[med-svn] [galaxy] 02/03: Import Debian patch 16.10-1
Olivier Sallou
osallou at debian.org
Sun Jan 15 12:48:33 UTC 2017
This is an automated email from the git hooks/post-receive script.
osallou pushed a commit to branch master
in repository galaxy.
commit d6dbeaf71a320d0a7e670e8721e4005acd56de41
Author: Olivier Sallou <osallou at debian.org>
Date: Sun Jan 15 10:34:35 2017 +0000
Import Debian patch 16.10-1
---
debian/README.source | 64 +++++++++++++++++++++++++
debian/changelog | 5 ++
debian/compat | 1 +
debian/control | 65 ++++++++++++++++++++++++++
debian/copyright | 26 +++++++++++
debian/galaxy-run.sh | 5 ++
debian/galaxy.dirs | 4 ++
debian/galaxy.install | 17 +++++++
debian/galaxy.links | 8 ++++
debian/patches/fix_debian_tests.patch | 20 ++++++++
debian/patches/fix_routes_version_breaks.patch | 13 ++++++
debian/patches/series | 2 +
debian/rules | 38 +++++++++++++++
debian/source/format | 1 +
debian/upstream/metadata | 11 +++++
debian/watch | 4 ++
16 files changed, 284 insertions(+)
diff --git a/debian/README.source b/debian/README.source
new file mode 100644
index 0000000..f0a774b
--- /dev/null
+++ b/debian/README.source
@@ -0,0 +1,64 @@
+# TODO
+
+* generate doc
+
+# About
+
+this repo is for development purpose of galaxy in Debian. It is not ready for packaging.
+some files certainly need to be excluded from source.
+
+copyright is not up to date
+
+# Javascript dependencies status
+
+For runtime and build
+
+ "jquery": "~1.12", <= 3.1 !!
+ "ravenjs": "~3", NO!
+ "underscore": "~1", <= 1.8.3
+ "backbone": "~1.3", <= 1.3.3
+ "bootstrap": "~3.3.2", <= 3.3.7
+ "bootstrap-tour": "~0.10.2", <= 0.11
+ "d3": "~3", <= 3.5.17
+ "farbtastic": "~2.0.0-alpha.1", <= NO
+ "toastr": "~2.1.0", <= NO
+ "jQTouch": "git://github.com/senchalabs/jQTouch#~1.0.0", <= NO
+ "bib2json": "git://github.com/galaxyproject/bib2json#galaxy", <= NO
+ "jquery-form": "~3.46.0", <= 11 ??
+ "jquery-autocomplete": "git://github.com/dyve/jquery-autocomplete", <= NO
+ "select2": "~3.5.2", <= 4.0.1
+ "jStorage": "~0.4.12", <= 0.3.1
+ "jquery.cookie": "~1.4.1", <= 11 ?
+ "dynatree": "~1.2.5", <= NO
+ "jquery-mousewheel": "~3.1.12", <= 11?
+ "wymeditor": "~1.0.0-rc.1", <= NO
+ "jstree": "~3.0.9", <= NO
+ "jquery-ui": "git://github.com/jquery/jquery-ui.git#~1.11.2", <= 1.12.1
+ "jquery.complexify": "git://github.com/danpalmer/jquery.complexify.js.git#~0.5.1", <= NO
+ "threedubmedia.jquery.event": "*", <= NO
+ "jquery-migrate": "~1.4", <= 1.4.1
+ "requirejs": "~2" <= 2.3.2
+
+To build libraries:
+
+ "amdi18n-loader": "^0.2.0", <= NO
+ "grunt": "^0.4.5", <= OK
+ "grunt-bower-install-simple": "^1.1.0", <= NO
+ "grunt-check-modules": "^1.0.0", <= NO
+ "grunt-cli": "^0.1.13", <= 1.2
+ "grunt-contrib-clean": "^0.6.0", <= 1.0
+ "grunt-contrib-copy": "^0.5.0", <= 1.0
+ "grunt-contrib-less": "^1.1.0", <= NO
+ "grunt-contrib-uglify": "^0.8.0", <= 2.0
+ "grunt-contrib-watch": "^0.6.1", <= NO
+ "grunt-exec": "^0.4.6", <= NO
+ "grunt-spritesmith": "^4.7.1", <= NO
+ "i18n-webpack-plugin": "^0.2.7", <= NO
+ "webpack": "^1.10.1", <= NO
+ "webpack-dev-server": "^1.7.0" <= NO
+
+
+Several dependencies are not yet python3 compatible and will impact Galaxy code (https://github.com/galaxyproject/galaxy/issues/1715). Upstream is working on this, but no roadmap yet. No python3 support is blocking, need to maintain python2 only deps in debianmed.
