Snake8

.circleci/config.yml

@@ -34,7 +34,7 @@ jobs:
               source activate ./atlasenv
               conda list
             else
-              mamba env create -p ./atlasenv --file atlasenv.yml
+              conda env create -p ./atlasenv --file atlasenv.yml
             fi
       - save_cache:
           key: atlasenv-d-{{ checksum "atlasenv.yml" }}

Dockerfile

@@ -0,0 +1,33 @@
+# Start with the Miniconda base image
+FROM continuumio/miniconda3:24.9.2-0
+
+# Set the working directory in the container
+WORKDIR /main
+
+# Copy the environment file and project code
+COPY atlasenv.yml .
+
+# Create a user with a specific UID and GID
+RUN groupadd -g 1000 atlasgroup && \
+    useradd -m -u 1000 -g atlasgroup -s /bin/bash atlasuser
+
+# Set the HOME environment variable
+ENV HOME=/home/atlasuser
+
+# Change ownership of the home directory
+RUN chown -R atlasuser:atlasgroup $HOME
+
+# Switch to the new user
+USER atlasuser
+
+# Create and activate the environment
+RUN conda env create -n atlas -f atlasenv.yml && \
+    conda clean -afy && \
+    echo "source activate atlas" > ~/.bashrc
+
+# Set the working directory
+WORKDIR /main
+
+
+# Set the default command
+CMD ["bash"]

README.md

@@ -13,7 +13,7 @@
 
 You can start using atlas with three commands:
 ```
-    mamba install -y -c bioconda -c conda-forge metagenome-atlas={latest_version}
+    conda install -y -c bioconda -c conda-forge metagenome-atlas={latest_version}
     atlas init --db-dir databases path/to/fastq/files
     atlas run all
 ```
@@ -38,7 +38,7 @@
 > doi: [10.1186/s12859-020-03585-4](https://doi.org/10.1186/s12859-020-03585-4)
 
 
 # Developpment/Extensions
 
 Here are some ideas I work or want to work on when I have time. If you want to contribute or have some ideas let me know via a feature request issue.
 

atlas/atlas.py

@@ -7,7 +7,7 @@
 import click
 
 
-from snakemake.io import load_configfile
+from snakemake.common.configfile import load_configfile
 from .make_config import validate_config
 from .init.atlas_init import run_init  # , run_init_sra
 
@@ -247,7 +247,7 @@ def run_download(db_dir, jobs, snakemake_args):
     cmd = (
         "snakemake --snakefile {snakefile} "
         "--jobs {jobs} --rerun-incomplete "
-        "--conda-frontend mamba --scheduler greedy "
+        "--scheduler greedy "
         "--nolock  --use-conda  --conda-prefix {conda_prefix} "
         " --show-failed-logs "
         "--config database_dir='{db_dir}' {add_args} "

atlas/make_config.py

@@ -1,6 +1,6 @@
 from .default_values import *
 from snakemake.utils import update_config as snakemake_update_config
-from snakemake.io import load_configfile
+from snakemake.common.configfile import load_configfile
 import tempfile
 import sys
 import os

atlasenv.yml

@@ -3,16 +3,16 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - python >=3.8, < 3.12
-  - mamba
+  - python >=3.10, < 3.12
+  - libmamba= 2
   - bbmap >= 39.01, <40
-  - snakemake-minimal >= 7.18.1, <7.26
+  - snakemake-minimal >= 8.12, <8.26
   - pygments
   - networkx
   - graphviz
   - pandas >=1.2, <1.6
   - pyarrow # for parquet reading
   - click >=7
   - ruamel.yaml >=0.17
-  - cookiecutter
   - wget
+  - snakemake-executor-plugin-slurm

docs/index.rst

@@ -26,7 +26,7 @@ It handles all steps from QC, Assembly, Binning, to Annotation.
 
 You can start using atlas with three commands::
 
-      mamba install -c bioconda -c conda-forge metagenome-atlas={latest_version}
+      conda install -c bioconda -c conda-forge metagenome-atlas={latest_version}
       atlas init --db-dir databases path/to/fastq/files
       atlas run
 

docs/usage/getting_started.rst

@@ -1,5 +1,5 @@
 .. _conda: http://anaconda.org/
-.. _mamba: https://github.com/TheSnakePit/mamba
+
 
 Getting Started
 ***************
@@ -30,15 +30,8 @@ Setting strict channel priority can prevent quite some annoyances.
 
 The order is important by the way.
 
-Install mamba
--------------
-
-Conda can be a bit slow because there are so many packages. A good way around this is to use mamba_ (another snake).::
-
-    conda install mamba
-
-
-From now on, you can replace ``conda install`` with ``mamba install`` and see how much faster this snake is.
+_Previously atalas reccomended to use of mamba, which was faster. Since conda 24.9, conda uses the same library as backend.
+So we sugest to update conda ``conda update -n base conda``` and to use it._::
 
 Install metagenome-atlas
 ------------------------
@@ -48,7 +41,7 @@ We also recommend to specify the latest version of metagenome-atlas.
 
