Merge remote-tracking branch 'origin/3.0'

.github/workflows/python-publish.yml

@@ -0,0 +1,31 @@
+# This workflows will upload a Python Package using Twine when a release is created
+# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
+
+name: Upload Python Package
+
+on:
+  release:
+    types: [created]
+
+jobs:
+  deploy:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.7'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install setuptools wheel twine
+    - name: Build and publish
+      env:
+        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
+        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+      run: |
+        python setup.py sdist bdist_wheel
+        twine upload dist/*

.github/workflows/pythonpackage.yml

@@ -0,0 +1,40 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Build MetaPhlAn package
+
+on:
+  push:
+    branches: [ "3.0"]
+  pull_request:
+    branches: [ "3.0" ]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [ 3.7 ]
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python 3.7
+      uses: actions/setup-python@v1
+      with:
+        python-version: 3.7
+    - name: Install dependencies
+      run: |
+        pip install numpy scipy cython
+        sudo apt install bowtie2 muscle ncbi-blast+ raxml
+        pip install .
+    - name: Test 
+      run: |
+        metaphlan -v
+        strainphlan -h
+        extract_markers.py -h
+        merge_metaphlan_tables.py -h
+        read_fastx.py -h
+        add_metadata_tree.py -h
+        plot_tree_graphlan.py -h
+        sample2markers.py -h
+        strain_transmission.py -h

.gitmodules

@@ -1,3 +1,10 @@
-[submodule "utils/hclust2"]
-	path = utils/hclust2
-	url = https://github.com/SegataLab/hclust2
+[submodule "metaphlan/utils/hclust2"]
+path = metaphlan/utils/hclust2
+url = https://github.com/SegataLab/hclust2
+
+[submodule "metaphlan/utils/cmseq"]
+path = metaphlan/utils/cmseq
+url = https://github.com/SegataLab/cmseq
+[submodule "phylophlan"]
+path = metaphlan/utils/phylophlan
+url = https://github.com/biobakery/phylophlan

bioconda_recipe/meta.yaml

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+{% set name = "metaphlan" %}
+{% set version = "3.0" %}
+
+package:
+  name: {{ name }}
+  version: {{ version }}
+
+source:
+  # url: https://github.com/biobakery/MetaPhlAn/archive/{{version}}.tar.gz
+  # sha256: 3a86b7010f0b8e006ecb536fb56e85ebd1e7665360adb7ef840fdfd7108c3594
+  # git_url: https://github.com/biobakery/MetaPhlAn.git
+  # git_rev: 30c19aa97328a09e3e2c44baf89eaa0fa93cd93b
+  path: ..
+
+build:
+  noarch: python
+  script: {{ PYTHON }} -m pip install . -vv --no-dependencies
+
+requirements:
+  host:
+    - python >=3
+    - setuptools
+    - cython
+    - numpy
+  run:
+    - python >=3
+    - bowtie2 >=2.0.0
+    - dendropy
+    - numpy
+    - cmseq
+    - phylophlan
+    - biom-format
+    - matplotlib-base
+    - biopython
+    - pandas
+    - scipy
+    - requests
+    - blast >=2.6.0
+    - muscle >=3.8.1551
+    - pysam
+    - raxml >=8.2.10
+    - samtools >=1.9
+
+test:
+  commands:
+    - metaphlan -v
+    - strainphlan -h
+    - extract_markers.py -h
+    - merge_metaphlan_tables.py -h
+    - read_fastx.py -h
+    - add_metadata_tree.py -h
+    - plot_tree_graphlan.py -h
+    - sample2markers.py -h
+    - strain_transmission.py -h
+
+about:
+  home: https://github.com/biobakery/metaphlan
+  license: MIT License
+  license_family: MIT
+  license_file: license.txt
+  summary: Metagenomic Phylogenetic Analysis
+  description: |
+    MetaPhlAn is a computational tool for profiling the composition of microbial
+    communities (Bacteria, Archaea and Eukaryotes) from metagenomic
+    shotgun sequencing data with species level resolution. From version 2.0
+    MetaPhlAn is also able to identify specific strains (in the not-so-frequent
+    cases in which the sample contains a previously sequenced strains) and to
+    track strains across samples for all species.

changeset.txt

@@ -1,4 +1,14 @@
-== Version 2.2.0
+=== Version 3.0
+* New MetaPhlAn marker genes extracted with a newer version of ChocoPhlAn based on UniRef
+* Estimation of metagenome composed by unknown microbes with parameter `--unknown_estimation`
+* Automatic retrieval and installation of the latest MetaPhlAn database  with parameter `--index latest`
+* Virus profiling with `--add_viruses`
+* Calculation of metagenome size for improved estimation of reads mapped to a given clade
+* Inclusion of NCBI taxonomy ID in the ouput file
+* CAMI (Taxonomic) Profiling Output Format included
+* Removal of reads with low MAPQ values
+
+=== Version 2.2.0
 - added option "marker_counts" (by Nicola)
 
 === Version 2.1.0