galaxy-commits November 2015

galaxy-commits@lists.galaxyproject.org

2 participants
160 discussions

[galaxyproject/galaxy] d20677: Fix Remote User failures due to apache null header...
by GitHub 03 Nov '15

03 Nov '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: d20677bb640de726574ae7f3e8d86739a8702cb5 https://github.com/galaxyproject/galaxy/commit/d20677bb640de726574ae7f3e8d8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-29 (Thu, 29 Oct 2015) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- Fix Remote User failures due to apache null headers. Commit: 3b8edf6aebfb10d1b52b57701eb4cb07558e9c9e https://github.com/galaxyproject/galaxy/commit/3b8edf6aebfb10d1b52b57701eb4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-03 (Tue, 03 Nov 2015) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- Merge pull request #1003 from dannon/remote_user_apache_fix [15.10] Fix Remote User failures due to apache null headers. Compare: https://github.com/galaxyproject/galaxy/compare/3b133d0d9206...3b8edf6aebfb

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[galaxyproject/usegalaxy-playbook] 58fab7: Add Dan to reserved node users
by GitHub 03 Nov '15

03 Nov '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 58fab7545f5b61a23f61dbd0788379f04ba9bbf3 https://github.com/galaxyproject/usegalaxy-playbook/commit/58fab7545f5b61a2… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-03 (Tue, 03 Nov 2015) Changed paths: M files/galaxy/common/dynamic_rules/multi_dynamic_walltime.py M files/galaxy/common/dynamic_rules/reserved.py Log Message: ----------- Add Dan to reserved node users

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[galaxyproject/usegalaxy-playbook] f2cff9: Updated slide rotation.
by GitHub 02 Nov '15

02 Nov '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: f2cff9c9f1700c23e2280bde7b1b0578386df261 https://github.com/galaxyproject/usegalaxy-playbook/commit/f2cff9c9f1700c23… Author: tnabtaf <clements(a)galaxyproject.org> Date: 2015-11-02 (Mon, 02 Nov 2015) Changed paths: A files/galaxy/common/static/welcome_img/GCC2016TrVote.png A files/galaxy/common/static/welcome_img/MississippiGalaxy.png M templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- Updated slide rotation.

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[galaxyproject/infrastructure-playbook] 01cd5c: Update common roles.
by GitHub 02 Nov '15

02 Nov '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 01cd5c650d6be4c6f75934de976e157826d74279 https://github.com/galaxyproject/infrastructure-playbook/commit/01cd5c650d6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-20 (Tue, 20 Oct 2015) Changed paths: M common_roles Log Message: ----------- Update common roles. Commit: cf8a746f22e3596590a675729df9575f541cf504 https://github.com/galaxyproject/infrastructure-playbook/commit/cf8a746f22e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-02 (Mon, 02 Nov 2015) Changed paths: M common_roles A galaxyenv/group_vars/baseenv.yml M galaxyenv/host_vars/orval.galaxyproject.org.yml M galaxyenv/secret_group_vars/all.yml M galaxyenv/secret_host_vars/n2.galaxyproject.org.yml M galaxyenv/secret_host_vars/orval.galaxyproject.org.yml Log Message: ----------- depot stuff I forgot to commit + add Dannon to sites@orval Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/577c599fa6…

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[galaxyproject/galaxy] 8b630d: Update galaxy.jobs.runners.util from pulsar.manage...
by GitHub 01 Nov '15

