2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/501940d5c857/ Changeset: 501940d5c857 User: davebgx Date: 2014-04-01 17:04:32 Summary: Migrate 46 tools from the distribution to the tool shed: gatk, gops, regional variation. Affected #: 218 files diff -r 615d5040d90b23a3476ff2e8c388c338fb031c09 -r 501940d5c8573f8cff8a11f66a35010a322de37d lib/tool_shed/galaxy_install/migrate/versions/0010_tools.py --- /dev/null +++ b/lib/tool_shed/galaxy_install/migrate/versions/0010_tools.py @@ -0,0 +1,110 @@ +""" +The following tools have been eliminated from the distribution: + +1. Analyze Covariates +2. Base Coverage of all intervals +3. Perform Best-subsets Regression +4. Cluster +5. Complement intervals of a dataset +6. Compute q-values based on multiple simultaneous tests p-values +7. Concatenate two datasets into one dataset +8. Count Covariates on BAM files +9. Coverage of a set of intervals on second set of intervals +10. Depth of Coverage on BAM files +11. Feature coverage +12. Fetch closest non-overlapping feature for every interval +13. Get flanks - returns flanking region/s for every gene +14. Estimate Indel Rates for 3-way alignments +15. Fetch Indels from pairwise alignments +16. Indel Realigner - perform local realignment +17. Intersect the intervals of two datasets +18. Join the intervals of two datasets side-by-side +19. Perform Linear Regression +20. Perform Logistic Regression with vif +21. Mask CpG/non-CpG sites from MAF file +22. Merge the overlapping intervals of a dataset +23. Extract Orthologous Microsatellites from pair-wise alignments +24. Estimate microsatellite mutability by specified attributes +25. Compute partial R square +26. Print Reads from BAM files +27. Filter nucleotides based on quality scores +28. Compute RCVE +29. Realigner Target Creator for use in local realignment +30. Estimate substitution rates for non-coding regions +31. Fetch substitutions from pairwise alignments +32. Subtract the intervals of two datasets +33. Subtract Whole Dataset from another dataset +34. Table Recalibration on BAM files +35. Arithmetic Operations on tables +36. Unified Genotyper SNP and indel caller +37. Variant Annotator +38. Apply Variant Recalibration +39. Combine Variants +40. Eval Variants +41. Variant Filtration on VCF files +42. Variant Recalibrator +43. Select Variants from VCF files +44. Validate Variants +45. Assign weighted-average of the values of features overlapping an interval +46. Make windows + +The tools are now available in the repositories respectively: + +1. analyze_covariates +2. basecoverage +3. best_regression_subsets +4. cluster +5. complement +6. compute_q_values +7. concat +8. count_covariates +9. coverage +10. depth_of_coverage +11. featurecounter +12. flanking_features +13. get_flanks +14. getindelrates_3way +15. getindels_2way +16. indel_realigner +17. intersect +18. join +19. linear_regression +20. logistic_regression_vif +21. maf_cpg_filter +22. merge +23. microsats_alignment_level +24. microsats_mutability +25. partialr_square +26. print_reads +27. quality_filter +28. rcve +29. realigner_target_creator +30. substitution_rates +31. substitutions +32. subtract +33. subtract_query +34. table_recalibration +35. tables_arithmetic_operations +36. unified_genotyper +37. variant_annotator +38. variant_apply_recalibration +39. variant_combine +40. variant_eval +41. variant_filtration +42. variant_recalibrator +43. variant_select +44. variants_validate +45. weightedaverage +46. windowsplitter + +from the main Galaxy tool shed at http://toolshed.g2.bx.psu.edu +and will be installed into your local Galaxy instance at the +location discussed above by running the following command. + +""" + +def upgrade( migrate_engine ): + print __doc__ + +def downgrade( migrate_engine ): + pass diff -r 615d5040d90b23a3476ff2e8c388c338fb031c09 -r 501940d5c8573f8cff8a11f66a35010a322de37d scripts/migrate_tools/0010_tools.sh --- /dev/null +++ b/scripts/migrate_tools/0010_tools.sh @@ -0,0 +1,4 @@ +#!