From e2e93b0d6e9f0bbdd6961ae05872d6891e9be6a8 Mon Sep 17 00:00:00 2001
From: Mainguy Jean <jmainguy@genoscope.cns.fr>
Date: Tue, 16 Jul 2024 09:30:53 +0200
Subject: [PATCH] Update 2 files
- /env/binning.yml
- /env/Singularity_recipe_binning
---
env/Singularity_recipe_binning | 10 ++--------
env/binning.yml | 19 ++-----------------
2 files changed, 4 insertions(+), 25 deletions(-)
diff --git a/env/Singularity_recipe_binning b/env/Singularity_recipe_binning
index ed343865..1f314315 100644
--- a/env/Singularity_recipe_binning
+++ b/env/Singularity_recipe_binning
@@ -7,20 +7,14 @@ env/binning.yml /
%post
# build-essential g++ are needed to pip install checkm2
-apt-get update && apt-get install -y procps build-essential g++ && apt-get clean -y
+apt-get update && apt-get install -y procps && apt-get clean -y
/opt/conda/bin/mamba env create -q -f /binning.yml && /opt/conda/bin/conda clean -a
export PATH=/opt/conda/envs/binning/bin:$PATH
-# install Binette
-wget https://github.com/genotoul-bioinfo/Binette/archive/refs/tags/v0.1.5.tar.gz
-tar -xf v0.1.5.tar.gz
-rm v0.1.5.tar.gz
-
-pip install Binette-0.1.5/
%environment
-export PATH=/opt/conda/envs/binning/bin/:/checkm2/bin/:$PATH
+export PATH=/opt/conda/envs/binning/bin/:$PATH
%runscript
"$@"
diff --git a/env/binning.yml b/env/binning.yml
index 77d3f734..1259ae2e 100644
--- a/env/binning.yml
+++ b/env/binning.yml
@@ -5,27 +5,12 @@ channels:
- conda-forge
dependencies:
- python>=3.6
- - scikit-learn=0.23.2
- - h5py=2.10.0
- - numpy=1.23.5
- - diamond>=2.0.4
- - tensorflow >= 2.3.0
- - lightgbm >= 3.2.1
- pandas
- - scipy
- - prodigal>=2.6.3
- - setuptools
- - requests
- - packaging
- - tqdm
- - networkx
- pyfastx
- - pyrodigal
- - biopython
- - matplotlib
- metabat2=2.15
- maxbin2=2.2.7
- concoct=1.1.0
- gtdbtk=2.1
- drep=3.0.0
- - pprodigal
+ - checkm2=1.0.2
+ - binette=1.0.1
--
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