[med-svn] [Git][med-team/strelka][master] 5 commits: Remove some code copies
Andreas Tille
gitlab at salsa.debian.org
Thu May 14 13:58:24 BST 2020
Andreas Tille pushed to branch master at Debian Med / strelka
Commits:
83ef519c by Andreas Tille at 2020-05-14T11:39:12+02:00
Remove some code copies
- - - - -
2a33aade by Andreas Tille at 2020-05-14T11:45:38+02:00
New upstream version 2.9.10+dfsg
- - - - -
31a3b9d5 by Andreas Tille at 2020-05-14T11:46:08+02:00
Update upstream source from tag 'upstream/2.9.10+dfsg'
Update to upstream version '2.9.10+dfsg'
with Debian dir e9c918718655c5a0bcf7da2ef30c01845217699a
- - - - -
707e18f7 by Andreas Tille at 2020-05-14T13:47:41+02:00
Use Debian packaged libs after removal of the code copies
- - - - -
d26f9031 by Andreas Tille at 2020-05-14T14:57:10+02:00
FIXME: WORKFLOW_VERSION needs to be set. Hardcoding is bad - but its the only idea I have for the moment
- - - - -
17 changed files:
- debian/changelog
- debian/control
- debian/copyright
- debian/patches/series
- + debian/patches/use_debian_packaged_redist.patch
- debian/rules
- debian/watch
- − redist/bgzf_extras-v0.1.tar.bz2
- − redist/boost_1_58_0_subset.tar.bz2
- − redist/cmake-2.8.12.tar.bz2
- − redist/cmake-modules-c99fd3/GetGitRevisionDescription.cmake
- − redist/cmake-modules-c99fd3/GetGitRevisionDescription.cmake.in
- − redist/cmake-modules-c99fd3/LICENSE_1_0.txt
- − redist/cmake-modules-c99fd3/README.markdown
- − redist/htslib-1.7-6-g6d2bfb7.tar.bz2
- − redist/pyflow-1.1.20.tar.bz2
- − redist/samtools-1.6.tar.bz2
Changes:
=====================================
debian/changelog
=====================================
@@ -1,4 +1,4 @@
-strelka (2.9.10-1) UNRELEASED; urgency=medium
+strelka (2.9.10+dfsg-1) UNRELEASED; urgency=medium
* Initial release (Closes: #<bug>)
=====================================
debian/control
=====================================
@@ -15,7 +15,9 @@ Build-Depends: debhelper-compat (= 12),
libboost-timer-dev,
libboost-chrono-dev,
libboost-test-dev,
- zlib1g-dev
+ zlib1g-dev,
+ libhts-dev,
+ rapidjson-dev,
Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/strelka
Vcs-Git: https://salsa.debian.org/med-team/strelka.git
=====================================
debian/copyright
=====================================
@@ -1,6 +1,12 @@
Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: strelka
Source: https://github.com/Illumina/strelka/releases
+Files-Excluded: redist/boost*
+ redist/bgzf_extras*
+ redist/cmake*
+ redist/htslib*
+ redist/pyflow*
+ redist/samtools*
Files: *
Copyright: 2009-2018 Illumina, Inc.
=====================================
debian/patches/series
=====================================
@@ -1 +1,2 @@
2to3.patch
+use_debian_packaged_redist.patch
=====================================
debian/patches/use_debian_packaged_redist.patch
=====================================
@@ -0,0 +1,72 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Wed, 13 May 2020 16:55:22 +0200
+Description: Use Debian packaged libs
+ FIXME: WORKFLOW_VERSION should not be hardcoded here!
