[med-svn] r18854 - in trunk/packages/spades/trunk/debian: . patches
Andreas Tille
tille at moszumanska.debian.org
Tue Feb 24 16:10:33 UTC 2015
Author: tille
Date: 2015-02-24 16:10:32 +0000 (Tue, 24 Feb 2015)
New Revision: 18854
Added:
trunk/packages/spades/trunk/debian/patches/bamtools-cmake.patch
trunk/packages/spades/trunk/debian/patches/use-debian-packaged-bwa.patch
trunk/packages/spades/trunk/debian/patches/use-debian-packaged-samtools.patch
Removed:
trunk/packages/spades/trunk/debian/patches/use_debian-packaged_boost.patch
Modified:
trunk/packages/spades/trunk/debian/changelog
trunk/packages/spades/trunk/debian/control
trunk/packages/spades/trunk/debian/copyright
trunk/packages/spades/trunk/debian/links
trunk/packages/spades/trunk/debian/patches/do_not_install_third_party_libs.patch
trunk/packages/spades/trunk/debian/patches/series
trunk/packages/spades/trunk/debian/patches/use_debian_packaged_python-yaml.patch
trunk/packages/spades/trunk/debian/rules
trunk/packages/spades/trunk/debian/watch
Log:
Some steps forward to adapt to latest version 3.5. There is a lot work remaining. For the moment it does not even build in pbuilder since it depends on a cmake control file in a not yet released bamtools package (I'll see whether this can be avoided)
Modified: trunk/packages/spades/trunk/debian/changelog
===================================================================
--- trunk/packages/spades/trunk/debian/changelog 2015-02-24 08:09:50 UTC (rev 18853)
+++ trunk/packages/spades/trunk/debian/changelog 2015-02-24 16:10:32 UTC (rev 18854)
@@ -1,5 +1,5 @@
-spades (3.0.0+dfsg-1) UNRELEASED; urgency=low
+spades (3.5.0+dfsg-1) UNRELEASED; urgency=low
* Initial release (Closes: #<bug>)
- -- Andreas Tille <tille at debian.org> Wed, 05 Feb 2014 15:12:36 +0100
+ -- Andreas Tille <tille at debian.org> Tue, 18 Feb 2014 15:48:55 +0100
Modified: trunk/packages/spades/trunk/debian/control
===================================================================
--- trunk/packages/spades/trunk/debian/control 2015-02-24 08:09:50 UTC (rev 18853)
+++ trunk/packages/spades/trunk/debian/control 2015-02-24 16:10:32 UTC (rev 18854)
@@ -7,9 +7,11 @@
cmake,
python-all-dev,
zlib1g-dev,
+ libbz2-dev,
libboost-dev,
+ libbamtools-dev,
lynx
-Standards-Version: 3.9.5
+Standards-Version: 3.9.6
Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/spades/trunk/
Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/spades/trunk/
Homepage: http://bioinf.spbau.ru/en/spades
@@ -20,7 +22,10 @@
${misc:Depends},
python,
python-joblib,
- python-yaml
+ python-yaml,
+ bwa,
+ bamtools,
+ samtools
Description: genome assembler for single-cell and isolates data sets
The SPAdes – St. Petersburg genome assembler is intended for both
standard isolates and single-cell MDA bacteria assemblies. It works
Modified: trunk/packages/spades/trunk/debian/copyright
===================================================================
--- trunk/packages/spades/trunk/debian/copyright 2015-02-24 08:09:50 UTC (rev 18853)