01 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8b630d6d6c121659c1f93f9b51df8ccc8871b83a https://github.com/galaxyproject/galaxy/commit/8b630d6d6c121659c1f93f9b51df… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-29 (Thu, 29 Oct 2015) Changed paths: A lib/galaxy/jobs/runners/util/drmaa/__init__.py A lib/galaxy/jobs/runners/util/retry.py A lib/galaxy/jobs/runners/util/sudo.py Log Message: ----------- Update galaxy.jobs.runners.util from pulsar.managers.util Commit: c46c7e082768ecd1c11fe20d3639ee5ada0ab61b https://github.com/galaxyproject/galaxy/commit/c46c7e082768ecd1c11fe20d3639… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-29 (Thu, 29 Oct 2015) Changed paths: A .ci/flake8_blacklist.txt A .ci/flake8_wrapper.sh M .gitignore A .travis.yml A CODE_OF_CONDUCT.md M CONTRIBUTING.md A CONTRIBUTORS.md M LICENSE.txt M README.rst M client/GruntFile.js A client/README.md R client/README.txt M client/bower.json M client/galaxy/scripts/base.js M client/galaxy/scripts/galaxy-app-base.js M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/galaxy.masthead.js M client/galaxy/scripts/galaxy.menu.js M client/galaxy/scripts/galaxy.panels.js R client/galaxy/scripts/galaxy.workflow_editor.canvas.js R client/galaxy/scripts/galaxy.workflows.js M client/galaxy/scripts/libs/backbone/backbone.js M client/galaxy/scripts/libs/d3.js M client/galaxy/scripts/libs/farbtastic.js M client/galaxy/scripts/libs/handlebars.runtime.js A client/galaxy/scripts/libs/jquery.sparklines.js M client/galaxy/scripts/libs/jquery/jqtouch.js M client/galaxy/scripts/libs/jquery/jquery.dynatree.js M client/galaxy/scripts/libs/jquery/jquery.js R client/galaxy/scripts/libs/lunr.js M client/galaxy/scripts/libs/raven.js M client/galaxy/scripts/libs/require.js M client/galaxy/scripts/libs/tracekit.js A client/galaxy/scripts/mvc/app/app-analysis.js A client/galaxy/scripts/mvc/app/app-view.js M 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client/toolshed/scripts/mvc/groups/group-list-view.js A client/toolshed/scripts/mvc/groups/group-listrow-view.js A client/toolshed/scripts/mvc/groups/group-model.js A client/toolshed/scripts/toolshed.groups.js A config/auth_conf.xml.sample M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced M config/object_store_conf.xml.sample M config/plugins/interactive_environments/common/templates/ie.mako M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/ipython/config/ipython.xml M config/plugins/interactive_environments/ipython/templates/ipython.mako M config/plugins/interactive_environments/ipython/templates/notebook.ipynb A config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample A config/plugins/interactive_environments/rstudio/config/rstudio.xml A config/plugins/interactive_environments/rstudio/static/js/crypto/base64.js A 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tools/data_source/genbank.xml M tools/data_source/import.xml M tools/data_source/metabolicmine.xml M tools/data_source/microbial_import.xml M tools/data_source/modmine.xml M tools/data_source/mousemine.xml M tools/data_source/ratmine.xml R tools/data_source/ucsc_archaea.xml R tools/data_source/ucsc_filter.py R tools/data_source/ucsc_proxy.py R tools/data_source/ucsc_proxy.xml M tools/data_source/ucsc_tablebrowser.xml M tools/data_source/ucsc_tablebrowser_archaea.xml M tools/data_source/ucsc_tablebrowser_test.xml R tools/data_source/ucsc_testproxy.xml M tools/data_source/upload.py M tools/data_source/upload.xml M tools/data_source/worm_modencode.xml M tools/data_source/wormbase_test.xml M tools/data_source/yeastmine.xml M tools/data_source/zebrafishmine.xml M tools/evolution/codingSnps.xml M tools/evolution/codingSnps_filter.py M tools/extract/extract_genomic_dna.py M tools/extract/extract_genomic_dna.xml M tools/extract/liftOver_wrapper.xml M tools/filters/CreateInterval.xml M tools/filters/axt_to_concat_fasta.xml M tools/filters/axt_to_fasta.xml M tools/filters/axt_to_lav.xml M tools/filters/axt_to_lav_code.py M tools/filters/catWrapper.xml M tools/filters/changeCase.xml M tools/filters/commWrapper.xml M tools/filters/condense_characters.xml M tools/filters/convert_characters.xml M tools/filters/cutWrapper.xml M tools/filters/fileGrep.xml M tools/filters/fixedValueColumn.xml M tools/filters/gff/extract_GFF_Features.xml M tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/gff/gff_filter_by_feature_count.xml M tools/filters/gff/gtf_filter_by_attribute_values_list.xml M tools/filters/gtf2bedgraph.xml M tools/filters/headWrapper.xml M tools/filters/joiner2.xml M tools/filters/lav_to_bed.py M tools/filters/lav_to_bed.xml M tools/filters/lav_to_bed_code.py M tools/filters/pasteWrapper.xml M tools/filters/remove_beginning.xml M tools/filters/tailWrapper.xml M tools/filters/ucsc_gene_bed_to_exon_bed.xml M tools/filters/ucsc_gene_bed_to_intron_bed.xml M tools/filters/ucsc_gene_table_to_intervals.xml M tools/filters/uniq.py M tools/filters/uniq.xml M tools/filters/wc_gnu.xml M tools/filters/wiggle_to_simple.xml M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_exporter.xml M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_file_browser_dev.xml M tools/genomespace/genomespace_file_browser_prod.xml M tools/genomespace/genomespace_file_browser_test.xml M tools/genomespace/genomespace_importer.py M tools/genomespace/genomespace_importer.xml M tools/maf/genebed_maf_to_fasta.xml M tools/maf/interval2maf.xml M tools/maf/interval2maf_pairwise.xml M tools/maf/interval_maf_to_merged_fasta.xml M tools/maf/maf_by_block_number.xml M tools/maf/maf_filter.py M tools/maf/maf_filter.xml M tools/maf/maf_limit_size.xml M tools/maf/maf_limit_to_species.xml M tools/maf/maf_reverse_complement.py M tools/maf/maf_reverse_complement.xml M tools/maf/maf_split_by_species.xml M tools/maf/maf_stats.xml M tools/maf/maf_thread_for_species.xml M