 .. code-block:: bash
 
-    mamba create -y -n atlasenv metagenome-atlas={latest_version}
+    conda create -y -n atlasenv metagenome-atlas={latest_version}
     source activate atlasenv
 
 where `{latest_version}` should be replaced by 
@@ -73,7 +66,7 @@ Alternatively, you can install metagenome Atlas directly from GitHub. This allow
     # git checkout branchname
 
     # create dependencies for atlas
-    mamba env create -n atlas-dev --file atlasenv.yml
+    conda env create -n atlas-dev --file atlasenv.yml
     conda activate atlas-dev
 
     # install atlas version. Changes in the files are directly available in the atlas dev version

docs/usage/output.rst

@@ -1,7 +1,6 @@
 .. |scheme| image:: ../../resources/images/atlas_list.png
   :alt: Atlas is a workflow for assembly and binning of metagenomic reads
 
-.. _thesis: https://github.com/TheSnakePit/mamba
 
 Expected output
 ***************

workflow/envs/fasta.yaml

@@ -3,7 +3,7 @@ channels:
     - bioconda
     - defaults
 dependencies:
-    - pyfastx=0.9
+    - pyfastx=2.1
     - pandas=1.2
     - pyarrow
     - biopython

workflow/envs/required_packages.yaml

@@ -9,4 +9,4 @@ dependencies:
     - bzip2 >=1.0
     - pandas >=1.2, <2
     - samtools >=1.13, <2
-    - sambamba <1
+    - sambamba

workflow/rules/assemble.smk

@@ -505,7 +505,7 @@ if config["filter_contigs"]:
         resources:
             mem_mb=config["mem"] * 1000,
         wrapper:
-            "v1.19.0/bio/minimap2/aligner"
+            "v5.5.0/bio/minimap2/aligner"
 
     rule pileup_prefilter:
         input:
@@ -635,7 +635,7 @@ rule align_reads_to_final_contigs:
     resources:
         mem_mb=config["mem"] * 1000,
     wrapper:
-        "v1.19.0/bio/minimap2/aligner"
+        "v5.5.0/bio/minimap2/aligner"
 
 
 rule pileup_contigs_sample:

workflow/rules/derep.smk

@@ -110,4 +110,4 @@ rule build_bin_report:
     log:
         "logs/binning/report_{binner}.log",
     script:
-        "../report/bin_report.py"
+        "../../report/bin_report.py"

workflow/rules/genecatalog.smk

@@ -234,7 +234,7 @@ rule index_genecatalog:
     params:
         index_size="12G",
     wrapper:
-        "v1.19.0/bio/minimap2/index"
+        "v5.5.0/bio/minimap2/index"
 
 
 rule concat_all_reads:
@@ -266,7 +266,7 @@ rule align_reads_to_Genecatalog:
         extra="-x sr --split-prefix {sample}_split_ ",
         sort="coordinate",
     wrapper:
-        "v1.19.0/bio/minimap2/aligner"
+        "v5.5.0/bio/minimap2/aligner"
 
 
 rule pileup_Genecatalog:

workflow/rules/genomes.smk

@@ -206,7 +206,7 @@ if config["genome_aligner"] == "minimap":
         resources:
             mem_mb=config["mem"] * 1000,
         wrapper:
-            "v1.19.0/bio/minimap2/index"
+            "v5.5.0/bio/minimap2/index"
 
     rule align_reads_to_genomes:
         input:
@@ -223,7 +223,7 @@ if config["genome_aligner"] == "minimap":
         resources:
             mem_mb=config["mem"] * 1000,
         wrapper:
-            "v1.19.0/bio/minimap2/aligner"
+            "v5.5.0/bio/minimap2/aligner"
 
 elif config["genome_aligner"] == "bwa":
 

workflow/rules/qc.smk

@@ -158,8 +158,7 @@ if not SKIP_QC:
                 dupesubs=config["duplicates_allow_substitutions"],
                 only_optical=("t" if config.get("duplicates_only_optical") else "f"),
             log:
-                sterr="{sample}/logs/QC/deduplicate.err",
-                stout="{sample}/logs/QC/deduplicate.log",
+                "{sample}/logs/QC/deduplicate.log",
             conda:
                 "%s/required_packages.yaml" % CONDAENV
             threads: config.get("threads", 1)
@@ -177,8 +176,7 @@ if not SKIP_QC:
                 " threads={threads} "
                 " pigz=t unpigz=t "
                 " -Xmx{resources.java_mem}G "
-                " 2> {log.sterr} "
-                " 1> {log.stout} "
+                " &> {log} "
 
     PROCESSED_STEPS.append("filtered")
 
@@ -229,8 +227,7 @@ if not SKIP_QC:
                 output.reads, key="out", allow_singletons=False
             ),
         log:
-            sterr="{sample}/logs/QC/quality_filter.err",
-            stout="{sample}/logs/QC/quality_filter.log",
+            "{sample}/logs/QC/quality_filter.log",
         conda:
             "%s/required_packages.yaml" % CONDAENV
         threads: config.get("threads", 1)
@@ -260,8 +257,7 @@ if not SKIP_QC:
             " prealloc={params.prealloc} "
             " pigz=t unpigz=t "
             " -Xmx{resources.java_mem}G "
-            " 2> {log.sterr} "
-            " 1> {log.stout} "
+            " &> {log} "
 
     # if there are no references, decontamination will be skipped
     if len(config.get("contaminant_references", {}).keys()) > 0: