Dev fpo (#44)

* Improve version checking of third-party software

* Update phylogeny.py

Raxml-ng is not available with version 1.0.0 in bioconda. We should ask for the version 1.0.1 (available in bioconda)

* Update conda badge

* Fix wrong link to conda badge

* Do not hardcode minimum software versions

---------

Co-authored-by: Amine Ghozlane <amine.ghozlane@pasteur.fr>

README.md

@@ -1,6 +1,6 @@
 # Meteor
 
-[![install with conda](https://img.shields.io/conda/vn/aghozlane/meteor?color=green&label=aghozlane%2Fmeteor&logo=anaconda)](https://anaconda.org/aghozlane/meteor)
+[![install with conda](https://img.shields.io/conda/vn/bioconda/meteor?color=green&label=bioconda%2Fmeteor&logo=anaconda)](https://anaconda.org/bioconda/meteor)
 [![PyPI](https://img.shields.io/pypi/v/METEOR?label=pypi%20package)](https://pypi.org/project/meteor/)
 [![dockerhub](https://img.shields.io/docker/v/aghozlane/meteor?label=aghozlane/meteor&logo=docker)](https://hub.docker.com/r/aghozlane/meteor/)
 ![Github Actions](https://github.com/metagenopolis/meteor/actions/workflows/main.yml/badge.svg)

meteor/mapper.py

@@ -16,7 +16,7 @@
 from dataclasses import dataclass
 from pathlib import Path
 from datetime import datetime
-from packaging.version import Version, parse
+from packaging.version import parse
 from re import findall
 from meteor.session import Session, Component
 from time import perf_counter
@@ -126,10 +126,10 @@ def execute(self) -> None:
             )
             sys.exit(1)
         bowtie_version = str(bowtie_exec.stdout).split("\\n", maxsplit=1)[0].split(" ")[2]
-        if parse(bowtie_version) < Version("2.3.5"):
+        if parse(bowtie_version) < self.meteor.MIN_BOWTIE2_VERSION:
             logging.error(
-                "The bowtie2 version %s is outdated for meteor. Please update bowtie2 to >=2.3.5.",
-                bowtie_version,
+                "The bowtie2 version %s is outdated for meteor. Please update bowtie2 to >= %s.",
+                bowtie_version, self.meteor.MIN_BOWTIE2_VERSION
             )
             sys.exit(1)
         # Start mapping

meteor/phylogeny.py

@@ -21,7 +21,7 @@
 from pathlib import Path
 import tempfile
 from tempfile import NamedTemporaryFile
-from packaging.version import Version, parse
+from packaging.version import parse
 from collections import OrderedDict
 from datetime import datetime
 from typing import Iterable
@@ -120,10 +120,10 @@ def execute(self) -> None:
             logging.error("Failed to determine the raxml-ng version.")
             sys.exit(1)
         raxml_ng_version = match.group(1)
-        if parse(raxml_ng_version) < Version("1.0.1"):
+        if parse(raxml_ng_version) < self.meteor.MIN_RAXML_NG_VERSION:
             logging.error(
-                "The raxml-ng version %s is outdated for meteor. Please update raxml-ng to >=1.0.1.",
-                raxml_ng_version,
+                "The raxml-ng version %s is outdated for meteor. Please update raxml-ng to >= %s.",
+                raxml_ng_version, self.meteor.MIN_RAXML_NG_VERSION
             )
             sys.exit(1)
 

meteor/referencebuilder.py

@@ -21,7 +21,7 @@
 from pathlib import Path
 from dataclasses import dataclass, field
 from datetime import datetime
-from packaging.version import Version, parse
+from packaging.version import parse
 from textwrap import fill
 from meteor.session import Session, Component
 from typing import Iterator, Tuple, ClassVar
@@ -140,10 +140,11 @@ def execute(self) -> None:
             )
             sys.exit(1)
         bowtie_version = bowtie_exec.stdout.decode("utf-8").split(" ")[2].split("\n")[0]
-        if parse(bowtie_version) < Version("2.3.5"):
+        if parse(bowtie_version) < self.meteor.MIN_BOWTIE2_VERSION:
             logging.error(
-                "The bowtie2 version %s is outdated for meteor. Please update bowtie2.",
+                "The bowtie2 version %s is outdated for meteor. Please update bowtie2 to >= %s.",
                 bowtie_version,
+                self.meteor.MIN_BOWTIE2_VERSION,
             )
             sys.exit(1)
         # Build the index with bowtie2

meteor/session.py

@@ -14,18 +14,24 @@
 
 from pathlib import Path
 from dataclasses import dataclass, field
-from typing import Protocol, Iterator
+from typing import Protocol, Iterator, ClassVar
 import logging
 import sys
 import json
 import lzma
 from importlib.metadata import version
+from packaging.version import Version
 
 
 @dataclass(kw_only=True)
 class Component:
     """Set of important constant for meteor"""
 
+    MIN_BOWTIE2_VERSION : ClassVar[Version] = Version('2.3.5')
+    MIN_BCFTOOLS_VERSION : ClassVar[Version] = Version('0.1.19')
+    MIN_BEDTOOLS_VERSION : ClassVar[Version] = Version('2.18')
+    MIN_RAXML_NG_VERSION : ClassVar[Version] = Version("1.0.1")
+
     threads: int | None
     fastq_dir: Path = field(default_factory=Path)
     mapping_dir: Path = field(default_factory=Path)

meteor/variantcalling.py

@@ -23,7 +23,7 @@
 from meteor.session import Session, Component
 from time import perf_counter
 from tempfile import NamedTemporaryFile
-from packaging.version import Version, parse
+from packaging.version import parse
 
 # from pysam import AlignmentFile
 # from collections import defaultdict
@@ -254,10 +254,10 @@ def execute(self) -> None:
         bcftools_version = (
             bcftools_exec.stdout.decode("utf-8").split("\n")[0].split(" ")[1]
         )
-        if parse(bcftools_version) < Version("0.1.19"):
+        if parse(bcftools_version) < self.meteor.MIN_BCFTOOLS_VERSION:
             logging.error(
-                "The bcftools version %s is outdated for meteor. Please update bcftools to >= 0.1.19.",
-                bcftools_version,
+                "The bcftools version %s is outdated for meteor. Please update bcftools to >= %s.",
+                bcftools_version, self.meteor.MIN_BCFTOOLS_VERSION
             )
             sys.exit(1)
         bedtools_exec = run(["bedtools", "--version"], check=False, capture_output=True)
@@ -267,10 +267,10 @@ def execute(self) -> None:
             )
             sys.exit(1)
         bedtools_version = bedtools_exec.stdout.decode("utf-8").split(" ")[1][1:]
-        if parse(bedtools_version) < Version("2.18"):
+        if parse(bedtools_version) < self.meteor.MIN_BEDTOOLS_VERSION:
             logging.error(
-                "Error, the bedtools version %s is outdated for meteor. Please update bedtools to >= 2.18.",
-                bedtools_version,
+                "The bedtools version %s is outdated for meteor. Please update bedtools to >= %s.",
+                bedtools_version, self.meteor.MIN_BEDTOOLS_VERSION
             )
             sys.exit(1)
         start = perf_counter()