[med-svn] [Git][med-team/paleomix][master] 4 commits: routine-update: New upstream version
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Sat Dec 11 20:34:47 GMT 2021
Étienne Mollier pushed to branch master at Debian Med / paleomix
Commits:
67476a8c by Étienne Mollier at 2021-12-11T21:22:59+01:00
routine-update: New upstream version
- - - - -
4ecb3fd4 by Étienne Mollier at 2021-12-11T21:23:00+01:00
New upstream version 1.3.6
- - - - -
0fcd63e5 by Étienne Mollier at 2021-12-11T21:23:06+01:00
Update upstream source from tag 'upstream/1.3.6'
Update to upstream version '1.3.6'
with Debian dir a522019c57d3cc7aae9a28615b07e5d24f058326
- - - - -
d27cf3fb by Étienne Mollier at 2021-12-11T21:26:55+01:00
routine-update: Ready to upload to unstable
- - - - -
8 changed files:
- CHANGES.md
- debian/changelog
- docs/conf.py
- docs/installation.rst
- paleomix/__init__.py
- paleomix/nodes/adapterremoval.py
- paleomix/pipelines/bam/makefile.py
- paleomix_environment.yaml
Changes:
=====================================
CHANGES.md
=====================================
@@ -1,5 +1,15 @@
# Changelog
+## [1.3.6] - 2021-11-28
+
+### Added
+ - Added explicit support for the AdapterRemoval `--trim5p` and `--trim3p` options,
+ which may take one or two values (as a list).
+
+### Changed
+ - User options for AdapterRemoval are no longer restricted by a whitelist.
+
+
## [1.3.5] - 2021-10-12
### Added
@@ -758,6 +768,7 @@ the (partially) updated documentation now hosted on ReadTheDocs.
- Switching to more traditional version-number tracking.
+[1.3.6]: https://github.com/MikkelSchubert/paleomix/compare/v1.3.5...v1.3.6
[1.3.5]: https://github.com/MikkelSchubert/paleomix/compare/v1.3.4...v1.3.5
[1.3.4]: https://github.com/MikkelSchubert/paleomix/compare/v1.3.3...v1.3.4
[1.3.3]: https://github.com/MikkelSchubert/paleomix/compare/v1.3.2...v1.3.3
=====================================
debian/changelog
=====================================
@@ -1,3 +1,9 @@
+paleomix (1.3.6-1) unstable; urgency=medium
+
+ * New upstream version
+
+ -- Étienne Mollier <emollier at debian.org> Sat, 11 Dec 2021 21:23:21 +0100
+
paleomix (1.3.5-1) unstable; urgency=medium
* New upstream version
=====================================
docs/conf.py
=====================================
@@ -26,7 +26,7 @@ author = "Mikkel Schubert"
# The short X.Y version
version = "1.3"
# The full version, including alpha/beta/rc tags
-release = "1.3.5"
+release = "1.3.6"
# -- General configuration ---------------------------------------------------
=====================================
docs/installation.rst
=====================================
@@ -17,13 +17,13 @@ In addition, some libraries used by PALEOMIX may require additional development
Once all requirements have been installed, PALEOMIX may be installed using `pip`::
- $ python3 -m pip install paleomix==1.3.5
+ $ python3 -m pip install paleomix==1.3.6
To verify that the installation was carried out correctly, run the command `paleomix`::
$ paleomix
PALEOMIX - pipelines and tools for NGS data analyses
- Version: v1.3.5
+ Version: v1.3.6
...
@@ -45,7 +45,7 @@ This installation method requires the `venv` module. On Debian based systems, th
Once `venv` is installed, creation of a virtual environment and installation of PALEOMIX may be carried out as shown here::
$ python3 -m venv venv
- $ ./venv/bin/pip install paleomix==v1.3.5
+ $ ./venv/bin/pip install paleomix==v1.3.6
Following successful completion of these commands, the `paleomix` executable will be accessible in the `./venv/bin/` folder. However, as this folder also contains a copy of Python itself, it is not recommended to add it to your `PATH`. Instead, simply link the `paleomix` executable to a folder in your `PATH`. This can be accomplished as follows::
@@ -78,7 +78,7 @@ To install `conda` and also set it up so it can use the `bioconda`_ bioinformati
Next, run the following commands to download the conda environment template for this release of PALEOMIX and to create a new conda environment named `paleomix` using that template::
- $ curl -fL https://github.com/MikkelSchubert/paleomix/releases/download/v1.3.5/paleomix_environment.yaml > paleomix_environment.yaml
+ $ curl -fL https://github.com/MikkelSchubert/paleomix/releases/download/v1.3.6/paleomix_environment.yaml > paleomix_environment.yaml
$ conda env create -n paleomix -f paleomix_environment.yaml
You can now activate the paleomix environment with::
=====================================
paleomix/__init__.py
=====================================
@@ -21,5 +21,5 @@
# SOFTWARE.
#
-__version_info__ = (1, 3, 5)
+__version_info__ = (1, 3, 6)
__version__ = "%i.%i.%i" % __version_info__
=====================================
paleomix/nodes/adapterremoval.py
=====================================
@@ -142,4 +142,14 @@ def _get_common_parameters(options, threads=1):
cmd.cmd.set_option("--adapter-list", "%(IN_ADAPTER_LIST)s")
cmd.command.set_kwargs(IN_ADAPTER_LIST=adapter_list)
+ for key in ("--trim5p", "--trim3p"):
+ values = options.pop(key, None)
+ if values is not None:
+ cmd.add_value(key)
+ if isinstance(values, list):
+ for value in values:
+ cmd.add_value(value)
+ else:
+ cmd.add_value(values)
+
return cmd
=====================================
paleomix/pipelines/bam/makefile.py
=====================================
@@ -173,6 +173,9 @@ _VALIDATION_OPTIONS = {
"--preserve5p": Or(IsNone, IsBoolean),
"--collapse-deterministic": Or(IsNone, IsBoolean),
"--collapse-conservatively": Or(IsNone, IsBoolean),
+ "--trim5p": Or(IsInt, IsListOf(IsInt)),
+ "--trim3p": Or(IsInt, IsListOf(IsInt)),
+ StringStartsWith("--"): Or(IsStr, IsInt, IsFloat, IsNone),
},
# Which aliger/mapper to use (BWA/Bowtie2)
"Aligners": {
=====================================
paleomix_environment.yaml
=====================================
@@ -17,4 +17,4 @@ dependencies:
- r-gam
- r-inline
- pip:
- - paleomix==1.3.5
+ - paleomix==1.3.6
View it on GitLab: https://salsa.debian.org/med-team/paleomix/-/compare/9f14424d8136cbc2755dba4d6fd4790f6580f84b...d27cf3fbffff3e29b7ebd39dcb05357c64a780b3
--
View it on GitLab: https://salsa.debian.org/med-team/paleomix/-/compare/9f14424d8136cbc2755dba4d6fd4790f6580f84b...d27cf3fbffff3e29b7ebd39dcb05357c64a780b3
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