+
+Auto install of dependencies by Galaxy in a virtualenv, shared with installation of toolshed means code modification in Debian to use system libs. To avoid this:
+run.sh options --skip-venv --skip-eggs --skip-wheels seem to disable virtualenv and packages installation.
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..d202fa2
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+galaxy (16.10-1) UNRELEASED; urgency=medium
+
+ * Package for Galaxy (Closes: #NNNN).
+
+ -- Olivier Sallou <osallou at debian.org> Sun, 15 Jan 2017 10:34:35 +0000
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..ec63514
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+9
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..d19201a
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,65 @@
+Source: galaxy
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Olivier Sallou <osallou at debian.org>
+Section: science
+Priority: optional
+#TODO add python-bx
+Build-Depends: debhelper (>= 9),
+ python-all,
+ python-all-dev,
+ python-setuptools,
+ python-nose,
+ python-nosehtmloutput,
+ python-docutils,
+ python-markupsafe,
+ python-yaml,
+ python-sqlalchemy,
+ mercurial,
+ python-numpy,
+ python-crypto,
+ python-paste,
+ python-pastedeploy,
+ python-wchartype,
+ python-repoze.lru,
+ python-routes,
+ python-webob,
+ python-webhelpers,
+ python-mako,
+ python-tz,
+ python-babel,
+ python-beaker,
+ python-dictobj,
+ python-parsley,
+ python-six,
+ python-whoosh,
+ python-cheetah,
+ python-markdown,
+ python-bioblend,
+ python-boto,
+ python-requests,
+ python-requests-toolbelt,
+ python-kombu,
+ python-amqp,
+ python-anyjson,
+ python-psutil,
+ python-migrate,
+ python-decorator,
+ python-tempita,
+ python-sqlparse,
+ python-pbr,
+ python-svgwrite,
+ python-paramiko,
+ python-ecdsa,
+ python-pysam,
+ perl
+Standards-Version: 3.9.8
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/galaxy.git
+Vcs-Git: https://anonscm.debian.org/git/debian-med/galaxy.git
+Homepage: http://
+
+Package: galaxy
+Architecture: all
+Depends: ${misc:Depends},
+ ${perl:Depends}
+Description: XXX
+ YYYY
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..d237ca3
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,26 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: galaxy
+Source: https://github.com/galaxyproject/galaxy
+
+Files: *
+Copyright: 2010-2015 TODO
+License: TODO
+
+Files: debian/*
+Copyright: 2017 Olivier Sallou <osallou at debian.org>
+License: GPL-2+
+ This package is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <https://www.gnu.org/licenses/>
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
diff --git a/debian/galaxy-run.sh b/debian/galaxy-run.sh
new file mode 100644