tools/maf/maf_to_bed.xml M tools/maf/maf_to_fasta.xml M tools/maf/maf_to_interval.xml M tools/maf/vcf_to_maf_customtrack.xml M tools/next_gen_conversion/solid2fastq.xml M tools/phenotype_association/master2gd_snp.xml M tools/phenotype_association/master2pg.xml M tools/phenotype_association/pagetag.py M tools/phenotype_association/senatag.py M tools/plotting/bar_chart.xml M tools/plotting/boxplot.xml M tools/solid_tools/maq_cs_wrapper_code.py M tools/sr_mapping/bfast_wrapper.xml M tools/sr_mapping/fastq_statistics.xml M tools/sr_mapping/mosaik.xml M tools/sr_mapping/srma_wrapper.xml M tools/stats/filtering.xml M tools/stats/grouping.py M tools/stats/gsummary.py M tools/stats/gsummary.xml M tools/stats/gsummary.xml.groups M tools/validation/fix_errors.xml M tools/visualization/LAJ.xml M tools/visualization/LAJ_code.py A tox.ini Log Message: ----------- Merge branch 'dev' into pulsar-client-update Commit: 1e2863dd1c7db1020ceba0a0cffb77c771c7e788 https://github.com/galaxyproject/galaxy/commit/1e2863dd1c7db1020ceba0a0cffb… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-29 (Thu, 29 Oct 2015) Changed paths: M lib/galaxy/tools/lint.py A lib/galaxy/tools/lint_util.py M lib/galaxy/tools/linters/command.py M lib/galaxy/tools/linters/help.py M lib/galaxy/tools/linters/inputs.py M lib/galaxy/tools/linters/outputs.py A lib/galaxy/tools/linters/stdio.py M lib/galaxy/tools/linters/tests.py M lib/galaxy/tools/linters/top_level.py A lib/galaxy/tools/linters/xml_order.py A lib/galaxy/tools/linters/xsd.py A lib/galaxy/tools/linters/xsd_util.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/util/xml_macros.py Log Message: ----------- Merge linting and tool loader changes from Planemo Commit: 36eb1142c4c9bae876185d79f5d7229bf08c0b8d https://github.com/galaxyproject/galaxy/commit/36eb1142c4c9bae876185d79f5d7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-29 (Thu, 29 Oct 2015) Changed paths: M lib/galaxy/tools/linters/tests.py Log Message: ----------- PEP-8 fix for linters Commit: a9d79b34e65c914e569bc1713ee82dd8877c2d6f https://github.com/galaxyproject/galaxy/commit/a9d79b34e65c914e569bc1713ee8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-29 (Thu, 29 Oct 2015) Changed paths: M lib/galaxy/tools/deps/commands.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/tools/deps/dockerfiles.py M lib/galaxy/tools/deps/resolvers/modules.py Log Message: ----------- Merge Planemo and Galaxy tools.deps changes (and a PEP-8 fix) Commit: 12fdd3f9d5758f8957d57591c4bbd777bd1d5723 https://github.com/galaxyproject/galaxy/commit/12fdd3f9d5758f8957d57591c4bb… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-29 (Thu, 29 Oct 2015) Changed paths: M lib/galaxy/jobs/metrics/instrumenters/collectl.py Log Message: ----------- Correct a mistakenly reformatted comment. Inline isn't possible because hanging an inline violates E113 (although PEP-8 does not explicitly say it's not allowed, but it does say "An inline comment is a comment on the same line as a statement"), so convert the comments to block. Commit: a1726d205d167a8eb30de427d56b81fdd7529397 https://github.com/galaxyproject/galaxy/commit/a1726d205d167a8eb30de427d56b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-29 (Thu, 29 Oct 2015) Changed paths: M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py Log Message: ----------- Python 3-ify the object store (from Pulsar, for Planemo) Commit: aefc35ae0309d7a9a4418cdf479821e07e154fbd https://github.com/galaxyproject/galaxy/commit/aefc35ae0309d7a9a4418cdf4798… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-30 (Fri, 30 Oct 2015) Changed paths: R lib/galaxy/tools/linters/xsd.py R lib/galaxy/tools/linters/xsd_util.py Log Message: ----------- Remove old XSD linting code. Commit: 45e3257f04b3a3858f0a4f6298076d1f91acc712 https://github.com/galaxyproject/galaxy/commit/45e3257f04b3a3858f0a4f629807… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-30 (Fri, 30 Oct 2015) Changed paths: M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py Log Message: ----------- Restore changes to tool shed package resolver. Commit: 4e9e9a17d1dfd322ffbcb2ecebc184fe5538ec7e https://github.com/galaxyproject/galaxy/commit/4e9e9a17d1dfd322ffbcb2ecebc1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-01 (Sun, 01 Nov 2015) Changed paths: M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py R lib/galaxy/tools/linters/xsd.py R lib/galaxy/tools/linters/xsd_util.py Log Message: ----------- Merge pull request #1 from jmchilton/pulsar-planemo-lib-update Remove old XSD linting code. Commit: 99319f59c88715e74290267d93018d1f172512ca https://github.com/galaxyproject/galaxy/commit/99319f59c88715e74290267d9301… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-01 (Sun, 01 Nov 2015) Changed paths: M lib/galaxy/jobs/metrics/instrumenters/collectl.py A lib/galaxy/jobs/runners/util/drmaa/__init__.py A lib/galaxy/jobs/runners/util/retry.py A lib/galaxy/jobs/runners/util/sudo.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py M lib/galaxy/tools/deps/commands.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/tools/deps/dockerfiles.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py M lib/galaxy/tools/lint.py A lib/galaxy/tools/lint_util.py M lib/galaxy/tools/linters/command.py M lib/galaxy/tools/linters/help.py M lib/galaxy/tools/linters/inputs.py M lib/galaxy/tools/linters/outputs.py A lib/galaxy/tools/linters/stdio.py M lib/galaxy/tools/linters/tests.py M lib/galaxy/tools/linters/top_level.py A lib/galaxy/tools/linters/xml_order.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/util/xml_macros.py Log Message: ----------- Merge pull request #1005 from natefoo/pulsar-planemo-lib-update Merge changes to common modules shared between Galaxy, Planemo, and Pulsar. Compare: https://github.com/galaxyproject/galaxy/compare/cbc8c44f60b4...99319f59c887

