Merge pull request #285 from pirovc/dev

ganon version 2.1.0

.travis.yml

@@ -7,20 +7,15 @@ matrix:
       os: linux
       addons:
         apt:
-          sources:
-            - ubuntu-toolchain-r-test
           packages:
             - g++-11
             - parallel
       env:
         - MATRIX_EVAL="CC=gcc-11 && CXX=g++-11 && BUILD_TYPE=Release"
-
     - name: "linux gcc-12"
       os: linux
       addons:
         apt:
-          sources:
-            - ubuntu-toolchain-r-test
           packages:
             - g++-12
             - parallel
@@ -31,8 +26,6 @@ matrix:
       os: linux
       addons:
         apt:
-          sources:
-            - ubuntu-toolchain-r-test
           packages:
             - g++-11
             - parallel
@@ -43,22 +36,34 @@ matrix:
 before_install:
   - eval "${MATRIX_EVAL}"
   - python3 -m pip install --upgrade pip
-  - python3 -m pip install "pandas>=1.1.0"
+  - wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
+  - bash miniconda.sh -b -p $HOME/miniconda
+  - source "$HOME/miniconda/etc/profile.d/conda.sh"
+  - conda config --set always_yes yes --set changeps1 no
+  - conda update -q conda
+  - conda info -a
+  - conda activate base
+
+install:
+  - python3 -m pip install "pandas>=1.2.0"
   - python3 -m pip install "multitax>=1.3.1"
+  - python3 -m pip install "parameterized>=0.9.0"
   - if [ "$BUILD_TYPE" == "Coverage" ]; then 
       python3 -m pip install coverage;
     fi
-
-script:
+  - conda install -c bioconda -c conda-forge "raptor=3.0.1"
   - mkdir build && cd build 
   - cmake -DCMAKE_BUILD_TYPE=$BUILD_TYPE -DVERBOSE_CONFIG=ON -DCMAKE_EXPORT_COMPILE_COMMANDS=ON -DCONDA=OFF ..
   - cat compile_commands.json
   - cmake --build . -- -j2
   - ctest -VV .
   - sudo make install
-  - ganon-build -h  # ret 0
-  - ganon-classify -h  # ret 0
   - cd ..
+
+script:
+  - ganon-build --version
+  - ganon-classify --version
+  - raptor --version
   - if [ "$BUILD_TYPE" == "Coverage" ]; then 
       python3 -m coverage run --omit="/usr/*,tests/*" -m unittest discover -s tests/ganon/integration/ -v;
     else

CMakeLists.txt

@@ -3,7 +3,7 @@
 # =============================================================================
 
 cmake_minimum_required( VERSION 3.4 FATAL_ERROR )
-project( ganon VERSION 2.0.1 LANGUAGES CXX )
+project( ganon VERSION 2.1.0 LANGUAGES CXX )
 
 # -----------------------------------------------------------------------------
 # build setup

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2023 Vitor C. Piro pirovc.github.io
+Copyright (c) 2024 Vitor C. Piro pirovc.github.io
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

docs/classification.md

@@ -12,7 +12,7 @@ Output files:
  - `results.rep`: plain report of the run, used to further generate tree-like reports
  - `results.tre`: tree-like report with cumulative abundances by taxonomic ranks (can be re-generated with `ganon report`)
 
-By default, `ganon classify` only write report files. To get files with the classification of each read, use `--output-one` and/or `--output-all`. More information about output files [here](../outputfiles/#ganon-classify).
+By default, `ganon classify` only write report files. To get files with the classification of each read, use `--output-one` and/or `--output-all`. More information about output files [here](outputfiles.md#ganon-classify).
 
 !!! Note
     ganon performs **taxonomic profiling** and/or **binning** (one tax. assignment for each read) at a taxonomic, strain or sequence level. Some guidelines are listed below, please choose the parameters according to your application.
@@ -23,15 +23,15 @@ By default, `ganon classify` only write report files. To get files with the clas
 
  - strict thresholds: `--rel-cutoff 0.75` and `--rel-filter 0.1`
  - `--min-count 0.00005` (0.005%) to exclude very low abundant taxa
- - `--report-type abundance` to generate taxonomic abundances, correcting for genome sizes  (more infos [here](../reports/#report-type-report-type))
+ - `--report-type abundance` to generate taxonomic abundances, correcting for genome sizes  (more infos [here](reports.md#report-type-report-type))
 
 ### Binning
 
 To achieve better results for taxonomic binning or sequence classification, `ganon classify` can be configured with `--binning`, that is the same as:
 
  - less strict thresholds: `--rel-cutoff 0.25 --rel-filter 0`
  - `--min-count 0` reports all taxa with at least one read assigned to it
- - `--report-type reads` will report sequence abundances instead of taxonomic abundances (more infos [here](../reports/#report-type-report-type))
+ - `--report-type reads` will report sequence abundances instead of taxonomic abundances (more infos [here](reports.md#report-type-report-type))
 
 !!! Tip
     Database parameters in `ganon build` can also influence your results. Lower `--max-fp` (e.g. 0.1, 0.001) and higher `--kmer-size` (e.g. `23`, `27`) will improve sensitivity of your results at cost of a larger database and memory usage.