update to v2.1.0

ohmeta · May 24, 2022 · dd637e2 · dd637e2
1 parent e6d0acb
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Showing 6 changed files with 23 additions and 98 deletions.
diff --git a/README.md b/README.md
@@ -8,25 +8,25 @@
 A general metagenomics data mining system focus on robust microbiome research.
 
 ## Overview
-### MAG workflow
+### MAG workflow (WIP figure)
 <div align=center><img width="600" height="800" src="docs/mag_workflow.svg"></div>
 
 ## Installation
 
-metapi works with Python 3.6+.
+metapi works with Python 3.7+.
 You can install it via [bioconda](https://bioconda.github.io/):
 
 ```
 ➤ mamba install -c conda-forge -c bioconda metapi
 
-# specific version, recommand to install latest version
-➤ mamba install -c conda-forge -c bioconda metapi=1.1.0
+# It is recommended to install the latest version
+➤ mamba install -c conda-forge -c bioconda metapi=2.1.0
 ```
 
 Or via pip:
 
 ```
-➤ pip3 install metapi=1.1.0
+➤ pip3 install metapi=2.1.0
 ```
 
 ## Run
@@ -178,10 +178,16 @@ positional arguments:
   binning_vamb_all,
   binning_report_all,
   binning_all,
+  identify_virsorter2_all,
+  identify_deepvirfinder_all,
+  identify_single_all,
+  identify_phamb_all,
+  identify_multi_all,
+  identify_all,
   predict_scaftigs_gene_prodigal_all,
   predict_scaftigs_gene_prokka_all,
   predict_bins_gene_prodigal_all,
-  predict_bins_gene_prokka_all, 
+  predict_bins_gene_prokka_all,
   predict_scaftigs_gene_all,
   predict_bins_gene_all,
   predict_all,
@@ -247,9 +253,12 @@ optional arguments:
 # run assembly
 ➤ metapi mag_wf assembly_all --run-local
 
-# run binning
+# run binning (microbial MAG)
 ➤ metapi mag_wf binning_all --run-local
 
+# run identify (virus MAG)
+➤ metapi mag_wf identify_all --run-local
+
 # run gene predict
 ➤ metapi mag_wf predict_all --run-local
 
@@ -396,7 +405,7 @@ Then metapi will use [InSilicoSeq](https://github.com/HadrienG/InSilicoSeq) to g
   |  s2          |   s2.bin.2.fa   |
   |  s2          |   s3.bin.3.fa   |
 
-## Output Structure (begin from trimming)
+## Default output structure (begin from trimming)
 ```
 - config.yaml
 - logs/
@@ -410,6 +419,7 @@ Then metapi will use [InSilicoSeq](https://github.com/HadrienG/InSilicoSeq) to g
     04.assembly/
     05.alignment/
     06.binning/
+    06.identify/
     07.predict/
     08.checkm/
     09.dereplicate/

diff --git a/environment.yml b/environment.yml
@@ -6,35 +6,8 @@ channels:
 dependencies:
   - setuptools
   - pandas
-  - ruamel.yaml
-  - snakemake >=5.10
   - numpy
-  - pandas
-  - openpyxl
-  - biopython>=1.73
   - ruamel.yaml
-  - snakemake >=5.10
-  - insilicoseq
-  - fastqc
-  - seqtk
-  - seqkit
-  - multiqc
-  - pigz
-  - fastp
-  - sickle-trim
-  - bwa
-  - bowtie2
-  - samtools
-  - megahit
-  - idba
-  - spades
-  - quast
-  - metabat2
-  - maxbin2
-  - vsearch
-  - prodigal
-  - prokka
-  - checkm-genome
-  - drep
-  - kraken
-  - gtdbtk
+  - snakemake >=6.10
+  - openpyxl
+  - biopython >=1.73
diff --git a/metapi/__about__.py b/metapi/__about__.py
@@ -1,4 +1,4 @@
 #!/usr/bin/env python3
 
-__version__ = '2.0.0'
+__version__ = '2.1.0'
 __author__ = "Jie Zhu, Fangming Yang"
diff --git a/pyproject.toml b/pyproject.toml
diff --git a/requirements.txt b/requirements.txt
@@ -3,4 +3,4 @@ pandas
 openpyxl
 snakemake
 ruamel.yaml
-biopython>=1.73
+biopython >=1.73
diff --git a/setup.py b/setup.py
@@ -41,7 +41,6 @@
     "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
     "Natural Language :: English",
     "Operating System :: OS Independent",
-    "Programming Language :: Python :: 3.6",
     "Programming Language :: Python :: 3.7",
     "Programming Language :: Python :: 3.8",
     "Programming Language :: Python :: 3.9",