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[galaxyproject/galaxy] 602d05: Log TS installation commands with repository name
by GitHub 01 Nov '15

01 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 602d05408465bb69e2594d95c5a0d479bc7f5ce1 https://github.com/galaxyproject/galaxy/commit/602d05408465bb69e2594d95c5a0… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-10-29 (Thu, 29 Oct 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Log TS installation commands with repository name Fixes #436 Commit: 7813148d9a09198d1d00d4326403adf0aa1f2250 https://github.com/galaxyproject/galaxy/commit/7813148d9a09198d1d00d4326403… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-10-30 (Fri, 30 Oct 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Fix review comments Commit: cbc8c44f60b45c8cefb0c34fa9abc9c5aa067af9 https://github.com/galaxyproject/galaxy/commit/cbc8c44f60b45c8cefb0c34fa9ab… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-01 (Sun, 01 Nov 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge pull request #1008 from erasche/installation_logging Log TS installation commands with repository name Compare: https://github.com/galaxyproject/galaxy/compare/f406cdefc79e...cbc8c44f60b4

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[galaxyproject/galaxy] 9c2a07: Add run_framework_tests.html to .gitignore .
by GitHub 01 Nov '15

01 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9c2a07d4242110642da7ca7f28eca772e8342acb https://github.com/galaxyproject/galaxy/commit/9c2a07d4242110642da7ca7f28ec… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-10-26 (Mon, 26 Oct 2015) Changed paths: M .gitignore Log Message: ----------- Add run_framework_tests.html to .gitignore . Commit: 3c7082c64a31fa8a0296d5655039ed772d4de3b0 https://github.com/galaxyproject/galaxy/commit/3c7082c64a31fa8a0296d5655039… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-10-26 (Mon, 26 Oct 2015) Changed paths: M doc/source/lib/galaxy.auth.providers.rst M doc/source/lib/galaxy.datatypes.rst A doc/source/lib/galaxy.dependencies.rst M doc/source/lib/galaxy.eggs.rst M doc/source/lib/galaxy.jobs.runners.rst M doc/source/lib/galaxy.rst M doc/source/lib/galaxy.tools.deps.resolvers.rst M doc/source/lib/galaxy.web.framework.middleware.rst M doc/source/lib/galaxy.webapps.galaxy.controllers.rst M doc/source/lib/galaxy.webapps.reports.controllers.rst M doc/source/lib/galaxy.webapps.rst M doc/source/lib/galaxy.webapps.tool_shed.api.rst M doc/source/lib/modules.rst R doc/source/lib/pkg_resources.rst Log Message: ----------- Fix doc/source/lib using "sphinx-apidoc -M -f -o doc/source/lib/ lib/" Commit: 69cda4869051edce338e3e585345a500015b80ac https://github.com/galaxyproject/galaxy/commit/69cda4869051edce338e3e585345… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-10-26 (Mon, 26 Oct 2015) Changed paths: M .ci/flake8_blacklist.txt M lib/pulsar/client/transport/curl.py M scripts/tools/maf/check_loc_file.py M tools/data_source/data_source.py M tools/evolution/add_scores.py M tools/extract/extract_genomic_dna.py M tools/extract/liftOver_wrapper.py M tools/filters/axt_to_concat_fasta.py M tools/filters/axt_to_fasta.py M tools/filters/axt_to_lav.py M tools/filters/catWrapper.py M tools/filters/gff/extract_GFF_Features.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/sort_gtf.py M tools/filters/gff_to_bed_converter.py M tools/filters/lav_to_bed.py M tools/filters/secure_hash_message_digest.py M tools/filters/wiggle_to_simple.py M tools/genomespace/genomespace_exporter.py M tools/maf/interval2maf.py M tools/maf/interval2maf.xml M tools/maf/interval_maf_to_merged_fasta.py M tools/maf/maf_by_block_number.py M tools/maf/maf_filter.py M tools/maf/maf_limit_size.py M tools/maf/maf_limit_to_species.py M tools/maf/maf_reverse_complement.py M tools/maf/maf_split_by_species.py M tools/maf/maf_stats.py M tools/maf/maf_thread_for_species.py M tools/maf/maf_to_bed.py M tools/maf/maf_to_bed_code.py M tools/maf/maf_to_fasta_concat.py M tools/maf/maf_to_fasta_multiple_sets.py M tools/maf/maf_to_interval.py M tools/maf/vcf_to_maf_customtrack.py M tools/next_gen_conversion/fastq_conversions.py M tools/next_gen_conversion/fastq_gen_conv.py M tools/next_gen_conversion/solid2fastq.py M tools/next_gen_conversion/solid_to_fastq.py M tools/ngs_simulation/ngs_simulation.py M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py Log Message: ----------- Remove remaining references to galaxy.eggs . flake8 some files in tools/ . Commit: f406cdefc79e6ecf7801b7da0dd98dad9dc43955 https://github.com/galaxyproject/galaxy/commit/f406cdefc79e6ecf7801b7da0dd9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-01 (Sun, 01 Nov 2015) Changed paths: M .ci/flake8_blacklist.txt M .gitignore M doc/source/lib/galaxy.auth.providers.rst M doc/source/lib/galaxy.datatypes.rst A doc/source/lib/galaxy.dependencies.rst M doc/source/lib/galaxy.eggs.rst M doc/source/lib/galaxy.jobs.runners.rst M doc/source/lib/galaxy.rst M doc/source/lib/galaxy.tools.deps.resolvers.rst M doc/source/lib/galaxy.web.framework.middleware.rst M doc/source/lib/galaxy.webapps.galaxy.controllers.rst M doc/source/lib/galaxy.webapps.reports.controllers.rst M doc/source/lib/galaxy.webapps.rst M doc/source/lib/galaxy.webapps.tool_shed.api.rst M doc/source/lib/modules.rst R doc/source/lib/pkg_resources.rst M lib/pulsar/client/transport/curl.py M scripts/tools/maf/check_loc_file.py M tools/data_source/data_source.py M tools/evolution/add_scores.py M tools/extract/extract_genomic_dna.py M tools/extract/liftOver_wrapper.py M tools/filters/axt_to_concat_fasta.py M tools/filters/axt_to_fasta.py M tools/filters/axt_to_lav.py M tools/filters/catWrapper.py M tools/filters/gff/extract_GFF_Features.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/sort_gtf.py M tools/filters/gff_to_bed_converter.py M tools/filters/lav_to_bed.py M tools/filters/secure_hash_message_digest.py M tools/filters/wiggle_to_simple.py M tools/genomespace/genomespace_exporter.py M tools/maf/interval2maf.py M tools/maf/interval2maf.xml M tools/maf/interval_maf_to_merged_fasta.py M tools/maf/maf_by_block_number.py M tools/maf/maf_filter.py M tools/maf/maf_limit_size.py M tools/maf/maf_limit_to_species.py M tools/maf/maf_reverse_complement.py M tools/maf/maf_split_by_species.py M tools/maf/maf_stats.py M tools/maf/maf_thread_for_species.py M tools/maf/maf_to_bed.py M tools/maf/maf_to_bed_code.py M tools/maf/maf_to_fasta_concat.py M tools/maf/maf_to_fasta_multiple_sets.py M tools/maf/maf_to_interval.py M tools/maf/vcf_to_maf_customtrack.py M tools/next_gen_conversion/fastq_conversions.py M tools/next_gen_conversion/fastq_gen_conv.py M tools/next_gen_conversion/solid2fastq.py M tools/next_gen_conversion/solid_to_fastq.py M tools/ngs_simulation/ngs_simulation.py M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py Log Message: ----------- Merge pull request #990 from nsoranzo/post_eggs_smash Remove remaining references to galaxy.eggs . flake8 some tools. Compare: https://github.com/galaxyproject/galaxy/compare/d9d746675a60...f406cdefc79e

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[galaxyproject/galaxy] bd95d7: Updates to default welcome page.
by GitHub 01 Nov '15

01 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bd95d7672d0cf9f164abd9bcb43485c946150fa7 https://github.com/galaxyproject/galaxy/commit/bd95d7672d0cf9f164abd9bcb434… Author: James Taylor <james(a)jamestaylor.org> Date: 2015-11-01 (Sun, 01 Nov 2015) Changed paths: M static/welcome.html.sample Log Message: ----------- Updates to default welcome page. Reference CONTRIBUTORS.md, update institution references, update to HTML5, use some standard classes for formatting, include links for configuring and installling tools. Commit: 12b6d43c81c2d1dadd24248ea329b662465633fb https://github.com/galaxyproject/galaxy/commit/12b6d43c81c2d1dadd24248ea329… Author: James Taylor <james(a)jamestaylor.org> Date: 2015-11-01 (Sun, 01 Nov 2015) Changed paths: M client/galaxy/style/less/base.less M static/style/blue/base.css M static/welcome.html.sample Log Message: ----------- Change a.btn style, fix welcome link targets. "a" elements styled with .btn will have no underline by default. Commit: 2d60665ab503878731a4aacd8bd9873fc938281c https://github.com/galaxyproject/galaxy/commit/2d60665ab503878731a4aacd8bd9… Author: James Taylor <james(a)jamestaylor.org> Date: 2015-11-01 (Sun, 01 Nov 2015) Changed paths: M static/welcome.html.sample Log Message: ----------- Fix link target in welcome Commit: d9d746675a6072701197b2b3123b7eb51c3618f3 https://github.com/galaxyproject/galaxy/commit/d9d746675a6072701197b2b3123b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-01 (Sun, 01 Nov 2015) Changed paths: M client/galaxy/style/less/base.less M static/style/blue/base.css M static/welcome.html.sample Log Message: ----------- Merge pull request #1013 from jxtx/fix-default-welcome-references Updates to default welcome page. Compare: https://github.com/galaxyproject/galaxy/compare/6b0898c32785...d9d746675a60

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[galaxyproject/galaxy] 4cbeba: Show masthead if login is required, add login page...
by GitHub 01 Nov '15

01 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4cbeba4d601d16755c334c713df44370c0553600 https://github.com/galaxyproject/galaxy/commit/4cbeba4d601d16755c334c713df4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-10-21 (Wed, 21 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-analysis.js A client/galaxy/scripts/mvc/app/app-login.js M client/galaxy/scripts/mvc/app/app-view.js M lib/galaxy/managers/configuration.py M static/maps/mvc/app/app-analysis.js.map A static/maps/mvc/app/app-login.js.map M static/maps/mvc/app/app-view.js.map M static/scripts/mvc/app/app-analysis.js A static/scripts/mvc/app/app-login.js M static/scripts/mvc/app/app-view.js Log Message: ----------- Show masthead if login is required, add login page to front end Style fix Commit: 66d3289b383e34093bf14c4dc3e696c9b66b6f48 https://github.com/galaxyproject/galaxy/commit/66d3289b383e34093bf14c4dc3e6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-10-21 (Wed, 21 Oct 2015) Changed paths: M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/mvc/app/app-analysis.js M client/galaxy/scripts/mvc/history/history-panel.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/library/library-model.js M client/galaxy/scripts/mvc/list/list-panel.js M client/galaxy/style/less/library.less M client/galaxy/style/less/list-item.less M lib/galaxy/objectstore/s3.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/galaxy.library.js.map M static/maps/mvc/app/app-analysis.js.map M static/maps/mvc/history/history-panel.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-librarylist-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/maps/mvc/library/library-model.js.map M static/maps/mvc/list/list-panel.js.map M static/scripts/galaxy.library.js M static/scripts/mvc/app/app-analysis.js M static/scripts/mvc/history/history-panel.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/library/library-model.js M static/scripts/mvc/list/list-panel.js M static/style/blue/base.css M static/style/blue/library.css M templates/webapps/galaxy/root/index.mako M tools/filters/cutWrapper.xml Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into fix_require_login_003 Conflicts: static/maps/mvc/app/app-analysis.js.map static/scripts/mvc/app/app-analysis.js Commit: 27bde1bb1de8bf0fbd873b7dc8db215235b2126e https://github.com/galaxyproject/galaxy/commit/27bde1bb1de8bf0fbd873b7dc8db… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-10-28 (Wed, 28 Oct 2015) Changed paths: M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/libs/jquery/jquery.dynatree.js M client/galaxy/scripts/mvc/app/app-analysis.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/grid/grid-model.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/tools.js M client/galaxy/scripts/mvc/tools/tools-form-base.js M client/galaxy/scripts/reports_webapp/run_stats.js M client/galaxy/scripts/utils/deferred.js M create_db.sh R dist-eggs.ini M doc/source/index.rst A doc/source/project/issues.rst R eggs.ini M lib/galaxy/__init__.py M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py M lib/galaxy/datatypes/converters/bgzip.py M lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py M lib/galaxy/datatypes/converters/interval_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/interval_to_fli.py M lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py M lib/galaxy/datatypes/converters/maf_to_fasta_converter.py M lib/galaxy/datatypes/converters/maf_to_interval_converter.py M lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py M lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py M lib/galaxy/datatypes/coverage.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/dataproviders/dataset.py M lib/galaxy/datatypes/display_applications/util.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/metadata.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/util/gff_util.py A lib/galaxy/dependencies/__init__.py A lib/galaxy/dependencies/conditional-requirements.txt A lib/galaxy/dependencies/dev-requirements.txt A lib/galaxy/dependencies/requirements.txt M lib/galaxy/eggs/__init__.py R lib/galaxy/eggs/dist.py R lib/galaxy/eggs/scramble.py M lib/galaxy/exceptions/__init__.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/pbs.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/managers/base.py M lib/galaxy/managers/citations.py M lib/galaxy/managers/configuration.py M lib/galaxy/managers/histories.py M 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lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/data_manager.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library.py M lib/galaxy/webapps/galaxy/controllers/library_admin.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/request_type.py M lib/galaxy/webapps/galaxy/controllers/requests.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py M lib/galaxy/webapps/galaxy/controllers/requests_common.py M lib/galaxy/webapps/galaxy/controllers/tool_runner.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/userskeys.