[med-svn] [gbrowse] 02/04: Merge tag 'upstream/2.56+dfsg'
Andreas Tille
tille at debian.org
Mon Jan 16 04:36:36 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository gbrowse.
commit 4ef5ba8b13886ca231aa04a010585d258b7c074c
Merge: 840dd13 84a0626
Author: Andreas Tille <tille at 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(-)
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