+
+--- a/redist/CMakeLists.txt
++++ b/redist/CMakeLists.txt
+@@ -68,7 +68,7 @@ endif ()
+
+ superset(THIS_ADDITIONAL_LIB "${THIS_ADDITIONAL_LIB}")
+
+-
++if(!DEBIAN_BUILD)
+ #
+ # htslib
+ #
+@@ -194,7 +194,7 @@ set (RAPIDJSON_FINAL_TASK ${RAPIDJSON_IN
+
+ set(THIS_RAPIDJSON "${THIS_PROJECT_NAME}_rapidjson")
+ add_custom_target(${THIS_RAPIDJSON} DEPENDS "${RAPIDJSON_FINAL_TASK}")
+-
++endif()
+
+
+ #
+@@ -213,6 +213,7 @@ add_custom_command(
+ set(THIS_CODEMIN "${THIS_PROJECT_NAME}_codemin")
+ add_custom_target(${THIS_CODEMIN} DEPENDS "${CODEMIN_MARK}")
+
++if(!DEBIAN_BUILD)
+ #
+ # pyflow
+ #
+@@ -242,13 +243,15 @@ install_python_lib_dir("${PYFLOW_DIR}/sr
+
+ set (THIS_PYFLOW "${THIS_PROJECT_NAME}_pyflow")
+ add_custom_target(${THIS_PYFLOW} DEPENDS "${PYFLOW_DEPENDS}")
+-
++endif()
+
+ # tie results back to parent:
+ #
+ add_dependencies(${THIS_OPT} ${THIS_SAMTOOLS} ${THIS_RAPIDJSON} ${THIS_CODEMIN} ${THIS_PYFLOW})
+
++if(!DEBIAN_BUILD)
++# FIXME: obviously we should provide THIS_BGZFX
+ if (NOT WIN32)
+ add_dependencies(${THIS_OPT} ${THIS_BGZFX})
+ endif ()
+-
++endif()
+--- a/src/cmake/getBuildTimeConfigInfo.cmake
++++ b/src/cmake/getBuildTimeConfigInfo.cmake
+@@ -33,6 +33,7 @@
+ #
+ # generate git describe tag
+ #
++if(!DEBIAN_BUILD)
+ set (GETGIT_CMAKE "${REDIST_DIR}/cmake-modules-c99fd3/GetGitRevisionDescription.cmake")
+ include ("${GETGIT_CMAKE}")
+ git_describe(GIT_VERSION "${SRC_DIR}" --match "v[0-9]*" --dirty)
+@@ -47,6 +48,10 @@ else ()
+ STRING(REGEX REPLACE "^v" "" GIT_VERSION ${GIT_VERSION})
+ endif ()
+ set(WORKFLOW_VERSION ${GIT_VERSION})
++else()
++# FIXME: needs to read WORKFLOW_VERSION from d/rules
++set(WORKFLOW_VERSION 2.9.10)
++endif()
+ message(STATUS "Detected workflow version: ${WORKFLOW_VERSION}")
+ file(WRITE ${CONFIG_FILE} "WORKFLOW_VERSION\t${WORKFLOW_VERSION}\n")
+
=====================================
debian/rules
=====================================
@@ -17,11 +17,14 @@ include /usr/share/dpkg/default.mk
# for hardening you might like to uncomment this:
# export DEB_BUILD_MAINT_OPTIONS=hardening=+all
+CMAKE_EXTRA_FLAGS += -DDEBIAN_BUILD=1 \
+ -DWORKFLOW_VERSION=$(DEB_VERSION_UPSTREAM)
+
%:
dh $@ --buildsystem=cmake
override_dh_auto_configure:
- dh_auto_configure -- -DCMAKE_BUILD_TYPE=RelWithDebInfo
+ dh_auto_configure -- -DCMAKE_BUILD_TYPE=RelWithDebInfo $(CMAKE_EXTRA_FLAGS)
### When overriding auto_test make sure DEB_BUILD_OPTIONS will be respected
#override_dh_auto_test:
=====================================
debian/watch
=====================================
@@ -1,4 +1,4 @@
version=4
-opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%@PACKAGE at -$1.tar.gz%" \
-https://github.com/Illumina/strelka//releases .*/archive/v?@ANY_VERSION@\.tar\.gz
+opts="repacksuffix=+dfsg,dversionmangle=auto,repack,compression=xz,filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%@PACKAGE at -$1.tar.gz%" \
+ https://github.com/Illumina/strelka//releases .*/archive/v?@ANY_VERSION@\.tar\.gz
=====================================
redist/bgzf_extras-v0.1.tar.bz2 deleted
=====================================
Binary files a/redist/bgzf_extras-v0.1.tar.bz2 and /dev/null differ
=====================================
redist/boost_1_58_0_subset.tar.bz2 deleted
=====================================
Binary files a/redist/boost_1_58_0_subset.tar.bz2 and /dev/null differ
=====================================
redist/cmake-2.8.12.tar.bz2 deleted
=====================================
Binary files a/redist/cmake-2.8.12.tar.bz2 and /dev/null differ
=====================================
redist/cmake-modules-c99fd3/GetGitRevisionDescription.cmake deleted
=====================================
@@ -1,128 +0,0 @@
-# - Returns a version string from Git
-#
-# These functions force a re-configure on each git commit so that you can
-# trust the values of the variables in your build system.
-#
-# get_git_head_revision(<refspecvar> <hashvar> [<additional arguments to git describe> ...])
-#
-# Returns the refspec and sha hash of the current head revision
-#
-# git_describe(<var> [<additional arguments to git describe> ...])
-#
-# Returns the results of git describe on the source tree, and adjusting
-# the output so that it tests false if an error occurs.
-#
-# git_get_exact_tag(<var> [<additional arguments to git describe> ...])
-#
-# Returns the results of git describe --exact-match on the source tree,
-# and adjusting the output so that it tests false if there was no exact
-# matching tag.
-#
-# Requires CMake 2.6 or newer (uses the 'function' command)
-#
-# Original Author:
-# 2009-2010 Ryan Pavlik <rpavlik at iastate.edu> <abiryan at ryand.net>
-# http://academic.cleardefinition.com
-# Iowa State University HCI Graduate Program/VRAC
-#
-# Copyright Iowa State University 2009-2010.
-# Distributed under the Boost Software License, Version 1.0.
-# (See accompanying file LICENSE_1_0.txt or copy at
-# http://www.boost.org/LICENSE_1_0.txt)
-
-if(__get_git_revision_description)
- return()
-endif()
-set(__get_git_revision_description YES)
-
-# We must run the following at "include" time, not at function call time,
-# to find the path to this module rather than the path to a calling list file
-get_filename_component(_gitdescmoddir ${CMAKE_CURRENT_LIST_FILE} PATH)
-
-# csaunders: modify to take srcdir as an argument instead of using CMAKE(_CURRENT|)_SOURCE_DIR
-function(get_git_head_revision _refspecvar _hashvar _srcdir)
- set(GIT_PARENT_DIR "${_srcdir}")
- set(GIT_DIR "${GIT_PARENT_DIR}/.git")
- while(NOT EXISTS "${GIT_DIR}") # .git dir not found, search parent directories
- set(GIT_PREVIOUS_PARENT "${GIT_PARENT_DIR}")
- get_filename_component(GIT_PARENT_DIR ${GIT_PARENT_DIR} PATH)
- if(GIT_PARENT_DIR STREQUAL GIT_PREVIOUS_PARENT)
- # We have reached the root directory, we are not in git
- set(${_refspecvar} "GITDIR-NOTFOUND" PARENT_SCOPE)
- set(${_hashvar} "GITDIR-NOTFOUND" PARENT_SCOPE)
- return()
- endif()
- set(GIT_DIR "${GIT_PARENT_DIR}/.git")
- endwhile()
- # check if this is a submodule
- if(NOT IS_DIRECTORY ${GIT_DIR})
- file(READ ${GIT_DIR} submodule)
- string(REGEX REPLACE "gitdir: (.*)\n$" "\\1" GIT_DIR_RELATIVE ${submodule})
- get_filename_component(SUBMODULE_DIR ${GIT_DIR} PATH)
- get_filename_component(GIT_DIR ${SUBMODULE_DIR}/${GIT_DIR_RELATIVE} ABSOLUTE)
- endif()
- set(GIT_DATA "${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/git-data")
- if(NOT EXISTS "${GIT_DATA}")
- file(MAKE_DIRECTORY "${GIT_DATA}")
- endif()
-
- if(NOT EXISTS "${GIT_DIR}/HEAD")
- return()
- endif()
- set(HEAD_FILE "${GIT_DATA}/HEAD")
- configure_file("${GIT_DIR}/HEAD" "${HEAD_FILE}" COPYONLY)
-
- configure_file("${_gitdescmoddir}/GetGitRevisionDescription.cmake.in"
- "${GIT_DATA}/grabRef.cmake"
- @ONLY)
- include("${GIT_DATA}/grabRef.cmake")
-
- set(${_refspecvar} "${HEAD_REF}" PARENT_SCOPE)
- set(${_hashvar} "${HEAD_HASH}" PARENT_SCOPE)
-endfunction()
-
-# csaunders: modify to take srcdir as an argument instead of using CMAKE(_CURRENT|)_SOURCE_DIR
-function(git_describe _var _srcdir)
- if(NOT GIT_FOUND)
- find_package(Git QUIET)
- endif()
- get_git_head_revision(refspec hash ${_srcdir})
- if(NOT GIT_FOUND)
- set(${_var} "GIT-NOTFOUND" PARENT_SCOPE)
- return()
- endif()
- if(NOT hash)
- set(${_var} "HEAD-HASH-NOTFOUND" PARENT_SCOPE)
- return()
- endif()
-
- # TODO sanitize
- #if((${ARGN}" MATCHES "&&") OR
- # (ARGN MATCHES "||") OR
- # (ARGN MATCHES "\\;"))
- # message("Please report the following error to the project!")