/bin/sh + +cd `dirname $0`/../.. +python ./scripts/migrate_tools/migrate_tools.py 0010_tools.xml $@ diff -r 615d5040d90b23a3476ff2e8c388c338fb031c09 -r 501940d5c8573f8cff8a11f66a35010a322de37d scripts/migrate_tools/0010_tools.xml --- /dev/null +++ b/scripts/migrate_tools/0010_tools.xml @@ -0,0 +1,141 @@ +<?xml version="1.0"?> +<toolshed name="toolshed.g2.bx.psu.edu"> + <repository owner="devteam" name="analyze_covariates" changeset_revision="be6bede22459" description="Analyze Covariates"> + <tool id="gatk_analyze_covariates" version="0.0.5" file="gatk/analyze_covariates.xml" /> + </repository> + <repository owner="devteam" name="basecoverage" changeset_revision="1e6a9e97fa41" description="Base Coverage of all intervals"> + <tool id="gops_basecoverage_1" version="0.0.1" file="new_operations/basecoverage.xml" /> + </repository> + <repository owner="devteam" name="best_regression_subsets" changeset_revision="54c7a01a2cc7" description="Perform Best-subsets Regression"> + <tool id="BestSubsetsRegression1" version="0.0.1" file="regVariation/best_regression_subsets.xml" /> + </repository> + <repository owner="devteam" name="cluster" changeset_revision="d5677eecbad4" description="Cluster"> + <tool id="gops_cluster_1" version="0.0.1" file="new_operations/cluster.xml" /> + </repository> + <repository owner="devteam" name="complement" changeset_revision="d958d5a0d1e8" description="Complement intervals of a dataset"> + <tool id="gops_complement_1" version="0.0.1" file="new_operations/complement.xml" /> + </repository> + <repository owner="devteam" name="compute_q_values" changeset_revision="63abfc350814" description="Compute q-values based on multiple simultaneous tests p-values"> + <tool id="compute_q_values" version="1.0.1" file="regVariation/compute_q_values.xml" /> + </repository> + <repository owner="devteam" name="concat" changeset_revision="8aa939ace6ba" description="Concatenate two datasets into one dataset"> + <tool id="gops_concat_1" version="1.0.1" file="new_operations/concat.xml" /> + </repository> + <repository owner="devteam" name="count_covariates" changeset_revision="14e304b70425" description="Count Covariates on BAM files"> + <tool id="gatk_count_covariates" version="0.0.5" file="gatk/count_covariates.xml" /> + </repository> + <repository owner="devteam" name="coverage" changeset_revision="1e864693a1c0" description="Coverage of a set of intervals on second set of intervals"> + <tool id="gops_coverage_1" version="0.0.1" file="new_operations/coverage.xml" /> + </repository> + <repository owner="devteam" name="depth_of_coverage" changeset_revision="c3f08370fc82" description="Depth of Coverage on BAM files"> + <tool id="gatk_depth_of_coverage" version="0.0.2" file="gatk/depth_of_coverage.xml" /> + </repository> + <repository owner="devteam" name="featurecounter" changeset_revision="ac6218e2b686" description="Feature coverage"> + <tool id="featureCoverage1" version="2.0.0" file="regVariation/featureCounter.xml" /> + </repository> + <repository owner="devteam" name="flanking_features" changeset_revision="90100b587723" description="Fetch closest non-overlapping feature for every interval"> + <tool id="flanking_features_1" version="4.0.1" file="new_operations/flanking_features.xml" /> + </repository> + <repository owner="devteam" name="get_flanks" changeset_revision="a72f0decd7b3" description="Get flanks - returns flanking region/s for every gene"> + <tool id="get_flanks1" version="0.0.1" file="new_operations/get_flanks.xml" /> + </repository> + <repository owner="devteam" name="getindelrates_3way" changeset_revision="d427e5acb9ee" description="Estimate Indel Rates for 3-way alignments"> + <tool id="indelRates_3way" version="1.0.0" file="regVariation/getIndelRates_3way.xml" /> + </repository> + <repository owner="devteam" name="getindels_2way" changeset_revision="91655316fcf0" description="Fetch Indels from pairwise alignments"> + <tool