+++ trunk/packages/spades/trunk/debian/copyright 2015-02-24 16:10:32 UTC (rev 18854)
@@ -5,6 +5,17 @@
Files-Excluded:
ext/include/boost
ext/src/python_libs
+ ext/tools/bwa-0.6.2
+ ext/*/bamtools
+ ext/*/samtools/samtools
+ ext/*/samtools/misc/ace2sam
+ ext/*/samtools/misc/bamcheck
+ ext/*/samtools/misc/maq2sam-*
+ ext/*/samtools/misc/md5fa
+ ext/*/samtools/misc/md5sum-lite
+ ext/*/samtools/misc/wgsim
+ ext/*/samtools/bcftools/bcftools
+ ext/*/samtools/win32
Files: *
Copyright: 2011-2013 Saint-Petersburg Academic University
Modified: trunk/packages/spades/trunk/debian/links
===================================================================
--- trunk/packages/spades/trunk/debian/links 2015-02-24 08:09:50 UTC (rev 18853)
+++ trunk/packages/spades/trunk/debian/links 2015-02-24 16:10:32 UTC (rev 18854)
@@ -1,2 +1,3 @@
usr/bin/spades usr/bin/dipspades
usr/lib/spades/share/spades/test_dataset usr/share/doc/spades/examples
+usr/bin/bwa usr/lib/spades/bin/bwa-spades
Added: trunk/packages/spades/trunk/debian/patches/bamtools-cmake.patch
===================================================================
--- trunk/packages/spades/trunk/debian/patches/bamtools-cmake.patch (rev 0)
+++ trunk/packages/spades/trunk/debian/patches/bamtools-cmake.patch 2015-02-24 16:10:32 UTC (rev 18854)
@@ -0,0 +1,38 @@
+--- /dev/null
++++ b/src/cmake/bamtools-config.cmake
+@@ -0,0 +1,35 @@
++# - Config file for the BamTools package
++# Found at
++# https://bitbucket.org/lunacab/ccdeep/raw/229ad7adb3700eec272a6cce36966b458bdaaa7a/bamtools-config.cmake
++# It defines the following variables
++# bamtools_FOUND - System has bamtols
++# bamtools_INCLUDE_DIRS - include directories for BamTools
++# bamtools_LIBRARIES - libraries to link against
++# bamtools_EXECUTABLE - the bar executable
++
++
++include(FindPackageHandleStandardArgs)
++find_path(bamtools_INCLUDE_DIR api/BamReader.h
++ HINTS ENV BAMTOOLS_INC
++ PATH_SUFFIXES bamtools
++ )
++
++find_library(bamtools_LIBRARY NAMES bamtools
++ HINTS ${CMAKE_SYSTEM_LIB_PATH}
++ PATH_SUFFIXES bamtools
++ )
++
++get_filename_component(bamtools_LIB_DIR ${bamtools_LIBRARY}
++ PATH)
++
++set(bamtools_LIBRARIES ${bamtools_LIB_DIR})
++set(bamtools_INCLUDE_DIRS ${bamtools_INCLUDE_DIR})
++get_filename_component(bamtools_REAL_LIBRARY ${bamtools_LIBRARY} REALPATH)
++get_filename_component(bamtools_LIB_FILE ${bamtools_REAL_LIBRARY} NAME)
++
++find_package_handle_standard_args(bamtools DEFAULT_MSG
++ bamtools_LIBRARY bamtools_INCLUDE_DIR)
++
++mark_as_advanced(bamtools_LIBRARY bamtools_INCLUDE_DIR )
++
++
Modified: trunk/packages/spades/trunk/debian/patches/do_not_install_third_party_libs.patch
===================================================================
--- trunk/packages/spades/trunk/debian/patches/do_not_install_third_party_libs.patch 2015-02-24 08:09:50 UTC (rev 18853)
+++ trunk/packages/spades/trunk/debian/patches/do_not_install_third_party_libs.patch 2015-02-24 16:10:32 UTC (rev 18854)
@@ -4,16 +4,124 @@
python-yaml and python-joblib. These code copies are removed
and this patch is just fixing the cmake input file