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/reports/controllers/home.py M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/reports/controllers/query.py M lib/galaxy/webapps/reports/controllers/sample_tracking.py M lib/galaxy/webapps/reports/controllers/system.py M lib/galaxy/webapps/reports/controllers/users.py M lib/galaxy/webapps/reports/controllers/workflows.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/api/repository_revisions.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/controllers/hg.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/controllers/repository_review.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/webapps/tool_shed/model/mapping.py M lib/galaxy/webapps/tool_shed/model/migrate/check.py M lib/galaxy/webapps/tool_shed/search/repo_search.py M lib/galaxy/webapps/tool_shed/search/tool_search.py M lib/galaxy/webapps/tool_shed/security/__init__.py M lib/galaxy/webapps/util.py M lib/galaxy/workflow/render.py M lib/galaxy_ext/metadata/set_metadata.py R lib/pkg_resources.py M lib/pulsar/client/config_util.py M lib/pulsar/client/transport/poster.py M lib/pulsar/client/transport/requests.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/installed_repository_manager.py M lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py M lib/tool_shed/galaxy_install/migrate/check.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/galaxy_install/update_repository_manager.py M lib/tool_shed/grids/admin_grids.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/repository_review_grids.py M lib/tool_shed/managers/groups.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/repository_registry.py M lib/tool_shed/repository_types/metadata.py M lib/tool_shed/repository_types/repository_suite_definition.py M lib/tool_shed/repository_types/tool_dependency_definition.py M lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py M lib/tool_shed/scripts/check_repositories_for_functional_tests.py M lib/tool_shed/scripts/check_s3_for_empty_tool_dependency_installation_paths.py M lib/tool_shed/scripts/check_tool_dependency_definition_repositories.py M lib/tool_shed/scripts/deprecate_repositories_without_metadata.py M lib/tool_shed/tools/tool_version_manager.py M lib/tool_shed/util/basic_util.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/hg_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/review_util.py M lib/tool_shed/util/search_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_dependency_util.py M manage_db.sh M manage_tools.sh M requirements.txt M run.sh M run_reports.sh M run_tests.sh M run_tool_shed.sh M scripts/api/common.py A scripts/binary_compatibility.py R scripts/check_eggs.py M scripts/check_galaxy.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/pgcleanup.py M scripts/common_startup.sh M scripts/data_libraries/build_lucene_index.py M scripts/data_libraries/build_whoosh_index.py M scripts/db_shell.py R scripts/dist-scramble.py M scripts/drmaa_external_killer.py M scripts/drmaa_external_runner.py R scripts/egg_packager_template.py R scripts/fetch_eggs.py M scripts/functional_tests.py R scripts/make_egg_packager.py M scripts/manage_db.py M scripts/manage_tools.py M scripts/nosetests.py M scripts/others/incorrect_gops_jobs.py M scripts/others/incorrect_gops_join_jobs.py M scripts/paster.py R scripts/scramble.py R scripts/scramble/lib/scramble_lib.py R scripts/scramble/patches/Cheetah/SetupConfig.py R scripts/scramble/patches/MySQL_python/site.cfg R scripts/scramble/patches/PasteScript/setup.py R scripts/scramble/patches/python_daemon/setup.py R scripts/scramble/scripts/DRMAA_python-macosx.py R scripts/scramble/scripts/DRMAA_python-solaris.py R scripts/scramble/scripts/DRMAA_python.py R scripts/scramble/scripts/MySQL_python-solaris.py R scripts/scramble/scripts/MySQL_python.py R scripts/scramble/scripts/PyRods.py R scripts/scramble/scripts/bx_python-solaris.py R scripts/scramble/scripts/generic.py R scripts/scramble/scripts/pbs_python.py R scripts/scramble/scripts/psycopg2-linux.py R scripts/scramble/scripts/psycopg2-macosx.py R scripts/scramble/scripts/psycopg2-solaris.py R scripts/scramble/scripts/psycopg2.py R scripts/scramble/scripts/pysam-solaris.py R scripts/scramble/scripts/pysqlite.py M scripts/summarize_timings.py R scripts/test_dist_egg.py M scripts/tool_shed/build_ts_whoosh_index.py M scripts/tool_shed/migrate_tools_to_repositories.py M scripts/tools/maf/check_loc_file.py M scripts/transfer.py M scripts/update_shed_config_path.py M set_metadata.sh M static/maps/galaxy.library.js.map M static/maps/libs/jquery/jquery.dynatree.js.map M static/maps/mvc/app/app-analysis.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/grid/grid-view.js.map M static/maps/mvc/tools.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/maps/reports_webapp/run_stats.js.map M static/maps/utils/deferred.js.map M static/scripts/galaxy.library.js M static/scripts/libs/jquery/jquery.dynatree.js M static/scripts/mvc/app/app-analysis.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/tools.