index 0000000..f58f90a
--- /dev/null
+++ b/debian/galaxy-run.sh
@@ -0,0 +1,5 @@
+#!/bin/bash
+
+cd /usr/share/galaxy
+
+./run.sh --skip-venv --skip-eggs --skip-wheels $@
diff --git a/debian/galaxy.dirs b/debian/galaxy.dirs
new file mode 100644
index 0000000..7c2648c
--- /dev/null
+++ b/debian/galaxy.dirs
@@ -0,0 +1,4 @@
+usr/bin
+var/lib/galaxy
+etc/galaxy
+usr/share/galaxy
diff --git a/debian/galaxy.install b/debian/galaxy.install
new file mode 100644
index 0000000..b132c04
--- /dev/null
+++ b/debian/galaxy.install
@@ -0,0 +1,17 @@
+display_applications etc/galaxy
+external_service_types etc/galaxy
+scripts usr/share/galaxy
+templates usr/share/galaxy
+tools var/lib/galaxy
+tool-data var/lib/galaxy
+config/*.xml etc/galaxy/config
+config/*.sample etc/galaxy/config
+config/plugins usr/share/galaxy
+database var/lib/galaxy
+locale usr/share/galaxy
+*.sh usr/share/galaxy
+integrated_tool_panel.xml etc/galaxy
+openid usr/share/galaxy
+static usr/share/galaxy
+lib usr/share/galaxy
+cron usr/share/galaxy
diff --git a/debian/galaxy.links b/debian/galaxy.links
new file mode 100644
index 0000000..3038cb9
--- /dev/null
+++ b/debian/galaxy.links
@@ -0,0 +1,8 @@
+var/lib/galaxy/database usr/share/galaxy/database
+var/lib/galaxy/tools usr/share/galaxy/tools
+var/lib/galaxy/tool-data usr/share/galaxy/tool-data
+etc/galaxy/config usr/share/galaxy/config
+etc/galaxy/display_applications usr/share/galaxy/display_applications
+etc/galaxy/external_service_types usr/share/galaxy/external_service_types
+etc/galaxy/integrated_tool_panel.xml usr/share/galaxy/integrated_tool_panel.xml
+
diff --git a/debian/patches/fix_debian_tests.patch b/debian/patches/fix_debian_tests.patch
new file mode 100644
index 0000000..60a677b
--- /dev/null
+++ b/debian/patches/fix_debian_tests.patch
@@ -0,0 +1,20 @@
+--- a/run_tests.sh
++++ b/run_tests.sh
+@@ -443,7 +443,7 @@
+ GALAXY_CONFIG_OVERRIDE_DATABASE_CONNECTION=$GALAXY_TEST_DBURI
+ export GALAXY_CONFIG_OVERRIDE_DATABASE_CONNECTION
+ fi
+- ./scripts/common_startup.sh $skip_venv $no_create_venv $no_replace_pip $replace_pip --dev-wheels || exit 1
++ ./scripts/common_startup.sh $skip_venv $no_create_venv $no_replace_pip $replace_pip --skip-eggs --skip-wheels || exit 1
+ fi
+
+ GALAXY_VIRTUAL_ENV="${GALAXY_VIRTUAL_ENV:-.venv}"
+@@ -509,7 +509,7 @@
+ GALAXY_TEST_TOOL_CONF="config/tool_conf.xml.sample,test/functional/tools/samples_tool_conf.xml"
+ export GALAXY_TEST_TOOL_CONF
+ fi
+- python $test_script $coverage_arg -v --with-nosehtml --html-report-file $report_file $xunit_args $structured_data_args $extra_args
++ python $test_script $coverage_arg -v --with-html-output --html-out-file $report_file $xunit_args $structured_data_args $extra_args
+ exit_status=$?
