update to v0.7.1

ohmeta · Apr 25, 2020 · 8137628 · 8137628
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diff --git a/README.md b/README.md
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+# metapi
+
+[![bioconda-badge](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io)
+[![PyPI version](https://badge.fury.io/py/metapi.svg)](https://badge.fury.io/py/metapi)
+[![star this repo](http://githubbadges.com/star.svg?user=ohmeta&repo=metapi&style=flat)](https://github.com/ohmeta/metapi)
+[![Anaconda-Server Badge](https://anaconda.org/bioconda/metapi/badges/downloads.svg)](https://anaconda.org/bioconda/metapi)
+
+A pipeline to construct genome catalogue from metagenomcis data.
+
+## Installation
+
+metapi works with Python 3.6+.
+You can install it via [bioconda](https://bioconda.github.io/):
+
+```
+$ conda install metapi
+```
+
+Or via pip:
+
+```
+$ pip install metapi
+```
+
+## Run
+
+### help
+
+```
+$ metapi --help
+
+  .___  ___.  _______ .___________.    ___      .______    __
+  |   \/   | |   ____||           |   /   \     |   _  \  |  |
+  |  \  /  | |  |__   `---|  |----`  /  ^  \    |  |_)  | |  |
+  |  |\/|  | |   __|      |  |      /  /_\  \   |   ___/  |  |
+  |  |  |  | |  |____     |  |     /  _____  \  |  |      |  |
+  |__|  |__| |_______|    |__|    /__/     \__\ | _|      |__|
+
+            Omics for All, Open Source for All
+
+  A pipeline to construct a genome catalogue from metagenomics data
+
+    optional arguments:
+    -h, --help     show this help message and exit
+    -v, --version  print software version and exit
+
+    available subcommands:
+
+    init         init project
+    denovo_wf    denovo_wf pipeline
+```
+
+### init
+
+```
+$ metapi init --help
+
+  usage: metapi init [-h] [-d WORKDIR] [-s SAMPLES]
+                    [-b {simulate,trimmingrmhost,assembly}]
+
+  arguments:
+      -h, --help            show this help message and exit
+      -d WORKDIR, --workdir WORKDIR
+                            project workdir
+      -s SAMPLES, --samples SAMPLES
+                            samples list, tsv format required if begin from
+                            trimming, rmhost, or assembly: if it is fastq: the
+                            header is [id, fq1, fq2], else it is sra: the header
+                            is [id, sra] else begin from simulate: the header is
+                            [id, genome, abundance, reads_num, model]
+    -b {simulate,trimming,rmhost,assembly}, --begin {simulate,trimming,rmhost,assembly}
+                            pipeline starting point
+```
+
+### denovo_wf
+
+```
+$ metapi denovo_wf --help
+
+  usage: metapi denovo_wf [-h] [-d WORKDIR] [--cores CORES] [--jobs JOBS]
+                          [--list] [--run] [--debug] [--dry_run] [--qsub]
+                          [--wait WAIT] [--snake [SNAKEMAKEARGS]]
+                          [TASK]
+
+  positional arguments:
+    TASK                  pipeline end point. Allowed values are simulate_all,
+                          prepare_reads_all, raw_fastqc_all, rmhost_bwa_all,
+                          rmhost_bowtie2_all, rmhost_all, assebmly_megahit_all,
+                          assembly_idba_ud_all, assembly_metaspades_all,
+                          assembly_spades_all, assembly_metaquast_all,
+                          assembly_report_all, assembly_all,
+                          alignment_base_depth_all, alignment_all,
+                          binning_metabat2_all, binning_maxbin2_all,
+                          binning_all, predcit_scafitgs_gene_all,
+                          predict_bins_gene_all, predcit_all, checkm_link_bins,
+                          checkm_all, dereplicate_drep_all, dereplicate_all,
+                          classify_short_reads_kraken2_all,
+                          classify_hmq_bins_gtdbtk_all, classify_all,
+                          profiling_metaphlan2_all, profiling_jgi_all,
+                          profiling_humann2_all, profiling_all,
+                          upload_sequencing_all, upload_assembly_all,
+                          upload_all, all
+
+  arguments:
+    -h, --help            show this help message and exit
+    -d WORKDIR, --workdir WORKDIR
+                          project workdir, default: ./
+    --cores CORES         CPU cores
+    --jobs JOBS           qsub job numbers
