[med-svn] [gbrowse] branch upstream updated (4299a4d -> 84a0626)
Andreas Tille
tille at debian.org
Mon Jan 16 04:36:37 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch upstream
in repository gbrowse.
from 4299a4d Imported Upstream version 2.54+dfsg
new 84a0626 New upstream version 2.56+dfsg
The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
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(-)
create mode 100755 bin/gbrowse_aws_balancer.pl
delete mode 100755 bin/gbrowse_launch_aws_slaves.pl
create mode 100755 bin/gbrowse_sync_aws_slave.pl
create mode 100755 bin/split_wig.pl
mode change 100755 => 100644 cgi-bin/das
mode change 100755 => 100644 cgi-bin/gbgff
mode change 100755 => 100644 cgi-bin/gbrowse
mode change 100755 => 100644 cgi-bin/gbrowse_details
mode change 100755 => 100644 cgi-bin/gbrowse_gmap
mode change 100755 => 100644 cgi-bin/gbrowse_img
mode change 100755 => 100644 cgi-bin/gbrowse_key_img
mode change 100755 => 100644 cgi-bin/gbrowse_login
mode change 100755 => 100644 cgi-bin/gbrowse_syn
create mode 100644 conf/aws_balancer.conf
rename conf/synteny/{oryza.synconf.disabled => oryza.synconf.disabled.conf} (84%)
create mode 100644 etc/default/gbrowse-aws-balancer
create mode 100755 etc/init.d/gbrowse-aws-balancer
create mode 100644 htdocs/images/buttons/pop_in.png
create mode 100644 htdocs/images/buttons/pop_out.png
create mode 100644 htdocs/images/help/sugarcane_sorghum_synteny.png
create mode 100644 htdocs/js/toggle.js
create mode 100644 lib/Bio/DB/SeqFeature/Store/LoadHelper.pm
create mode 100644 lib/Bio/Graphics/Browser2/DataLoader/archive.pm
create mode 100644 lib/Bio/Graphics/Browser2/DataLoader/bigbed.pm
create mode 100644 lib/Bio/Graphics/Browser2/DataLoader/useq.pm
create mode 100644 lib/Bio/Graphics/Browser2/Render/Slave/AWS_Balancer.pm
create mode 100644 sample_data/yeast_chr1+2/dummy.fa
create mode 100755 t/07.balancer.t
create mode 100644 t/testdata/conf/aws_slave.conf
create mode 100644 t/testdata/data/volvox/dummy.fa
create mode 100644 t/testdata/data/volvox2/dummy.fa
create mode 100644 t/testdata/data/volvox3/dummy.fa
create mode 100644 t/testdata/data/volvox4/dummy.fa
--
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