-
--- a/ext/src/CMakeLists.txt
+++ b/ext/src/CMakeLists.txt
-@@ -2,9 +2,5 @@
+@@ -2,11 +2,6 @@
add_subdirectory(jemalloc)
- add_subdirectory(otkpp)
+ add_subdirectory(nlopt)
-add_subdirectory(python_libs/joblib2)
-add_subdirectory(python_libs/joblib3)
-add_subdirectory(python_libs/pyyaml2)
-add_subdirectory(python_libs/pyyaml3)
add_subdirectory(yaml-cpp)
add_subdirectory(ConsensusCore)
+-add_subdirectory(bamtools)
+ add_subdirectory(samtools)
+--- a/src/cmake/includes.cmake
++++ b/src/cmake/includes.cmake
+@@ -1,6 +1,7 @@
+ # -*- cmake -*-
+
+ set(CMAKE_INCLUDE_CURRENT_DIR ON)
++### include_directories(SYSTEM "-I/usr/include/bamtools")
+ set(CMAKE_INCLUDE_SYSTEM_FLAG_C "-isystem ")
+ set(CMAKE_INCLUDE_SYSTEM_FLAG_CXX "-isystem ")
+ include_directories(${SPADES_MAIN_INCLUDE_DIR} ${SPADES_BUILT_INCLUDE_DIR})
+--- a/src/cmake/deps.cmake
++++ b/src/cmake/deps.cmake
+@@ -16,6 +16,21 @@ endif()
+ find_package(OpenMP)
+ find_package(ZLIB REQUIRED)
+ find_package(BZip2 REQUIRED)
++
++# BamTools
++## SET(BAMTOOLS_DIR "/usr")
++FIND_LIBRARY(BAMTOOLS_LIB bamtools ${BAMTOOLS_DIR}/lib)
++## Hmmm, this seems to be quite brutal and should be rather set by FIND_LIBRARY
++ADD_DEFINITIONS(-I/usr/include/bamtools)
++ADD_DEFINITIONS(-L/usr/lib)
++ADD_DEFINITIONS(-lbamtools)
++
++MESSAGE(status "** BAMTOOLS Include: ${INCLUDE_DIRECTORIES}")
++MESSAGE(status "** BAMTOOLS Link: ${LINK_DIRECTORIES}")
++MESSAGE(status "** BAMTOOLS Lib: ${BAMTOOLS_DIR}")
++
++
++find_package(BamTools REQUIRED)
+ find_package(Readline QUIET)
+ set(CURSES_NEED_NCURSES TRUE)
+ find_package(Curses QUIET)
+--- a/src/dipspades/CMakeLists.txt
++++ b/src/dipspades/CMakeLists.txt
+@@ -27,7 +27,7 @@ add_executable(dipspades
+ utils/files_utils.cpp
+ main.cpp)
+
+-target_link_libraries(dipspades input mph_index BamTools yaml-cpp nlopt ${COMMON_LIBRARIES} ssw)
++target_link_libraries(dipspades input mph_index bamtools yaml-cpp nlopt ${COMMON_LIBRARIES} ssw)
+
+ if (SPADES_STATIC_BUILD)
+ set_target_properties(dipspades PROPERTIES LINK_SEARCH_END_STATIC 1)
+--- a/src/debruijn/CMakeLists.txt
++++ b/src/debruijn/CMakeLists.txt
+@@ -25,7 +25,7 @@ add_executable(spades
+ # We have to do this to minimize changes in ConsensusCore itself
+ include_directories(${EXT_DIR}/include/ConsensusCore)
+
+-target_link_libraries(spades ConsensusCore input mph_index nlopt BamTools yaml-cpp ${COMMON_LIBRARIES})
++target_link_libraries(spades ConsensusCore input mph_index nlopt bamtools yaml-cpp ${COMMON_LIBRARIES})
+
+ if (SPADES_STATIC_BUILD)
+ set_target_properties(spades PROPERTIES LINK_SEARCH_END_STATIC 1)
+--- a/src/hammer/CMakeLists.txt
++++ b/src/hammer/CMakeLists.txt
+@@ -21,7 +21,7 @@ add_executable(hammer
+ # add_subdirectory(quake_count)
+ # add_subdirectory(gen_test_data)
+
+-target_link_libraries(hammer input mph_index BamTools yaml-cpp ${COMMON_LIBRARIES})
++target_link_libraries(hammer input mph_index bamtools yaml-cpp ${COMMON_LIBRARIES})
+
+ if (SPADES_STATIC_BUILD)
+ set_target_properties(hammer PROPERTIES LINK_SEARCH_END_STATIC 1)
+--- a/src/io/CMakeLists.txt
++++ b/src/io/CMakeLists.txt
+@@ -12,5 +12,5 @@ add_library(input STATIC
+ copy_file.cpp
+ library.cpp)
+
+-target_link_libraries(input BamTools yaml-cpp)
++target_link_libraries(input bamtools yaml-cpp)
+
+--- a/src/ionhammer/CMakeLists.txt
++++ b/src/ionhammer/CMakeLists.txt
+@@ -19,7 +19,7 @@ add_executable(ionhammer
+ seqeval/TreephaserLite.cpp
+ main.cpp)
+
+-target_link_libraries(ionhammer input mph_index BamTools yaml-cpp ${COMMON_LIBRARIES})
++target_link_libraries(ionhammer input mph_index bamtools yaml-cpp ${COMMON_LIBRARIES})
+
+ if (SPADES_STATIC_BUILD)
+ set_target_properties(ionhammer PROPERTIES LINK_SEARCH_END_STATIC 1)
+--- a/src/corrector/CMakeLists.txt
++++ b/src/corrector/CMakeLists.txt
+@@ -19,7 +19,8 @@ add_executable(corrector
+ config_struct.cpp
+ main.cpp)
+
+-target_link_libraries(corrector samtools input yaml-cpp ${COMMON_LIBRARIES})
++target_link_libraries(corrector samtools input yaml-cpp ${COMMON_LIBRARIES} -lhts)
++# target_link_libraries(corrector input yaml-cpp ${COMMON_LIBRARIES})
+
+
+
+--- a/ext/src/samtools/CMakeLists.txt
++++ b/ext/src/samtools/CMakeLists.txt
+@@ -28,4 +28,4 @@ add_library (samtools
+ bam_reheader.c
+ kprobaln.c
+ bam_cat.c)
+-target_link_libraries(samtools BamTools)
++target_link_libraries(samtools bamtools)
Modified: trunk/packages/spades/trunk/debian/patches/series
===================================================================
--- trunk/packages/spades/trunk/debian/patches/series 2015-02-24 08:09:50 UTC (rev 18853)
+++ trunk/packages/spades/trunk/debian/patches/series 2015-02-24 16:10:32 UTC (rev 18854)
@@ -1,4 +1,6 @@
do_not_install_third_party_libs.patch
adapt_to_debian_pathes.patch
use_debian_packaged_python-yaml.patch
-use_debian-packaged_boost.patch
+use-debian-packaged-bwa.patch
+# use-debian-packaged-samtools.patch
+# bamtools-cmake.patch
Added: trunk/packages/spades/trunk/debian/patches/use-debian-packaged-bwa.patch
===================================================================
--- trunk/packages/spades/trunk/debian/patches/use-debian-packaged-bwa.patch (rev 0)
+++ trunk/packages/spades/trunk/debian/patches/use-debian-packaged-bwa.patch 2015-02-24 16:10:32 UTC (rev 18854)
@@ -0,0 +1,22 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Changed: Tue, 18 Feb 2014 15:48:55 +0100
+Description: SPAdes originally contained a code copy of bwa since the version
+ of bwa which was current of the time of release did not builded with recent
+ gcc versions. Since this is not the case with Debian shipped bwa this code
+ copy is skipped.
+ .
+ See https://lists.debian.org/debian-med/2014/02/msg00192.html
+ .
+ Note: I tried to patch the Python scripts which were calling bwa-spades to
+ rather call /usr/bin/bwa but the test suite failed. So as an alternative
+ the package contains a symlink
+ ln -s /usr/bin/bwa /usr/lib/spades/bin/bwa-spades
+ which enables successfull run of the test suite
+
+--- a/ext/tools/CMakeLists.txt
++++ b/ext/tools/CMakeLists.txt
+@@ -4,4 +4,3 @@
+ # See file LICENSE for details.
