diff --git a/.coveragerc b/.coveragerc new file mode 100644 index 00000000000..26050442d35 --- /dev/null +++ b/.coveragerc @@ -0,0 +1,3 @@ +[run] +branch = True +include = lib/galaxy/* diff --git a/.hgignore b/.hgignore index b5acfbd1abf..ffb0c07f9c3 100644 --- a/.hgignore +++ b/.hgignore @@ -60,7 +60,7 @@ shed_tool_data_table_conf.xml job_conf.xml data_manager_conf.xml shed_data_manager_conf.xml -visualizations_conf.xml +config/visualizations/*.xml static/welcome.html.* static/welcome.html @@ -82,6 +82,9 @@ tool-data/genome/* # Test output run_functional_tests.html test/tool_shed/tmp/* +.coverage +htmlcov +run_unit_tests.html # Project files *.kpf diff --git a/.hgtags b/.hgtags index 4b94f4612d6..843ac397c4d 100644 --- a/.hgtags +++ b/.hgtags @@ -2,3 +2,4 @@ a4113cc1cb5eaa68091c9a73375f00555b66dd11 release_2013.01.13 1c717491139269651bb59687563da9410b84c65d release_2013.02.08 75f09617abaadbc8cc732bb8ee519decaeb56ea7 release_2013.04.01 2cc8d10988e03257dc7b97f8bb332c7df745d1dd security_2013.04.08 +524f246ca85395082719ae7a6ff72260d7ad5612 release_2013.06.03 diff --git a/README.txt b/README.txt index 051f8f25e6f..e222728000c 100644 --- a/README.txt +++ b/README.txt @@ -7,7 +7,7 @@ website above. HOW TO START ============ -Galaxy requires Python 2.5, 2.6 or 2.7. To check your python version, run: +Galaxy requires Python 2.6 or 2.7. To check your python version, run: % python -V Python 2.7.3 diff --git a/buildbot_setup.sh b/buildbot_setup.sh index d4917e8c8e2..8eb2f73a372 100644 --- a/buildbot_setup.sh +++ b/buildbot_setup.sh @@ -65,6 +65,7 @@ LINKS=" " SAMPLES=" +tool_conf.xml.sample datatypes_conf.xml.sample universe_wsgi.ini.sample tool_data_table_conf.xml.sample diff --git a/config/visualizations/circster.xml.sample b/config/visualizations/circster.xml.sample new file mode 100644 index 00000000000..cf15d7b66b1 --- /dev/null +++ b/config/visualizations/circster.xml.sample @@ -0,0 +1,26 @@ + + + + + + HistoryDatasetAssociation + data.Data + dataset_id + hda_ldda + + + LibraryDatasetDatasetAssociation + data.Data + dataset_id + hda_ldda + + + + id + dataset_id + hda_ldda + dbkey + + + _top + diff --git a/config/visualizations/phyloviz.xml.sample b/config/visualizations/phyloviz.xml.sample new file mode 100644 index 00000000000..a2a879ef800 --- /dev/null +++ b/config/visualizations/phyloviz.xml.sample @@ -0,0 +1,18 @@ + + + + + + HistoryDatasetAssociation + data.Newick + data.Nexus + dataset_id + + + + dataset_id + tree_index + + + _top + diff --git a/config/visualizations/scatterplot.xml.sample b/config/visualizations/scatterplot.xml.sample new file mode 100644 index 00000000000..3ab023cb5bc --- /dev/null +++ b/config/visualizations/scatterplot.xml.sample @@ -0,0 +1,15 @@ + + + + + + HistoryDatasetAssociation + tabular.Tabular + dataset_id + + + + dataset_id + + + diff --git a/config/visualizations/sweepster.xml.sample b/config/visualizations/sweepster.xml.sample new file mode 100644 index 00000000000..9dd19178756 --- /dev/null +++ b/config/visualizations/sweepster.xml.sample @@ -0,0 +1,25 @@ + + + + + + HistoryDatasetAssociation + data.Data + dataset_id + hda_ldda + + + LibraryDatasetDatasetAssociation + data.Data + dataset_id + hda_ldda + + + + visualization + dataset_id + hda_ldda + + + _top + diff --git a/config/visualizations/trackster.xml.sample b/config/visualizations/trackster.xml.sample new file mode 100644 index 00000000000..813fa97fbb2 --- /dev/null +++ b/config/visualizations/trackster.xml.sample @@ -0,0 +1,29 @@ + + + + + + + HistoryDatasetAssociation + data.Data + dataset_id + hda_ldda + dbkey + + + LibraryDatasetDatasetAssociation + data.Data + dataset_id + hda_ldda + + + + id + dataset_id + genome_region + dbkey + + tracks + + _top + diff --git a/config/visualizations/visualization.dtd b/config/visualizations/visualization.dtd new file mode 100644 index 00000000000..75722998007 --- /dev/null +++ b/config/visualizations/visualization.dtd @@ -0,0 +1,132 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/eggs.ini b/eggs.ini index 872ee3c0caa..26e0907b9ae 100644 --- a/eggs.ini +++ b/eggs.ini @@ -19,7 +19,7 @@ MarkupSafe = 0.12 mercurial = 2.2.3 MySQL_python = 1.2.3c1 numpy = 1.6.0 -pbs_python = 4.1.0 +pbs_python = 4.3.5 psycopg2 = 2.0.13 pycrypto = 2.5 pysam = 0.4.2 diff --git a/job_conf.xml.sample_advanced b/job_conf.xml.sample_advanced index 6a9a6c6e3e0..396b82b9c98 100644 --- a/job_conf.xml.sample_advanced +++ b/job_conf.xml.sample_advanced @@ -54,7 +54,15 @@ foo.example.org 24:00:00 - + + + 8 + + + ucsc_tools + bedtools + bedtools genomecov -bg -split -ibam $input -g $chromInfo diff --git a/lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml b/lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml index c0648f61481..68432c62aff 100644 --- a/lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml +++ b/lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml @@ -1,5 +1,9 @@