1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/8092639dd35b/
changeset: 8092639dd35b
user: guru
date: 2012-01-30 18:29:39
summary: added cacao genome to manual builds
affected #: 1 file
diff -r f8cf58d19ea0bda386ef4cf85a365596a37c3e64 -r 8092639dd35b048614cfaa444273a0458b8fa284 tool-data/shared/ucsc/manual_builds.txt
--- a/tool-data/shared/ucsc/manual_builds.txt
+++ b/tool-data/shared/ucsc/manual_builds.txt
@@ -704,3 +704,4 @@
Homo_sapiens_nuHg19_mtrCRS Homo sapiens (hg19 with mtDNA replaced with rCRS) chr1=249250621,chr2=243199373,chr3=198022430,chr4=191154276,chr5=180915260,chr6=171115067,chr7=159138663,chr8=146364022,chr9=141213431,chr10=135534747,chr11=135006516,chr12=133851895,chr13=115169878,chr14=107349540,chr15=102531392,chr16=90354753,chr17=81195210,chr18=78077248,chr19=59128983,chr20=63025520,chr21=48129895,chr22=51304566,chrX=155270560,chrY=59373566,chrM=16569,chr1_gl000191_random=106433,chr1_gl000192_random=547496,chr4_ctg9_hap1=590426,chr4_gl000193_random=189789,chr4_gl000194_random=191469,chr6_apd_hap1=4622290,chr6_cox_hap2=4795371,chr6_dbb_hap3=4610396,chr6_mann_hap4=4683263,chr6_mcf_hap5=4833398,chr6_qbl_hap6=4611984,chr6_ssto_hap7=4928567,chr7_gl000195_random=182896,chr8_gl000196_random=38914,chr8_gl000197_random=37175,chr9_gl000198_random=90085,chr9_gl000199_random=169874,chr9_gl000200_random=187035,chr9_gl000201_random=36148,chr11_gl000202_random=40103,chr17_ctg5_hap1=1680828,chr17_gl000203_random=37498,chr17_gl000204_random=81310,chr17_gl000205_random=174588,chr17_gl000206_random=41001,chr18_gl000207_random=4262,chr19_gl000208_random=92689,chr19_gl000209_random=159169,chr21_gl000210_random=27682,chrUn_gl000211=166566,chrUn_gl000212=186858,chrUn_gl000213=164239,chrUn_gl000214=137718,chrUn_gl000215=172545,chrUn_gl000216=172294,chrUn_gl000217=172149,chrUn_gl000218=161147,chrUn_gl000219=179198,chrUn_gl000220=161802,chrUn_gl000221=155397,chrUn_gl000222=186861,chrUn_gl000223=180455,chrUn_gl000224=179693,chrUn_gl000225=211173,chrUn_gl000226=15008,chrUn_gl000227=128374,chrUn_gl000228=129120,chrUn_gl000229=19913,chrUn_gl000230=43691,chrUn_gl000231=27386,chrUn_gl000232=40652,chrUn_gl000233=45941,chrUn_gl000234=40531,chrUn_gl000235=34474,chrUn_gl000236=41934,chrUn_gl000237=45867,chrUn_gl000238=39939,chrUn_gl000239=33824,chrUn_gl000240=41933,chrUn_gl000241=42152,chrUn_gl000242=43523,chrUn_gl000243=43341,chrUn_gl000244=39929,chrUn_gl000245=36651,chrUn_gl000246=38154,chrUn_gl000247=36422,chrUn_gl000248=39786,chrUn_gl000249=38502
Arabidopsis_thaliana_TAIR10 Arabidopsis thaliana TAIR10 (Arabidopsis_thaliana_TAIR10) chr1=30427671,chr2=19698289,chr3=23459830,chr4=18585056,chr5=26975502,chrM=366924,chrC=154478
dp4 D. pseudoobscura (dp4)
+Tcacao_1.0 Theobroma cacao Dec 2010 (CIRAD/Theobroma cacao Belizian Criollo) Tc01=31268538,Tc02=27754001,Tc03=25475297,Tc04=23504306,Tc05=25651337,Tc06=15484475,Tc07=14169093,Tc08=11535834,Tc09=28459094,Tc10=15164258,Tc00=108886888
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/f8cf58d19ea0/
changeset: f8cf58d19ea0
user: greg
date: 2012-01-30 18:17:56
summary: When storing tool panel section information for installed repository tools, make sure tool section id, name and version values are an empty string rather than None.
affected #: 3 files
diff -r 016630d4fb0e9b17b41781613951ae8c89353ca2 -r f8cf58d19ea0bda386ef4cf85a365596a37c3e64 lib/galaxy/tools/__init__.py
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -192,7 +192,19 @@
else:
# The tool_panel_section was introduced late, so set it's value if its missing in the metadata.
if section:
- tool_panel_section = dict( id=section.id, version=section.version, name=section.name )
+ if section.id is None:
+ section_id = ''
+ else:
+ section_id = section.id
+ if section.version is None:
+ section_version = ''
+ else:
+ section_version = section.version
+ if section.name is None:
+ section_name = ''
+ else:
+ section_name = section.name
+ tool_panel_section = dict( id=section_id, version=section_version, name=section_name )
update_needed = True
else:
tool_panel_section = dict( id='', version='', name='' )
diff -r 016630d4fb0e9b17b41781613951ae8c89353ca2 -r f8cf58d19ea0bda386ef4cf85a365596a37c3e64 lib/galaxy/util/shed_util.py
--- a/lib/galaxy/util/shed_util.py
+++ b/lib/galaxy/util/shed_util.py
@@ -166,6 +166,9 @@
datatypes_config = None
# Keep track of the section in the tool panel in which this repository's tools will be contained.
if tool_section_dict:
+ for k, v in tool_section_dict.items():
+ if v is None:
+ tool_section_dict[ k ] = ''
metadata_dict[ 'tool_panel_section' ] = tool_section_dict
else:
metadata_dict[ 'tool_panel_section' ] = dict( id='', version='', name='' )
@@ -604,9 +607,18 @@
distribution but are now in the main Galaxy tool shed.
"""
if tool_section:
- section_id = tool_section.id
- section_version = tool_section.version
- section_name = tool_section.name
+ if tool_section.id is None:
+ section_id = ''
+ else:
+ section_id = tool_section.id
+ if tool_section.version is None:
+ section_version = ''
+ else:
+ section_version = tool_section.version
+ if tool_section.name is None:
+ section_name = ''
+ else:
+ section_name = tool_section.name
else:
section_id = ''
section_version = ''
diff -r 016630d4fb0e9b17b41781613951ae8c89353ca2 -r f8cf58d19ea0bda386ef4cf85a365596a37c3e64 templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako
--- a/templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako
+++ b/templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako
@@ -81,11 +81,11 @@
<div class="toolParamHelp" style="clear: both;">
* The repository record's deleted column in the tool_shed_repository database table will be set to True.
</div>
+ <div class="toolParamHelp" style="clear: both;">
+ * The repository record's uninstalled column in the tool_shed_repository database table will be set to True.
+ </div>
%if repository.dist_to_shed:
<div class="toolParamHelp" style="clear: both;">
- * The repository record's uninstalled column in the tool_shed_repository database table will be set to True.
- </div>
- <div class="toolParamHelp" style="clear: both;">
* All records associated with this repository will be eliminated from the tool_id_guid_map database table.
</div>
%endif
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/cb458aca542e/
changeset: cb458aca542e
user: natefoo
date: 2012-01-27 21:35:57
summary: Ensure that the history export dataset is created when the job is created.
affected #: 1 file
diff -r 56bdee21dc785c5f941510537978d71c4e9799c5 -r cb458aca542e67c41d1139d0356a6d09d2b12443 lib/galaxy/tools/actions/history_imp_exp.py
--- a/lib/galaxy/tools/actions/history_imp_exp.py
+++ b/lib/galaxy/tools/actions/history_imp_exp.py
@@ -88,8 +88,8 @@
archive_dataset = trans.app.model.Dataset()
trans.sa_session.add( archive_dataset )
-
trans.sa_session.flush() #ensure job.id and archive_dataset.id are available
+ trans.app.object_store.create( archive_dataset ) # set the object store id, create dataset (if applicable)
#
# Setup job and job wrapper.
@@ -123,4 +123,4 @@
trans.app.job_queue.put( job.id, tool )
trans.log_event( "Added export history job to the job queue, id: %s" % str(job.id), tool_id=job.tool_id )
- return job, odict()
\ No newline at end of file
+ return job, odict()
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/56bdee21dc78/
changeset: 56bdee21dc78
user: natefoo
date: 2012-01-27 17:12:56
summary: Fix unit tests on Python 2.5 (can't load s3_multipart_upload.py).
affected #: 1 file
diff -r f9ca1c23ae7d2614c002257365d67a3eae98228e -r 56bdee21dc785c5f941510537978d71c4e9799c5 lib/galaxy/objectstore/s3_multipart_upload.py
--- a/lib/galaxy/objectstore/s3_multipart_upload.py
+++ b/lib/galaxy/objectstore/s3_multipart_upload.py
@@ -4,13 +4,19 @@
This parallelizes the task over available cores using multiprocessing.
Code mostly taken form CloudBioLinux.
"""
+from __future__ import with_statement
+
import os
+import sys
import glob
import subprocess
import contextlib
import functools
-import multiprocessing
-from multiprocessing.pool import IMapIterator
+
+if sys.version_info >= (2, 6):
+ # this is just to prevent unit tests from failing
+ import multiprocessing
+ from multiprocessing.pool import IMapIterator
from galaxy import eggs
eggs.require('boto')
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/7d0ea2879bc9/
changeset: 7d0ea2879bc9
user: dan
date: 2012-01-26 17:16:30
summary: Update tool test for GATK Print Reads.
affected #: 1 file
diff -r 8a440d85e13b83697220a2da4bb6f84d58027b60 -r 7d0ea2879bc9746e149e32381ea709a9aea33ff8 tools/gatk/print_reads.xml
--- a/tools/gatk/print_reads.xml
+++ b/tools/gatk/print_reads.xml
@@ -373,7 +373,7 @@
<param name="sample_file_repeat" value="0" /><param name="sample_name_repeat" value="0" /><param name="gatk_param_type_selector" value="basic" />
- <output name="output_bam" file="gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam" ftype="bam" sort="True"/>
+ <output name="output_bam" file="gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam" ftype="bam" compare="contains"/><output name="output_log" file="gatk/gatk_print_reads/gatk_print_reads_out_1.log.contains" compare="contains" /></test></tests>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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