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commit 4ef5ba8b13886ca231aa04a010585d258b7c074c Merge: 840dd13 84a0626 Author: Andreas Tille <ti...@debian.org> Date: Mon Jan 16 04:54:18 2017 +0100 Merge tag 'upstream/2.56+dfsg' Upstream version 2.56+dfsg Build.PL | 11 +- Changes | 30 + MANIFEST | 78 +- META.json | 317 +++--- META.yml | 197 ++-- Makefile.PL | 2 +- README | 4 +- README.IF.GBROWSE.ISNT.WORKING | 7 + bin/gbrowse_aws_balancer.pl | 562 +++++++++++ bin/gbrowse_configure_slaves.pl | 2 +- bin/gbrowse_launch_aws_slaves.pl | 222 ----- bin/gbrowse_syn_load_alignments_msa.pl | 40 +- bin/gbrowse_sync_aws_slave.pl | 176 ++++ bin/split_wig.pl | 74 ++ bin/wiggle2gff3.pl | 8 + cgi-bin/das | 6 + cgi-bin/gbgff | 6 + cgi-bin/gbrowse | 22 +- cgi-bin/gbrowse_details | 6 + cgi-bin/gbrowse_gmap | 6 + cgi-bin/gbrowse_img | 114 ++- cgi-bin/gbrowse_key_img | 6 + cgi-bin/gbrowse_login | 6 + cgi-bin/gbrowse_syn | 38 +- conf/GBrowse.conf | 23 +- conf/aws_balancer.conf | 28 + conf/languages/POSIX.pm | 4 + conf/plugins/Blat.pm | 112 ++- conf/plugins/FilterTest.pm | 2 +- conf/plugins/PrimerDesigner.pm | 9 +- conf/plugins/RestrictionAnnotator.pm | 5 +- conf/plugins/Submitter.pm | 9 +- conf/renderfarm.conf | 3 - conf/slave_preload.conf | 19 +- ...ynconf.disabled => oryza.synconf.disabled.conf} | 8 +- conf/synteny/rice_synteny.conf | 4 +- conf/synteny/wild_rice_synteny.conf | 4 +- conf/yeast_chr1+2.conf | 2 +- etc/default/gbrowse-aws-balancer | 16 + etc/default/gbrowse-slave | 4 +- etc/init.d/gbrowse-aws-balancer | 74 ++ etc/init.d/gbrowse-slave | 9 +- htdocs/annotation_help.html | 152 ++- htdocs/cloud_index.html | 1 + htdocs/css/karyotype.css | 8 +- htdocs/css/tracks.css | 13 + htdocs/gbrowse_syn_help.html | 110 +-- htdocs/images/buttons/pop_in.png | Bin 0 -> 189 bytes htdocs/images/buttons/pop_out.png | Bin 0 -> 201 bytes htdocs/images/help/sugarcane_sorghum_synteny.png | Bin 0 -> 17912 bytes htdocs/index.html | 18 +- htdocs/js/buttons.js | 2 + htdocs/js/controller.js | 134 ++- htdocs/js/dragdrop.js | 5 +- htdocs/js/login.js | 10 +- htdocs/js/overviewSelect.js | 40 +- htdocs/js/toggle.js | 58 ++ htdocs/js/track_pan.js | 5 +- htdocs/tutorial/conf_files/elegans_core.conf | 2 +- htdocs/tutorial/conf_files/elegans_extra.conf | 2 +- htdocs/tutorial/conf_files/volvox.conf | 2 +- htdocs/tutorial/conf_files/volvox_final.conf | 2 +- .../conf_files/volvox_final_withPhylo.conf | 2 +- htdocs/tutorial/conf_files/volvox_halfway.conf | 2 +- htdocs/tutorial/conf_files/volvox_quarter.conf | 2 +- htdocs/tutorial/conf_files/volvox_refactored.conf | 10 +- htdocs/tutorial/data_files/volvox_all.gff3 | 2 +- htdocs/tutorial/data_files/volvox_microarray.gff3 | 2 +- install_util/GBrowseGuessDirectories.pm | 10 +- install_util/GBrowseInstall.pm | 162 +++- lib/Bio/DB/SeqFeature/Store/LoadHelper.pm | 200 ++++ lib/Bio/Graphics/Browser2.pm | 29 +- lib/Bio/Graphics/Browser2/Action.pm | 30 +- lib/Bio/Graphics/Browser2/DataLoader/archive.pm | 318 ++++++ lib/Bio/Graphics/Browser2/DataLoader/bam.pm | 18 +- lib/Bio/Graphics/Browser2/DataLoader/bigbed.pm | 119 +++ lib/Bio/Graphics/Browser2/DataLoader/useq.pm | 361 +++++++ lib/Bio/Graphics/Browser2/DataSource.pm | 9 +- lib/Bio/Graphics/Browser2/Region.pm | 1 + lib/Bio/Graphics/Browser2/RegionSearch.pm | 1 + lib/Bio/Graphics/Browser2/Render.pm | 53 +- lib/Bio/Graphics/Browser2/Render/HTML.pm | 12 +- lib/Bio/Graphics/Browser2/Render/Login.pm | 3 +- lib/Bio/Graphics/Browser2/Render/Slave.pm | 16 +- .../Graphics/Browser2/Render/Slave/AWS_Balancer.pm | 1022 ++++++++++++++++++++ lib/Bio/Graphics/Browser2/Render/Slave/Status.pm | 17 +- lib/Bio/Graphics/Browser2/RenderPanels.pm | 305 +++--- lib/Bio/Graphics/Browser2/SendMail.pm | 2 +- lib/Bio/Graphics/Browser2/TrackDumper.pm | 2 + lib/Bio/Graphics/Browser2/UserDB.pm | 6 +- lib/Bio/Graphics/Browser2/UserTracks.pm | 79 +- lib/Bio/Graphics/Karyotype.pm | 1 - lib/Legacy/Graphics/Browser.pm | 2 +- lib/Legacy/Graphics/Browser/Synteny.pm | 17 +- sample_data/yeast_chr1+2/dummy.fa | 0 t/00.compile.t | 3 +- t/04.remoteserver.t | 298 +++--- t/07.balancer.t | 45 + t/testdata/conf/aws_slave.conf | 23 + t/testdata/conf/languages/POSIX.pm | 4 + t/testdata/data/volvox/dummy.fa | 0 t/testdata/data/volvox2/dummy.fa | 0 t/testdata/data/volvox3/dummy.fa | 0 t/testdata/data/volvox4/dummy.fa | 0 104 files changed, 4747 insertions(+), 1280 deletions(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/gbrowse.git _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit