++ b/lib/galaxy/tools/actions/upload_common.py
@@ -294,7 +294,7 @@
json_file.write( to_json_string( json ) + '\n' )
json_file.close()
return json_file_path
-def create_job( trans, params, tool, json_file_path, data_list, folder=None, return_job=False ):
+def create_job( trans, params, tool, json_file_path, data_list, folder=None ):
"""
Create the upload job.
"""
@@ -341,10 +341,7 @@
output = odict()
for i, v in enumerate( data_list ):
output[ 'output%i' % i ] = v
- if return_job:
- return job, output
- else:
- return output
+ return job, output
def active_folders( trans, folder ):
# Stolen from galaxy.web.controllers.library_common (importing from which causes a circular issues).
# Much faster way of retrieving all active sub-folders within a given folder than the
diff -r 537a42e5d26578413f20b369643110404502b7c3 -r 72cbac1ff125c8133f4ba4e6c2607d816dcd8e56 lib/galaxy/web/controllers/library_common.py
--- a/lib/galaxy/web/controllers/library_common.py
+++ b/lib/galaxy/web/controllers/library_common.py
@@ -1045,7 +1045,12 @@
status='error' ) )
json_file_path = upload_common.create_paramfile( trans, uploaded_datasets )
data_list = [ ud.data for ud in uploaded_datasets ]
- return upload_common.create_job( trans, tool_params, tool, json_file_path, data_list, folder=library_bunch.folder )
+ job, output = upload_common.create_job( trans, tool_params, tool, json_file_path, data_list, folder=library_bunch.folder )
+ # HACK: Prevent outputs_to_working_directory from overwriting inputs when "linking"
+ job.add_parameter( 'link_data_only', to_json_string( kwd.get( 'link_data_only', 'copy_files' ) ) )
+ trans.sa_session.add( job )
+ trans.sa_session.flush()
+ return output
def make_library_uploaded_dataset( self, trans, cntrller, params, name, path, type, library_bunch, in_folder=None ):
library_bunch.replace_dataset = None # not valid for these types of upload
uploaded_dataset = util.bunch.Bunch()
https://bitbucket.org/galaxy/galaxy-central/changeset/c658f8f1e6ea/
changeset: c658f8f1e6ea
user: natefoo
date: 2011-11-16 19:53:05
summary: Bugfix for the last commit, since JobWrapper.param_dict doesn't exist after a server restart.
affected #: 1 file
diff -r 72cbac1ff125c8133f4ba4e6c2607d816dcd8e56 -r c658f8f1e6ea651c7d9f7fc2ca77512cad6beeb5 lib/galaxy/jobs/__init__.py
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -886,7 +886,9 @@
method should be removed ASAP and replaced with some properly generic
and stateful way of determining link-only datasets. -nate
"""
- return self.tool.id == 'upload1' and self.param_dict.get( 'link_data_only', None ) == 'link_to_files'
+ job = self.get_job()
+ param_dict = job.get_param_values( self.app )
+ return self.tool.id == 'upload1' and param_dict.get( 'link_data_only', None ) == 'link_to_files'
class TaskWrapper(JobWrapper):
"""
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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