- # message(FATAL_ERROR "Looks like someone's doing something nefarious with git_describe! Passed arguments ${ARGN}")
- #endif()
-
- #message(STATUS "Arguments to execute_process: ${ARGN}")
-
- # csaunders: Modified to leave off explicit ${head} specification so that the --dirty flag
- # can be added in. This probably breaks various submodule/etc, usages, but I can't document which
- execute_process(COMMAND
- "${GIT_EXECUTABLE}" describe ${ARGN}
- WORKING_DIRECTORY ${_srcdir}
- RESULT_VARIABLE res
- OUTPUT_VARIABLE out
- ERROR_QUIET
- OUTPUT_STRIP_TRAILING_WHITESPACE)
- if(NOT res EQUAL 0)
- set(out "${out}-${res}-NOTFOUND")
- endif()
-
- set(${_var} "${out}" PARENT_SCOPE)
-endfunction()
-
-function(git_get_exact_tag _var)
- git_describe(out --exact-match ${ARGN})
- set(${_var} "${out}" PARENT_SCOPE)
-endfunction()
=====================================
redist/cmake-modules-c99fd3/GetGitRevisionDescription.cmake.in deleted
=====================================
@@ -1,38 +0,0 @@
-#
-# Internal file for GetGitRevisionDescription.cmake
-#
-# Requires CMake 2.6 or newer (uses the 'function' command)
-#
-# Original Author:
-# 2009-2010 Ryan Pavlik <rpavlik at iastate.edu> <abiryan at ryand.net>
-# http://academic.cleardefinition.com
-# Iowa State University HCI Graduate Program/VRAC
-#
-# Copyright Iowa State University 2009-2010.
-# Distributed under the Boost Software License, Version 1.0.
-# (See accompanying file LICENSE_1_0.txt or copy at
-# http://www.boost.org/LICENSE_1_0.txt)
-
-set(HEAD_HASH)
-
-file(READ "@HEAD_FILE@" HEAD_CONTENTS LIMIT 1024)
-
-string(STRIP "${HEAD_CONTENTS}" HEAD_CONTENTS)
-if(HEAD_CONTENTS MATCHES "ref")
- # named branch
- string(REPLACE "ref: " "" HEAD_REF "${HEAD_CONTENTS}")
- if(EXISTS "@GIT_DIR@/${HEAD_REF}")
- configure_file("@GIT_DIR@/${HEAD_REF}" "@GIT_DATA@/head-ref" COPYONLY)
- elseif(EXISTS "@GIT_DIR@/logs/${HEAD_REF}")
- configure_file("@GIT_DIR@/logs/${HEAD_REF}" "@GIT_DATA@/head-ref" COPYONLY)
- set(HEAD_HASH "${HEAD_REF}")
- endif()
-else()
- # detached HEAD
- configure_file("@GIT_DIR@/HEAD" "@GIT_DATA@/head-ref" COPYONLY)
-endif()
-
-if(NOT HEAD_HASH)
- file(READ "@GIT_DATA@/head-ref" HEAD_HASH LIMIT 1024)
- string(STRIP "${HEAD_HASH}" HEAD_HASH)
-endif()
=====================================
redist/cmake-modules-c99fd3/LICENSE_1_0.txt deleted
=====================================
@@ -1,23 +0,0 @@
-Boost Software License - Version 1.0 - August 17th, 2003
-
-Permission is hereby granted, free of charge, to any person or organization
-obtaining a copy of the software and accompanying documentation covered by
-this license (the "Software") to use, reproduce, display, distribute,
-execute, and transmit the Software, and to prepare derivative works of the
-Software, and to permit third-parties to whom the Software is furnished to
-do so, all subject to the following:
-
-The copyright notices in the Software and this entire statement, including
-the above license grant, this restriction and the following disclaimer,
-must be included in all copies of the Software, in whole or in part, and
-all derivative works of the Software, unless such copies or derivative
-works are solely in the form of machine-executable object code generated by
-a source language processor.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE, TITLE AND NON-INFRINGEMENT. IN NO EVENT
-SHALL THE COPYRIGHT HOLDERS OR ANYONE DISTRIBUTING THE SOFTWARE BE LIABLE
-FOR ANY DAMAGES OR OTHER LIABILITY, WHETHER IN CONTRACT, TORT OR OTHERWISE,
-ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
-DEALINGS IN THE SOFTWARE.