id="getIndels_2way" version="0.0.1" file="regVariation/getIndels_2way.xml" /> + </repository> + <repository owner="devteam" name="indel_realigner" changeset_revision="bb0beda6cf83" description="Indel Realigner - perform local realignment"> + <tool id="gatk_indel_realigner" version="0.0.6" file="gatk/indel_realigner.xml" /> + </repository> + <repository owner="devteam" name="intersect" changeset_revision="5b3c6135a982" description="Intersect the intervals of two datasets"> + <tool id="gops_intersect_1" version="0.0.1" file="new_operations/intersect.xml" /> + </repository> + <repository owner="devteam" name="join" changeset_revision="e56b47dce68a" description="Join the intervals of two datasets side-by-side"> + <tool id="gops_join_1" version="0.0.1" file="new_operations/join.xml" /> + </repository> + <repository owner="devteam" name="linear_regression" changeset_revision="cf431604ec3e" description="Perform Linear Regression"> + <tool id="LinearRegression1" version="1.0.1" file="regVariation/linear_regression.xml" /> + </repository> + <repository owner="devteam" name="logistic_regression_vif" changeset_revision="bd196d7c1ca9" description="Perform Logistic Regression with vif"> + <tool id="LogisticRegression" version="1.0.1" file="regVariation/logistic_regression_vif.xml" /> + </repository> + <repository owner="devteam" name="maf_cpg_filter" changeset_revision="7f2a12cb047d" description="Mask CpG/non-CpG sites from MAF file"> + <tool id="cpgFilter" version="1.0.0" file="regVariation/maf_cpg_filter.xml" /> + </repository> + <repository owner="devteam" name="merge" changeset_revision="b488a1fa07f6" description="Merge the overlapping intervals of a dataset"> + <tool id="gops_merge_1" version="0.0.1" file="new_operations/merge.xml" /> + </repository> + <repository owner="devteam" name="microsats_alignment_level" changeset_revision="d4368a5a3fc7" description="Extract Orthologous Microsatellites from pair-wise alignments"> + <tool id="microsats_align1" version="0.0.1" file="regVariation/microsats_alignment_level.xml" /> + </repository> + <repository owner="devteam" name="microsats_mutability" changeset_revision="4aa1ee5d8510" description="Estimate microsatellite mutability by specified attributes"> + <tool id="microsats_mutability1" version="1.1.0" file="regVariation/microsats_mutability.xml" /> + </repository> + <repository owner="devteam" name="partialr_square" changeset_revision="88ef41de020d" description="Compute partial R square"> + <tool id="partialRsq" version="1.0.0" file="regVariation/partialR_square.xml" /> + </repository> + <repository owner="devteam" name="print_reads" changeset_revision="e768f4851646" description="Print Reads from BAM files"> + <tool id="gatk_print_reads" version="0.0.1" file="gatk/print_reads.xml" /> + </repository> + <repository owner="devteam" name="quality_filter" changeset_revision="8d65bbc52dfe" description="Filter nucleotides based on quality scores"> + <tool id="qualityFilter" version="1.0.1" file="regVariation/quality_filter.xml" /> + </repository> + <repository owner="devteam" name="rcve" changeset_revision="7740956d197b" description="Compute RCVE"> + <tool id="rcve1" version="1.0.0" file="regVariation/rcve.xml" /> + </repository> + <repository owner="devteam" name="realigner_target_creator" changeset_revision="b83a853a3156" description="Realigner Target Creator for use in local realignment"> + <tool id="gatk_realigner_target_creator" version="0.0.4" file="gatk/realigner_target_creator.xml" /> + </repository> + <repository owner="devteam" name="substitution_rates" changeset_revision="d1b35bcdaacc" description="Estimate substitution rates for non-coding regions"> + <tool id="subRate1" version="1.0.0" file="regVariation/substitution_rates.xml" /> + </repository> + <repository owner="devteam" name="substitutions" changeset_revision="c54f5d0bbb58" description="Fetch substitutions from pairwise alignments"> + <tool