Étienne Mollier pushed to branch upstream at Debian Med / paleomix
Commits: 4ecb3fd4 by Étienne Mollier at 2021-12-11T21:23:00+01:00 New upstream version 1.3.6 - - - - - 7 changed files: - CHANGES.md - 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 ===================================== 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/-/commit/4ecb3fd49faf45b0f56280eb42f5af47f1fdfc77 -- View it on GitLab: https://salsa.debian.org/med-team/paleomix/-/commit/4ecb3fd49faf45b0f56280eb42f5af47f1fdfc77 You're receiving this email because of your account on salsa.debian.org.
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