diff --git a/README.rst b/README.rst index a3531b0..95a2936 100644 --- a/README.rst +++ b/README.rst @@ -71,17 +71,17 @@ QIIME2 is being used. Installing ITSxpress for use as a QIIME2 Plugin ---------------------------------------------------- -To install ITSxpress as a plugin for QIIME 2 first install QIIME 2 as a separate Conda/Mamba environemnt using thier instructions -https://docs.qiime2.org/2024.5/install/ then add ITSxress to the QIIME 2 Conda environment. The examples below are for QIIME2 2 -version 2024.2 an so please update the commands if you want a newer release. +To install ITSxpress as a plugin for QIIME 2, first install QIIME 2 Amplicon Distribution as a separate Conda/Mamba environemnt using their instructions +https://docs.qiime2.org/2024.10/install/native then add ITSxpress to the QIIME 2 Conda environment. The examples below are for QIIME2 +version 2024.10 an so please update the commands if you want a newer release. For Linux: .. code-block:: bash - conda env create -n qiime2-amplicon-2024.5 --file https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.5-py39-linux-conda.yml - conda activate qiime2-amplicon-2024.5 + conda env create -n qiime2-amplicon-2024.10 --file https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.10-py310-linux-conda.yml + conda activate qiime2-amplicon-2024.10 conda install -c bioconda -c conda-forge ITSxpress qiime dev refresh-cache @@ -89,16 +89,16 @@ For maxOS (Intel) and OS X: .. code-block:: bash - conda env create -n qiime2-amplicon-2024.5 --file https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.5-py39-osx-conda.yml - conda activate qiime2-amplicon-2024.5 + conda env create -n qiime2-amplicon-2024.10 --file https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.10-py310-osx-conda.yml + conda activate qiime2-amplicon-2024.10 conda install -c bioconda -c conda-forge ITSxpress qiime dev refresh-cache For macOS (Arm / Apple Silicon): .. code-block:: bash - CONDA_SUBDIR=osx-64 conda env create -n qiime2-amplicon-2024.5 --file https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.5-py39-osx-conda.yml - conda activate qiime2-amplicon-2024.5 + CONDA_SUBDIR=osx-64 conda env create -n qiime2-amplicon-2024.10 --file https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.10-py310-osx-conda.yml + conda activate qiime2-amplicon-2024.10 conda config --env --set subdir osx-64 CONDA_SUBDIR=osx-64 conda install -c bioconda -c conda-forge ITSxpress qiime dev refresh-cache @@ -111,16 +111,16 @@ For Linux, maxOS (Intel), and OS X: .. code-block:: bash - mamba create -n itsxpressenv -c bioconda -c conda-forge itsxpress - mamba activate itsxpressenv + conda create -n itsxpressenv -c bioconda -c conda-forge itsxpress + conda activate itsxpressenv For macOS (Arm/Apple Silicon): .. code-block:: bash - CONDA_SUBDIR=osx-64 mamba create -n itsxpressenv -c bioconda -c conda-forge itsxpress - mamba activate itsxpressenv + CONDA_SUBDIR=osx-64 conda create -n itsxpressenv -c bioconda -c conda-forge itsxpress + conda activate itsxpressenv conda config --env --set subdir osx-64 @@ -210,7 +210,7 @@ ITSxpress can take uncompressed, gzipped or zstd compressed FASTQ files and it c zstd compressed FASTQ files. It expects FASTQ files to end in: .fq, .fastq, .fq.gz, fastq.gz, .fq.zst or fastq.zst. Use case 2: Trimming the ITS2 region from a fungal amplicon sequencing dataset with -forward and reverse gzipped FASTQ files using two cpu threads. Return a forward +forward and reverse gzipped FASTQ files using two cpu threads. Return forward and reverse read files for use in Dada2. .. code-block:: bash diff --git a/changelog.md b/changelog.md index 39ab166..62eff81 100644 --- a/changelog.md +++ b/changelog.md @@ -1,6 +1,13 @@ +# 2.1.4 (2025-01-13) + +- Fixed a bug in [Issue 60](https://github.com/USDA-ARS-GBRU/itsxpress/issues/60) That caused the QIIME 2 plugin of ITSXpress to crash when running `.qza` files with more than one sample (thanks @hyphaltip). This bug was introduced in v2.1.2 or v2.1.3. +- Verified that the version will work with HMMER 3.4 and Vsearch 2.22.1 the current dependencies in QIIME 2 2024.11 Bioconda recipe was updated to allow later versions of HMMER. +- cleanup of setuptools-scm version file. +- Updates to the install instructions in the readme file. + # 2.1.3 (2024-11-14) -- fixed bug in [Issue 56](https://github.com/USDA-ARS-GBRU/itsxpress/issues/56) that caused some FASTQ files generated by PacBio to raise an error during validation. +- Fixed a bug in [Issue 56](https://github.com/USDA-ARS-GBRU/itsxpress/issues/56) that caused some FASTQ files generated by PacBio to raise an error during validation. these files now pass validation and the interleave check has been modified from raise a warning not an error. - Updated the citations.bib file to include the new Microbiology Spectrum article for ITSxpress diff --git a/itsxpress/main.py b/itsxpress/main.py index 4c7b464..64e75b0 100755 --- a/itsxpress/main.py +++ b/itsxpress/main.py @@ -140,7 +140,7 @@ def read_file(filename: str, mode: str ='r') -> contextlib.contextmanager: Args: filename: the filename to open - mode: 'r' for read 'w' for write. 't' will be adeed automacially for compressed files. + mode: 'r' for read 'w' for write. 't' will be added automatically for compressed files. Returns a context manager so the file can be opened using 'with' """ diff --git a/meta.yaml b/meta.yaml deleted file mode 100644 index c274eca..0000000 --- a/meta.yaml +++ /dev/null @@ -1,56 +0,0 @@ -{% set name = "itsxpress" %} -{% set version = "2.0.2" %} -{% set file_ext = "tar.gz" %} -{% set hash_type = "sha256" %} -{% set hash_value = "b5797107ee3f21cbaba0b9625aa931741babdee3eeb5a3218a8b8bc9783e2e72" %} - -package: - name: '{{ name|lower }}' - version: '{{ version }}' - -source: - url: "https://github.com/USDA-ARS-GBRU/{{ name }}/archive/v{{ version }}.tar.gz" - '{{ hash_type }}': '{{ hash_value }}' - -build: - noarch: python - number: 0 - entry_points: - - itsxpress=itsxpress.main:main - script: {{ PYTHON }} -m pip install --no-deps --no-build-isolation . -vvv - run_exports: - - {{ pin_subpackage('itsxpress', max_pin="x") }} - -requirements: - host: - - pip - - python =3.9.19 - run: - - pip - - python =3.9.19 - - biopython =1.84 - - hmmer =3.1b2 - - vsearch =2.22.1 - - pyzstd >=0.15.3 - -test: - imports: - - itsxpress - commands: - - itsxpress --help - -about: - home: http://github.com/usda-ars-gbru/itsxpress - license: CC0-1.0 - license_family: 'PUBLIC-DOMAIN' - summary: 'ITSxpress: Software to rapidly trim the Internally Transcribed Spacer (ITS) region from FASTQ files' - - -extra: - recipe-maintainers: - - arivers - - seina001 - identifiers: - - biotools:ITSxpress - - doi:10.5281/zenodo.1304349 - - doi:10.12688/f1000research.15704.1 \ No newline at end of file