id="substitutions1" version="1.0.0" file="regVariation/substitutions.xml" /> + </repository> + <repository owner="devteam" name="subtract" changeset_revision="5bc2dacbe729" description="Subtract the intervals of two datasets"> + <tool id="gops_subtract_1" version="0.0.1" file="new_operations/subtract.xml" /> + </repository> + <repository owner="devteam" name="subtract_query" changeset_revision="5f6ebef89722" description="Subtract Whole Dataset from another dataset"> + <tool id="subtract_query1" version="0.1" file="new_operations/subtract_query.xml" /> + </repository> + <repository owner="devteam" name="table_recalibration" changeset_revision="53dd1bfced54" description="Table Recalibration on BAM files"> + <tool id="gatk_table_recalibration" version="0.0.5" file="gatk/table_recalibration.xml" /> + </repository> + <repository owner="devteam" name="tables_arithmetic_operations" changeset_revision="82fa5062d611" description="Arithmetic Operations on tables"> + <tool id="tables_arithmetic_operations" version="1.0.0" file="new_operations/tables_arithmetic_operations.xml" /> + </repository> + <repository owner="devteam" name="unified_genotyper" changeset_revision="66dd4d4c1743" description="Unified Genotyper SNP and indel caller"> + <tool id="gatk_unified_genotyper" version="0.0.6" file="gatk/unified_genotyper.xml" /> + </repository> + <repository owner="devteam" name="variant_annotator" changeset_revision="ae9d0a543e9b" description="Variant Annotator"> + <tool id="gatk_variant_annotator" version="0.0.5" file="gatk/variant_annotator.xml" /> + </repository> + <repository owner="devteam" name="variant_apply_recalibration" changeset_revision="350a4d0d1678" description="Apply Variant Recalibration"> + <tool id="gatk_variant_apply_recalibration" version="0.0.4" file="gatk/variant_apply_recalibration.xml" /> + </repository> + <repository owner="devteam" name="variant_combine" changeset_revision="1a6e16391727" description="Combine Variants"> + <tool id="gatk_variant_combine" version="0.0.4" file="gatk/variant_combine.xml" /> + </repository> + <repository owner="devteam" name="variant_eval" changeset_revision="fbca1c0956d2" description="Eval Variants"> + <tool id="gatk_variant_eval" version="0.0.8" file="gatk/variant_eval.xml" /> + </repository> + <repository owner="devteam" name="variant_filtration" changeset_revision="da6e2503c62d" description="Variant Filtration on VCF files"> + <tool id="gatk_variant_filtration" version="0.0.5" file="gatk/variant_filtration.xml" /> + </repository> + <repository owner="devteam" name="variant_recalibrator" changeset_revision="cb7cf57397a7" description="Variant Recalibrator"> + <tool id="gatk_variant_recalibrator" version="0.0.4" file="gatk/variant_recalibrator.xml" /> + </repository> + <repository owner="devteam" name="variant_select" changeset_revision="135e8721ffc5" description="Select Variants from VCF files"> + <tool id="gatk_variant_select" version="0.0.2" file="gatk/variant_select.xml" /> + </repository> + <repository owner="devteam" name="variants_validate" changeset_revision="7e1ecaa64370" description="Validate Variants"> + <tool id="gatk_validate_variants" version="0.0.4" file="gatk/variants_validate.xml" /> + </repository> + <repository owner="devteam" name="weightedaverage" changeset_revision="9b7b4009f2c0" description="Assign weighted-average of the values of features overlapping an interval"> + <tool id="wtavg" version="1.0.0" file="regVariation/WeightedAverage.xml" /> + </repository> + <repository owner="devteam" name="windowsplitter" changeset_revision="e5490ea33640" description="Make windows"> + <tool id="winSplitter" version="0.0.1" file="regVariation/windowSplitter.xml" /> + </repository> +</toolshed> \ No newline at end of file This diff is so big that we needed to truncate the remainder. https://bitbucket.org/galaxy/galaxy-central/commits/7755367b0698/ Changeset: 7755367b0698 User: davebgx Date: 2014-04-01 17:05:31 Summary: Remove migrated tools from main's tool conf. Affected #: 1 