| Patch | Description | Author | Forwarded | Bugs | Origin | Last update |
|---|---|---|---|---|---|---|
| setup.patch | Do not check existence of third party tools since these are removed. We are using Debian packaged tools | Andreas Tille <tille@debian.org> | not-needed | 2020-05-24 | ||
| use_debian_packaged_guppy_from_pplacer.patch | Use Debian packaged guppy and hmm* An if statement is added because copy_tool_to_lib is also called for the jar that is generated before the Python part of the build. |
Andreas Tille <tille@debian.org> | not-needed | 2020-08-19 | ||
| change_java_version_for_ant.patch | More recent version of Java suppresses some warnings | Pierre Gruet <pgtdebian@free.fr> | not-needed | https://lists.debian.org/debian-med/2020/08/msg00104.html | 2020-09-18 | |
| json_collections.patch | Fix build issue | Pierre Gruet <pgtdebian@free.fr> | yes | https://lists.debian.org/debian-med/2020/08/msg00104.html | 2020-08-14 | |
| java_build.patch | Adapting the build.xml file of ant to Debian policy There are no embedded jars to include. The classpath thus has to be changed to include Debian-packaged jars. The .java files should not be included in the target jars. |
Pierre Gruet <pgtdebian@free.fr> | not-needed | 2020-09-18 | ||
| configuration_files_in_etc_and_per_user.patch | using configuration files that are in /etc or in ~/.sepp | Pierre Gruet <pgtdebian@free.fr> | not-needed | 2020-10-08 | ||
| looking_for_integer_in_placements.patch | looking for the right index in placements JSONArray Original code assumes the edge_num information is in the first position in the JSONArray placements, which is not always the case. We insert a loop to look for the right position. |
Pierre Gruet <pgtdebian@free.fr> | yes | 2020-10-08 | ||
| deactivating_log_test.patch | deactivating minor test relative to log verbosity level | Pierre Gruet <pgtdebian@free.fr> | yes | 2020-10-05 | ||
| make_split_sequences_script.patch | Marking split_sequences.py with a #! line | Pierre Gruet <pgtdebian@free.fr> | yes | 2020-10-05 | ||
| using_python3_interpreter.patch | Marking the Python interpreter as python3 This is to conform to Debian Python policy. =================================================================== |
Pierre Gruet <pgtdebian@free.fr> | yes | https://www.debian.org/doc/packaging-manuals/python-policy/programs.html#interpreter-directive | 2020-10-07 |