+    --list                list pipeline rules
+    --run                 run pipeline
+    --debug               debug pipeline
+    --dry_run             dry run pipeline
+    --qsub                qsub pipeline
+    --wait WAIT           wait given seconds
+    --snake [SNAKEMAKEARGS]
+                          other snakemake command options, if want --touch, just
+                          --snake touch
+```
+
+## input requirements
+
+The input samples file: `samples.tsv` format:
+
+Note: If `id` col contain same id, then the reads of each sample will be merged.
+
+- begin from trimming, rmhost or assembly:
+
+  - `Paired-end fastq`
+
+  | id  |   fq1   |   fq2   |
+  | :-: | :-----: | :-----: |
+  | s1  | aa.1.fq | aa.2.fq |
+  | s2  | bb.1.fq | bb.2.fq |
+  | s2  | cc.1.fq | cc.2.fq |
+  | s3  | dd.1.fq | dd.2.fq |
+
+  - `Single-end fastq`
+
+  | id  |   fq1   | fq2 |
+  | :-: | :-----: | :-: |
+  | s1  | aa.1.fq |     |
+  | s2  | bb.1.fq |     |
+  | s2  | cc.1.fq |     |
+  | s3  | dd.1.fq |     |
+
+  - `SRA`:
+
+  SRA can be dumpped to Paired-end fastq reads
+
+  | id  |  sra   |
+  | :-: | :----: |
+  | s1  | aa.sra |
+  | s2  | bb.sra |
+  | s2  | cc.sra |
+  | s3  | dd.sra |
+
+- begin from simulate
+
+  | id  | genome | abundance | reads_num | model |
+  | :-: | :----: | :-------: | :-------: | :---: |
+  | s1  | g1.fa  |    1.0    |    1M     | hiseq |
+  | s2  | g1.fa  |    0.5    |    2M     | hiseq |
+  | s2  | g2.fa  |    0.5    |    2M     | hiseq |
+  | s3  | g1.fa  |    0.2    |    3M     | hiseq |
+  | s3  | g2.fa  |    0.3    |    3M     | hiseq |
+  | s3  | g3.fa  |    0.5    |    3M     | hiseq |
+
+It means:
+
+The sample s1 contain 1M reads which come from g1, the relatative abundance of
+species g1 is 1.0.
+
+The sample s2 contain 2M reads, 1M reads come from g1
+and 1M reads come from g2. the relatative abundance of
+species g1 is 0.5, the relatative abundance of
+species g2 is 0.5.
+
+The sample s3 contain 3M reads, 0.6M reads come from g1, 0.9M reads come from
+g2 and 1.5M reads come from g3, the relatative abundance of
+species g1 is 0.2, the relatative abundance of
+species g1 is 0.3, the relatative abundance of
+species g1 is 0.5.
+
+Then metapi will use [InSilicoSeq] to generate metagenomics shutgun reads.
+
+## Getting help
+
+If you want to report a bug or issue, or have problems with installing or
+running the software, please create [a new
+issue](https://github.com/ohmeta/metapi/issues).
+This is the preferred way of getting support. Alternatively, you can [mail me](mailto:[email protected]).
+
+## Contributing
+
+Contributions welcome! Send me a pull request or get in [touch](mailto:[email protected])
+
+When contributing a PR, please use the [dev](https://github.com/ohmeta/metapi/tree/dev) branch.
+For style, code will be checked using flake8,
+[black](https://github.com/psf/black), and
+[smakefmt](https://github.com/snakemake/snakefmt). These modules can be
+installed via conda, `conda install black flake8 flake8-bugbear snakefmt` or via
+pip `pip install black flake8 flake8-bugbear snakefmt`.
+
+## Contributors
+
+- Jie Zhu - @alienzj
+
+## License
+
+This module is licensed under the terms of the [GPLv3 license](https://opensource.org/licenses/GPL-3.0).
diff --git a/README.org b/README.org
diff --git a/build.sh b/build.sh
@@ -1,3 +1,6 @@
 #!/bin/sh
+rm -rf build
+rm -rf metapi.egg-info
+rm -rf dist
 python3 setup.py sdist bdist_wheel
-twine upload dist/*
+twine upload dist/*
diff --git a/conda/meta.yaml b/conda/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "metapi" %}
 {% set version = "0.7.1" %}
-{% set sha256 = "5943b213b97f42bd13379c43c66949c543b35f1a84ff552d450021677306bf60" %}
+{% set sha256 = "bd5bf907cbe90d512d77f4fff75d3c16352f232aa22e7e43ba088cb7b6a6f583" %}
 
 package:
   name: {{ name|lower }}
@@ -20,27 +20,28 @@ build:
 
 requirements:
   build:
-    - python >=3.5
+    - python >=3.6
     - setuptools
     - pip
 
   host:
-    - python >=3.5
+    - python >=3.6
     - setuptools
     - pip
     - pandas
     - ruamel.yaml
     - snakemake >=5.10
 
   run:
-    - python >=3.5
+    - python >=3.6
     - numpy
     - pandas
     - openpyxl
     - biopython
     - ruamel.yaml
     - snakemake >=5.10
     - insilicoseq
+    - fastqc
     - seqtk
     - seqkit
     - multiqc