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/reports_webapp/run_stats.js M static/scripts/utils/deferred.js R static/style/blue/dynatree_skin/cbChecked.gif R static/style/blue/dynatree_skin/cbChecked_hover.gif R static/style/blue/dynatree_skin/cbIntermediate.gif R static/style/blue/dynatree_skin/cbIntermediate_hover.gif R static/style/blue/dynatree_skin/cbUnchecked.gif R static/style/blue/dynatree_skin/cbUnchecked_hover.gif R static/style/blue/dynatree_skin/customDoc1.gif R static/style/blue/dynatree_skin/customFolder1.gif A static/style/blue/dynatree_skin/icons-rtl.gif A static/style/blue/dynatree_skin/icons.gif A static/style/blue/dynatree_skin/loading.gif R static/style/blue/dynatree_skin/ltD_ne.gif R static/style/blue/dynatree_skin/ltD_nes.gif R static/style/blue/dynatree_skin/ltDoc.gif R static/style/blue/dynatree_skin/ltError.gif R static/style/blue/dynatree_skin/ltFld.gif R static/style/blue/dynatree_skin/ltFld_o.gif R static/style/blue/dynatree_skin/ltL_.gif R static/style/blue/dynatree_skin/ltL_ne.gif R static/style/blue/dynatree_skin/ltL_nes.gif R static/style/blue/dynatree_skin/ltL_ns.gif R static/style/blue/dynatree_skin/ltM_ne.gif R static/style/blue/dynatree_skin/ltM_nes.gif R static/style/blue/dynatree_skin/ltP_ne.gif R static/style/blue/dynatree_skin/ltP_nes.gif R static/style/blue/dynatree_skin/ltWait.gif R static/style/blue/dynatree_skin/rbChecked.gif R static/style/blue/dynatree_skin/rbChecked_hover.gif R static/style/blue/dynatree_skin/rbIntermediate.gif R static/style/blue/dynatree_skin/rbIntermediate_hover.gif R static/style/blue/dynatree_skin/rbUnchecked.gif R static/style/blue/dynatree_skin/rbUnchecked_hover.gif M static/style/blue/dynatree_skin/ui.dynatree.css A static/style/blue/dynatree_skin/vline-rtl.gif A static/style/blue/dynatree_skin/vline.gif M templates/admin/requests/select_datasets_to_transfer.mako M templates/admin/tool_shed_repository/common.mako M templates/base/base_panels.mako M templates/webapps/tool_shed/repository/common.mako M test/base/instrument.py M test/base/interactor.py M test/base/nose_util.py M test/base/test_db_util.py M test/base/twilltestcase.py M test/docker/base/Dockerfile M test/docker/base/ansible_vars.yml M test/functional/test_metadata_editing.py M test/install_and_test_tool_shed_repositories/base/test_db_util.py M test/install_and_test_tool_shed_repositories/base/twilltestcase.py M test/install_and_test_tool_shed_repositories/base/util.py M test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py M test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py M test/manual/workflows_scaling.py M test/tool_shed/base/test_db_util.py M test/tool_shed/base/twilltestcase.py M test/tool_shed/functional_tests.py M test/unit/jobs/test_runner_local.py M test/unit/managers/base.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HistoryManager.py M test/unit/managers/test_UserManager.py M test/unit/tools/test_execution.py M test/unit/workflows/test_modules.py M tools/genomespace/genomespace_importer.xml M tox.ini Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into fix_require_login_003 Conflicts: static/maps/mvc/app/app-analysis.js.map static/scripts/mvc/app/app-analysis.js Commit: f5a57b5f6ebf414fecfa2a6c325a5596fe11dd2b https://github.com/galaxyproject/galaxy/commit/f5a57b5f6ebf414fecfa2a6c325a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-10-29 (Thu, 29 Oct 2015) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- Undo 965 for dev Commit: bd383cc518f2f4335f3be97d50f33d66a081887f https://github.com/galaxyproject/galaxy/commit/bd383cc518f2f4335f3be97d50f3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-10-29 (Thu, 29 Oct 2015) Changed paths: M static/maps/mvc/app/app-analysis.js.map M static/scripts/mvc/app/app-analysis.js Log Message: ----------- Repack scripts Commit: 6b0898c3278504f3bcac4493f7724b8e4862613e https://github.com/galaxyproject/galaxy/commit/6b0898c3278504f3bcac4493f772… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-01 (Sun, 01 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-analysis.js A client/galaxy/scripts/mvc/app/app-login.js M client/galaxy/scripts/mvc/app/app-view.js M lib/galaxy/managers/configuration.py M lib/galaxy/web/framework/webapp.py M static/maps/galaxy.library.js.map M static/maps/mvc/app/app-analysis.js.map A static/maps/mvc/app/app-login.js.map M static/maps/mvc/app/app-view.js.map M static/scripts/galaxy.library.js M static/scripts/mvc/app/app-analysis.js A static/scripts/mvc/app/app-login.js M static/scripts/mvc/app/app-view.js Log Message: ----------- Merge pull request #968 from guerler/fix_require_login_003 Show masthead if login is required, add login page to front end Compare: https://github.com/galaxyproject/galaxy/compare/c8c2f96b041a...6b0898c32785

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[galaxyproject/usegalaxy-playbook] 165139: include more info at the Main's homepage
by GitHub 01 Nov '15

01 Nov '15

Branch: refs/heads/martenson-patch-1 Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 16513900e12388563df3d577c5a79c3fbc44e2bb https://github.com/galaxyproject/usegalaxy-playbook/commit/16513900e1238856… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-01 (Sun, 01 Nov 2015) Changed paths: M templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- include more info at the Main's homepage Please reword as proper but this message is really missing and I think we should highlight it as much as possible. This is a first step. I have met so many people at #GI2015 that knew Galaxy but did not understand any of these two concepts and it would benefit them very much.

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