+ ############################################################################
+
+-add_subdirectory(bwa-0.6.2)
Added: trunk/packages/spades/trunk/debian/patches/use-debian-packaged-samtools.patch
===================================================================
--- trunk/packages/spades/trunk/debian/patches/use-debian-packaged-samtools.patch (rev 0)
+++ trunk/packages/spades/trunk/debian/patches/use-debian-packaged-samtools.patch 2015-02-24 16:10:32 UTC (rev 18854)
@@ -0,0 +1,12 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Changed: Mon, 23 Feb 2015 21:24:39 +0100
+Description: SPAdes originally contained a code copy of samtools
+ Rather use the Debian packaged version
+
+--- a/ext/src/CMakeLists.txt
++++ b/ext/src/CMakeLists.txt
+@@ -4,4 +4,3 @@ add_subdirectory(jemalloc)
+ add_subdirectory(nlopt)
+ add_subdirectory(yaml-cpp)
+ add_subdirectory(ConsensusCore)
+-add_subdirectory(samtools)
Deleted: trunk/packages/spades/trunk/debian/patches/use_debian-packaged_boost.patch
===================================================================
--- trunk/packages/spades/trunk/debian/patches/use_debian-packaged_boost.patch 2015-02-24 08:09:50 UTC (rev 18853)
+++ trunk/packages/spades/trunk/debian/patches/use_debian-packaged_boost.patch 2015-02-24 16:10:32 UTC (rev 18854)
@@ -1,22 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Changed: Wed, 05 Feb 2014 15:12:36 +0100
-Description: SPAdes originally contained code copies of boost
- header files. The code copy was removed and this patch forces
- cmake to use the correct include dir of boost
-
---- a/src/cmake/deps.cmake
-+++ b/src/cmake/deps.cmake
-@@ -19,11 +19,7 @@ find_package(Readline QUIET)
- set(CURSES_NEED_NCURSES TRUE)
- find_package(Curses QUIET)
-
--# Use included boost unless explicitly specified
--if (NOT SPADES_BOOST_ROOT)
-- set(BOOST_ROOT "${EXT_DIR}/include")
--else()
-- set(BOOST_ROOT SPADES_BOOST_ROOT)
--endif()
-+# Use Debian packaged boost
-+set(BOOST_ROOT "/usr/include")
- set(Boost_USE_MULTITHREADED ON)
- find_package(Boost REQUIRED)
Modified: trunk/packages/spades/trunk/debian/patches/use_debian_packaged_python-yaml.patch
===================================================================
--- trunk/packages/spades/trunk/debian/patches/use_debian_packaged_python-yaml.patch 2015-02-24 08:09:50 UTC (rev 18853)
+++ trunk/packages/spades/trunk/debian/patches/use_debian_packaged_python-yaml.patch 2015-02-24 16:10:32 UTC (rev 18854)
@@ -6,7 +6,7 @@
--- a/spades.py
+++ b/spades.py
-@@ -31,10 +31,7 @@ import hammer_logic
+@@ -32,10 +32,7 @@ import hammer_logic
import spades_logic
import options_storage
addsitedir(ext_python_modules_home)
@@ -18,23 +18,9 @@
def print_used_values(cfg, log):
def print_value(cfg, section, param, pretty_param="", margin=" "):
---- a/src/spades_pipeline/corrector.py
-+++ b/src/spades_pipeline/corrector.py
-@@ -1253,10 +1253,7 @@ def main(args, joblib_path, log=None):
- tmp.append(os.path.getsize(contig_file))
- pairs.append(tmp)
- pairs.sort(key=lambda x: x[-1], reverse=True)
-- if sys.version.startswith('2.'):
-- from joblib2 import Parallel, delayed
-- elif sys.version.startswith('3.'):
-- from joblib3 import Parallel, delayed
-+ from joblib import Parallel, delayed
- Parallel(n_jobs=config["t"])(delayed(process_contig)(pair) for pair in pairs)
- # inserted += loc_ins
- # replaced += loc_rep
--- a/src/spades_pipeline/hammer_logic.py
+++ b/src/spades_pipeline/hammer_logic.py
-@@ -36,10 +36,7 @@ def compress_dataset_files(dataset_data,
+@@ -37,10 +37,7 @@ def compress_dataset_files(dataset_data,
support.sys_call([pigz_path, '-f', '-7', '-p', str(max_threads), reads_file], log)
else:
addsitedir(ext_python_modules_home)
@@ -46,7 +32,7 @@
n_jobs = min(len(to_compress), max_threads)