file diff -r 501940d5c8573f8cff8a11f66a35010a322de37d -r 7755367b06981f35fbc6911935513439c7e5445f tool_conf.xml.main --- a/tool_conf.xml.main +++ b/tool_conf.xml.main @@ -72,7 +72,6 @@ <section id="group" name="Join, Subtract and Group"><tool file="filters/joiner.xml" /><tool file="filters/compare.xml" /> - <tool file="new_operations/subtract_query.xml" /><tool file="stats/grouping.xml" /></section><section id="features" name="Extract Features"> @@ -99,17 +98,6 @@ <tool file="stats/aggregate_binned_scores_in_intervals.xml" /></section><section id="bxops" name="Operate on Genomic Intervals"> - <tool file="new_operations/intersect.xml" /> - <tool file="new_operations/subtract.xml" /> - <tool file="new_operations/merge.xml" /> - <tool file="new_operations/concat.xml" /> - <tool file="new_operations/basecoverage.xml" /> - <tool file="new_operations/coverage.xml" /> - <tool file="new_operations/complement.xml" /> - <tool file="new_operations/cluster.xml" id="cluster" /> - <tool file="new_operations/join.xml" /> - <tool file="new_operations/get_flanks.xml" /> - <tool file="new_operations/flanking_features.xml" /><tool file="annotation_profiler/annotation_profiler.xml" /></section><section id="stats" name="Statistics"> @@ -128,26 +116,6 @@ <tool file="maf/vcf_to_maf_customtrack.xml" /><tool file="mutation/visualize.xml" /></section> - <section id="regVar" name="Regional Variation"> - <tool file="regVariation/windowSplitter.xml" /> - <tool file="regVariation/featureCounter.xml" /> - <tool file="regVariation/WeightedAverage.xml" /> - <tool file="regVariation/quality_filter.xml" /> - <tool file="regVariation/maf_cpg_filter.xml" /> - <tool file="regVariation/getIndels_2way.xml" /> - <tool file="regVariation/getIndelRates_3way.xml" /> - <tool file="regVariation/substitutions.xml" /> - <tool file="regVariation/substitution_rates.xml" /> - <tool file="regVariation/microsats_alignment_level.xml" /> - <tool file="regVariation/microsats_mutability.xml" /> - </section> - <section id="multReg" name="Multiple regression"> - <tool file="regVariation/linear_regression.xml" /> - <tool file="regVariation/logistic_regression_vif.xml" /> - <tool file="regVariation/best_regression_subsets.xml" /> - <tool file="regVariation/rcve.xml" /> - <tool file="regVariation/partialR_square.xml" /> - </section><section id="multVar" name="Multivariate Analysis"><tool file="multivariate_stats/pca.xml" /><tool file="multivariate_stats/cca.xml" /> @@ -191,37 +159,4 @@ </section><section id="samtools" name="NGS: SAM Tools"></section> - <section id="gatk" name="NGS: GATK Tools (beta)"> - <label id="gatk_bam_utilities" text="Alignment Utilities" /> - <tool file="gatk/depth_of_coverage.xml" /> - <tool file="gatk/print_reads.xml" /> - - <label id="gatk_realignment" text="Realignment" /> - <tool file="gatk/realigner_target_creator.xml" /> - <tool file="gatk/indel_realigner.xml" /> - - <label id="gatk_recalibration" text="Base Recalibration" /> - <tool file="gatk/count_covariates.xml" /> - <tool file="gatk/table_recalibration.xml" /> - <tool file="gatk/analyze_covariates.xml" /> - - <label id="gatk_genotyping" text="Genotyping" /> - <tool file="gatk/unified_genotyper.xml" /> - - <label id="gatk_annotation" text="Annotation" /> - <tool file="gatk/variant_annotator.xml" /> - - <label id="gatk_filtration" text="Filtration" /> - <tool file="gatk/variant_filtration.xml" /> - <tool file="gatk/variant_select.xml" /> - - <label id="gatk_variant_quality_score_recalibration" text="Variant Quality Score Recalibration" /> - <tool file="gatk/variant_recalibrator.xml" /> - <tool file="gatk/variant_apply_recalibration.xml" /> - - <label id="gatk_variant_utilities" text="Variant Utilities" /> - <tool file="gatk/variants_validate.xml" /> - <tool file="gatk/variant_eval.xml" /> - <tool file="gatk/variant_combine.xml" /> - </section></toolbox> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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