=====================================
redist/cmake-modules-c99fd3/README.markdown deleted
=====================================
@@ -1,107 +0,0 @@
-Ryan's CMake Modules
-====================
-
-Ryan A. Pavlik, Ph.D.
-
-<ryan.pavlik at gmail.com> <abiryan at ryand.net>
-<http://academic.cleardefinition.com>
-
-Introduction
-------------
-
-This is a collection of CMake modules that I've produced during the course
-of a variety of software development. There are a number of find modules,
-especially for virtual reality and physical simulation packages, some utility
-modules of more general interest, and some patches or workarounds for
-CMake itself.
-
-Each module is generally documented, and depending on how busy I was
-when I created it, the documentation can be fairly complete.
-
-By now, it also includes contributions both from open-source projects I work on,
-as well as friendly strangers on the Internet contributing their modules. I am
-very grateful for improvements/fixes/pull requests!
-
-How to Integrate
-----------------
-
-These modules are probably best placed wholesale into a `cmake` subdirectory
-of your project source.
-
-If you use Git, try installing [git-subtree][1] (included by default on
-Git for Windows and perhaps for your Linux distro, especially post-1.9.1), so
-you can easily use this repository for subtree merges, updating simply.
-
-For the initial checkout:
-
- cd projectdir
-
- git subtree add --squash --prefix=cmake https://github.com/rpavlik/cmake-modules.git master
-
-For updates:
-
- cd projectdir
-
- git subtree pull --squash --prefix=cmake https://github.com/rpavlik/cmake-modules.git master
-
-If you originally installed this by just copying the files, you'll sadly have
-to delete the directory, commit that, then do the `git subtree add`. Annoying,
-but I don't know a workaround.
-
-If you use some other version control, you can export a copy of this directory
-without the git metadata by calling:
-
- ./export-to-directory.sh yourprojectdir/cmake
-
-You might also consider exporting to a temp directory and merging changes, since
-this will not overwrite by default. You can pass -f to overwrite existing files.
-
-How to Use
-----------
-
-At the minimum, all you have to do is add a line like this near the top
-of your root CMakeLists.txt file (but not before your `project()` call):
-
- list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
-
-You might also want the extra automatic features/fixes included with the
-modules, for that, just add another line following the first one:
-
- include(UseBackportedModules)
-
-Look at `module-help.html`/`.txt` (generated by `update-help.sh` on a unix-like shell with a pre-3.0 version of CMake.)
-either in this directory or online at <http://github.com/rpavlik/cmake-modules/blob/master/module-help.txt>
-for more information on individual modules. Since it requires an older CMake for generation,
-the docs might get out of date, sorry - but you can always look at the files themselves.
-
-
-Licenses
---------
-
-The modules that I wrote myself are all subject to this license:
-
-> Copyright Iowa State University 2009-2014,
-> or Copyright Sensics, Inc. 2014-2015,
-> or Copyright Ryan A. Pavlik 2009-2015
->
-> Distributed under the Boost Software License, Version 1.0.
->
-> (See accompanying file `LICENSE_1_0.txt` or copy at
-> <http://www.boost.org/LICENSE_1_0.txt>)
-
-Modules based on those included with CMake are under the OSI-approved
-BSD license, which is included in each of those modules. A few other modules
-are modified from other sources - when in doubt, look at the `.cmake`.
-
-If you'd like to contribute, that would be great! Just make sure to include
-the license boilerplate in your module, and send a pull request.
-
-Important License Note!
------------------------
-
-If you find this file inside of another project, rather at the top-level
-directory, you're in a separate project that is making use of these modules.
-That separate project can (and probably does) have its own license specifics.
-
-
-[1]: http://github.com/apenwarr/git-subtree "Git Subtree master"
=====================================
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=====================================
redist/pyflow-1.1.20.tar.bz2 deleted
=====================================
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=====================================
redist/samtools-1.6.tar.bz2 deleted
=====================================
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View it on GitLab: https://salsa.debian.org/med-team/strelka/-/compare/7fbdd9e5cf6633fe93e43b3e7e8e753a3a5a30f3...d26f9031df084d6110ef1d9746cd31a3793ebcc2
--
View it on GitLab: https://salsa.debian.org/med-team/strelka/-/compare/7fbdd9e5cf6633fe93e43b3e7e8e753a3a5a30f3...d26f9031df084d6110ef1d9746cd31a3793ebcc2
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