| Patch | Description | Author | Forwarded | Bugs | Origin | Last update |
|---|---|---|---|---|---|---|
| 0002_use_debian_packaged_python-joblib.patch | We are using Debian packaged python-joblib Debian has its own way to distinguish Python versions and there is no point in doing this inside the code. . The patch is non-intrusive since it conserves the original code and uses Debian pyyaml only if the original method fails. |
Andreas Tille <tille@debian.org> | no | |||
| 0003_accept-system-bwa.patch | Enable using Debian packaged bwa instead of bwa-spades Users might have installed a local version of bwa which is used independently from SPAdes. This is specifically true on Debian systems where the dependency system ensures the installation of bwa. This patch uses the local installed bwa as fallback if bwa-spades is not found. . The patch is non-intrusive since it conserves the original code and uses Debian bwa only if bwa-spades is not available. . Note: The duplicated which() in two files is for sure not the best solution. In case you consider taking over the patch I'd suggest to take it over into some common import file. |
Andreas Tille <tille@debian.org> | no | |||
| 0101_cmake_ignore_removed_python-yaml.patch | Since we are using Debian packaged python-yaml (see 0001_use_debian_packaged_python-yaml.patch) the dir needs to be excluded |
Andreas Tille <tille@debian.org> | no | |||
| 0102_cmake_ignore_removed_python-joblib.patch | Since we are using Debian packaged python-joblib (see 0002_use_debian_packaged_python-joblib.patch) the dir needs to be excluded |
Andreas Tille <tille@debian.org> | no | |||
| 0103_use-debian-packaged-bwa.patch | 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/libexec/spades/bwa-spades which enables successful run of the test suite |
Andreas Tille <tille@debian.org> | no | |||
| 0114_use_debian_provided_libs.patch | use more Debian packaged libraries Michael R. Crusoe <michael.crusoe@gmail.com> | Sascha Steinbiss <satta@debian.org>, | no | |||
| 0118_adjust_spades_home_again.patch | Adjust spades_home var to install files under /usr/share/spades | Alex Mestiashvili <amestia@rsh2.donotuse.de> | not-needed | |||
| fix-bool-cast | Make explicit cast to bool | Michael R. Crusoe <michael.crusoe@gmail.com> | no | |||
| python3.patch | Make sure Python3 interpreter is used in scripts | Andreas Tille <tille@debian.org> | no | 2019-11-12 | ||
| yaml_load.patch | Specify yaml loader see https://github.com/yaml/pyyaml/wiki/PyYAML-yaml.load(input)-Deprecation | Andreas Tille <tille@debian.org> | no | debian | 2022-10-23 | |
| debuginfo.patch | want debug info for the deb package | Juhani Numminen <juhaninumminen0@gmail.com> | not-needed | |||
| debian_bwa_zlib.patch | due to debian changes, bwa now refers to a system-wide libbwa.a and we need to manually link with zlib | Juhani Numminen <juhaninumminen0@gmail.com> | no | |||
| workdir_for_test.patch | set working directory so that the test finds its data | Juhani Numminen <juhaninumminen0@gmail.com> | no | |||
| disable_local_convertutf.patch | removal of ConvertUTF.cpp makes it necessary to link spades's LLVM with system-provided LLVMSupport.a | Juhani Numminen <juhaninumminen0@gmail.com> | not-needed | |||
| fix-sigill-on-non-popcnt-cpus.patch | fix baseline violation caused by asm calling popcnt | Étienne Mollier <etienne.mollier@mailoo.org> | yes | 2021-02-27 | ||
| fix-privacy-breaches.patch | fix privacy breaches identified by lintian. These breaches are caused by various badges, they may be safely remove. | Étienne Mollier <emollier@debian.org> | not-needed | 2022-06-25 | ||
| typos.patch | fix typo caught by lintian. | Étienne Mollier <emollier@debian.org> | no | 2022-06-25 |