+ echo "Testing complete. HTML report is in \"$report_file\"." 1>&2
+ exit ${exit_status}
diff --git a/debian/patches/fix_routes_version_breaks.patch b/debian/patches/fix_routes_version_breaks.patch
new file mode 100644
index 0000000..6beb234
--- /dev/null
+++ b/debian/patches/fix_routes_version_breaks.patch
@@ -0,0 +1,13 @@
+--- a/lib/galaxy/webapps/galaxy/buildapp.py
++++ b/lib/galaxy/webapps/galaxy/buildapp.py
+@@ -179,8 +179,8 @@
+ )
+
+ contents_archive_mapper = webapp.mapper.submapper( action='archive', controller='history_contents' )
+- contents_archive_mapper.connect( '/api/histories/{history_id}/contents/archive' )
+- contents_archive_mapper.connect( '/api/histories/{history_id}/contents/archive/{filename}{.format}' )
++ contents_archive_mapper.connect('history1', '/api/histories/{history_id}/contents/archive' )
++ contents_archive_mapper.connect('history2', '/api/histories/{history_id}/contents/archive/{filename}{.format}' )
+
+ # Legacy access to HDA details via histories/{history_id}/contents/{hda_id}
+ webapp.mapper.resource( 'content',
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..7afc11a
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1,2 @@
+fix_routes_version_breaks.patch
+fix_debian_tests.patch
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..f3a73f5
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,38 @@
+#!/usr/bin/make -f
+# See debhelper(7) (uncomment to enable)
+# output every command that modifies files on the build system.
+#export DH_VERBOSE = 1
+
+# see EXAMPLES in dpkg-buildflags(1) and read /usr/share/dpkg/*
+DPKG_EXPORT_BUILDFLAGS = 1
+include /usr/share/dpkg/default.mk
+
+# see FEATURE AREAS in dpkg-buildflags(1)
+# Fails to build when set to +all
+#export DEB_BUILD_MAINT_OPTIONS = hardening=+all
+export DEB_BUILD_MAINT_OPTIONS = hardening=+bindnow
+
+# see ENVIRONMENT in dpkg-buildflags(1)
+# package maintainers to append CFLAGS
+#export DEB_CFLAGS_MAINT_APPEND = -Wall -pedantic
+# package maintainers to append LDFLAGS
+#export DEB_LDFLAGS_MAINT_APPEND = -Wl,--as-needed
+
+
+# main packaging script based on dh7 syntax
+%:
+ dh $@
+
+override_dh_install:
+ cp debian/galaxy-run.sh debian/galaxy/usr/bin/galaxy-run.sh
+ dh_install
+ sed -i "s;config/plugin;plugin;g" debian/galaxy/etc/galaxy/config/galaxy.ini.sample
+ sed -i "s;#visualization_plugins_directory;visualization_plugins_directory/g" debian/galaxy/etc/galaxy/config/galaxy.ini.sample
+ sed -i "s;#interactive_environment_plugins_directory;interactive_environment_plugins_directory/g" debian/galaxy/etc/galaxy/config/galaxy.ini.sample
+ sed -i "s;#tour_config_dir;tour_config_dir/g" debian/galaxy/etc/galaxy/config/galaxy.ini.sample
+ sed -i "s;#webhooks_dir;webhook_dir/g" debian/galaxy/etc/galaxy/config/galaxy.ini.sample
+ find debian/galaxy -type f -name *.pyc | xargs rm -f
+
+override_dh_auto_build:
+ echo "skip make, nothing todo"
+
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
diff --git a/debian/upstream/metadata b/debian/upstream/metadata
new file mode 100644
index 0000000..3d90bfc
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,11 @@
+Reference:
+ Author: Marcel Martin
+ Title: "Cutadapt removes adapter sequences from high-throughput sequencing reads"
+ Journal: EMBnet.journal
+ Year: 2015
+ Volume: 17
+ Number: 1
+ Pages: 10-12
+ DOI: 10.14806/ej.17.1.200
+ URL: http://journal.embnet.org/index.php/embnetjournal/article/view/200
+ eprint: http://journal.embnet.org/index.php/embnetjournal/article/view/200/458
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..c61848c
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,4 @@
+version=4
+opts="repack,compression=xz,filenamemangle=s/.+\/v?(\d\S+)\.tar\.gz/galaxy-$1\.tar\.gz/" \
+ https://github.com/galaxyproject/galaxy/tags .*/v?(\d\S+)\.tar\.gz
+
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