outputs = Parallel(n_jobs=n_jobs)(delayed(support.sys_call)(['gzip', '-f', '-7', reads_file]) for reads_file in to_compress)
for output in outputs:
-@@ -72,10 +69,7 @@ def prepare_config_bh(filename, cfg, log
+@@ -73,10 +70,7 @@ def prepare_config_bh(filename, cfg, log
def prepare_config_ih(filename, cfg, ext_python_modules_home):
addsitedir(ext_python_modules_home)
@@ -57,8 +43,8 @@
+ import yaml as pyyaml
data = pyyaml.load(open(filename, 'r'))
- data["dataset"] = process_cfg.process_spaces(cfg.dataset_yaml_filename)
-@@ -89,10 +83,7 @@ def prepare_config_ih(filename, cfg, ext
+ data["dataset"] = cfg.dataset_yaml_filename
+@@ -90,10 +84,7 @@ def prepare_config_ih(filename, cfg, ext
def run_hammer(corrected_dataset_yaml_filename, configs_dir, execution_home, cfg,
not_used_dataset_data, ext_python_modules_home, log):
addsitedir(ext_python_modules_home)
@@ -67,9 +53,9 @@
- elif sys.version.startswith('3.'):
- import pyyaml3 as pyyaml
+ import yaml as pyyaml
-
dst_configs = os.path.join(cfg.output_dir, "configs")
if os.path.exists(dst_configs):
+ shutil.rmtree(dst_configs)
@@ -142,4 +133,4 @@ def run_hammer(corrected_dataset_yaml_fi
log.info("\n== Dataset description file was created: " + corrected_dataset_yaml_filename + "\n")
@@ -79,7 +65,7 @@
+ shutil.rmtree(cfg.tmp_dir)
--- a/src/spades_pipeline/spades_logic.py
+++ b/src/spades_pipeline/spades_logic.py
-@@ -59,10 +59,7 @@ def get_read_length(output_dir, K, ext_p
+@@ -68,10 +68,7 @@ def get_read_length(output_dir, K, ext_p
max_read_length = 0
if os.path.isfile(est_params_filename):
addsitedir(ext_python_modules_home)
Modified: trunk/packages/spades/trunk/debian/rules
===================================================================
--- trunk/packages/spades/trunk/debian/rules 2015-02-24 08:09:50 UTC (rev 18853)
+++ trunk/packages/spades/trunk/debian/rules 2015-02-24 16:10:32 UTC (rev 18854)
@@ -9,16 +9,8 @@
PREFIX:=/usr
BUILD_DIR:=build_spades
-DEB_CMAKE_EXTRA_FLAGS = \
- -DCMAKE_INSTALL_PREFIX:PATH=/usr \
- -DCMAKE_BUILD_TYPE:STRING=Release \
- -DCMAKE_CXX_FLAGS="-Wno-deprecated $(CXXFLAGS)" \
- -DCMAKE_VERBOSE_MAKEFILE=$(DH_VERBOSE) \
- -DCMAKE_SHARED_LINKER_FLAGS="-Wl,--as-needed $(LDFLAGS)" \
- -DCMAKE_EXE_LINKER_FLAGS="-Wl,--as-needed $(LDFLAGS)" \
- -DCMAKE_SKIP_RPATH:BOOL=ON \
+DEB_CMAKE_EXTRA_FLAGS = -DSPADES_BOOST_ROOT=/usr/include
-
%:
dh $@ --with python2 --sourcedirectory=src --buildsystem=cmake
@@ -38,6 +30,11 @@
# delete duplicate of license
find debian -type f -name GPLv2.txt -delete
find debian -type f -name LICENSE -delete
+ #
+ # for some strange reason the test suite fails if bwa is not build
+ # we just do not install it but rather remove the executable from
+ # installation dir and replace it by a link to the Debian packaged bwa
+ find debian -type f -name bwa-spades -delete
override_dh_installdocs:
dh_installdocs
@@ -48,3 +45,6 @@
lynx -dump changelog.html > changelog
dh_installchangelogs changelog
rm changelog
+
+get-orig-source:
+ uscan --verbose --force-download --repack --compression xz
Modified: trunk/packages/spades/trunk/debian/watch
===================================================================
--- trunk/packages/spades/trunk/debian/watch 2015-02-24 08:09:50 UTC (rev 18853)
+++ trunk/packages/spades/trunk/debian/watch 2015-02-24 16:10:32 UTC (rev 18854)
@@ -1,3 +1,3 @@
version=3
-opts="downloadurlmangle=s{release([\d.]+)/}{release${1}/SPAdes-${1}.tar.gz},filenamemangle=s{release([\d.]+)/}{SPAdes-${1}.tar.gz},dversionmangle=s/\+dfsg//" \
+opts="downloadurlmangle=s{release([\d.]+)/}{release${1}/SPAdes-${1}.tar.gz},filenamemangle=s{release([\d.]+)/}{SPAdes-${1}.tar.gz},repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g" \
http://spades.bioinf.spbau.ru/ release([\d.]+)/
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