From 3323ae805c866e3707c617c9c8678d02c107801e Mon Sep 17 00:00:00 2001 From: jfsanchezherrero Date: Wed, 10 Mar 2021 10:37:36 +0100 Subject: [PATCH] prepare release --- LICENSE | 22 ++++++++ VERSION | 2 +- devel/conda/build.sh | 4 ++ devel/conda/meta.yaml | 55 +++++++++++++++++++ ...guidelines.txt => developer_guidelines.md} | 4 +- devel/{ => pypi}/clean_devel.sh | 0 devel/{ => pypi}/create_distro.sh | 0 devel/{ => pypi}/requirements.txt | 0 devel/{ => pypi}/test_module.sh | 0 devel/{ => pypi}/upload_pypi.sh | 0 10 files changed, 85 insertions(+), 2 deletions(-) create mode 100644 devel/conda/build.sh create mode 100644 devel/conda/meta.yaml rename devel/{developer_guidelines.txt => developer_guidelines.md} (84%) rename devel/{ => pypi}/clean_devel.sh (100%) rename devel/{ => pypi}/create_distro.sh (100%) rename devel/{ => pypi}/requirements.txt (100%) rename devel/{ => pypi}/test_module.sh (100%) rename devel/{ => pypi}/upload_pypi.sh (100%) diff --git a/LICENSE b/LICENSE index e69de29..45c3830 100644 --- a/LICENSE +++ b/LICENSE @@ -0,0 +1,22 @@ + +MIT License + +Copyright (c) 2020-2021 HCGB-IGTP + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE. diff --git a/VERSION b/VERSION index 2b7c5ae..17b2ccd 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -0.4.2 +0.4.3 diff --git a/devel/conda/build.sh b/devel/conda/build.sh new file mode 100644 index 0000000..2f60f96 --- /dev/null +++ b/devel/conda/build.sh @@ -0,0 +1,4 @@ +# configure, make, and install +configure --prefix=$PREFIX --with-zlib=$PREFIX +make -j${CPU_COUNT} +make install \ No newline at end of file diff --git a/devel/conda/meta.yaml b/devel/conda/meta.yaml new file mode 100644 index 0000000..be520ed --- /dev/null +++ b/devel/conda/meta.yaml @@ -0,0 +1,55 @@ +package: + name: BacterialTyper + version: https://github.com/HCGB-IGTP/BacterialTyper/releases + +source: + git_url: https://github.com/HCGB-IGTP/BacterialTyper/releases + +build: + number: 0 + string: py{{CONDA_PY}}np{{CONDA_NPY}}_{{PKG_BUILDNUM}}_h{{PKG_HASH}}_g{{GIT_FULL_HASH[:7]}} + + +requirements: + host: + - python + - pip + run: + - python >=3.7 + - fastqc + - kma + - iqtree + - prokka + - spades + - trimmomatic + - snippy + - entrez-direct + - blast + - augustus + - bowtie2 + - busco + - cd-hit + - ariba + + +about: + home: https://github.com/HCGB-IGTP/BacterialTyper + license: + license_family: + summary: A bioinformatics pipeline for the integrative analysis of bacterial WGS + description: + We present BacterialTyper, a pipeline for the analysis of bacterial WGS data that integrates + and facilitates the interpretation of results generated from multiple software analysis. It is + capable of processing and identifying bacterial strains, identifying resistance and virulence genes, + and generating data for outbreak analysis using WGS data from isolated microbial cultured + colonies. The design of this bioinformatic tool allows comparing samples with an internal database + (previously identified samples) and external databases. + + The pipeline is written in Python with a modular architecture and based on open-source software and + databases engines. Multiple tasks are performed by each of several modules including: preparation of + raw data; assembly and annotation; bacterial strain identification; mobile genetic elements + identification (plasmids, putative pathogenicity islands or phage insertions regions); generation of + a virulence and resistance profile; clustering based on sequence similarity; phylogenetic analysis; + integration of metadata, etc. The tool allows to compare samples with previously identified samples + (collected and internal database) but it also uses, and updates periodically, external databases + from different sources. diff --git a/devel/developer_guidelines.txt b/devel/developer_guidelines.md similarity index 84% rename from devel/developer_guidelines.txt rename to devel/developer_guidelines.md index 8b67f08..8594e99 100644 --- a/devel/developer_guidelines.txt +++ b/devel/developer_guidelines.md @@ -1,3 +1,5 @@ +## Create + ## clean distribution packages sh devel/clean_devel.sh @@ -20,4 +22,4 @@ sh devel/upload_pypi.sh ## references https://dzone.com/articles/executable-package-pip-install -https://packaging.python.org/tutorials/packaging-projects/ \ No newline at end of file +https://packaging.python.org/tutorials/packaging-projects/ diff --git a/devel/clean_devel.sh b/devel/pypi/clean_devel.sh similarity index 100% rename from devel/clean_devel.sh rename to devel/pypi/clean_devel.sh diff --git a/devel/create_distro.sh b/devel/pypi/create_distro.sh similarity index 100% rename from devel/create_distro.sh rename to devel/pypi/create_distro.sh diff --git a/devel/requirements.txt b/devel/pypi/requirements.txt similarity index 100% rename from devel/requirements.txt rename to devel/pypi/requirements.txt diff --git a/devel/test_module.sh b/devel/pypi/test_module.sh similarity index 100% rename from devel/test_module.sh rename to devel/pypi/test_module.sh diff --git a/devel/upload_pypi.sh b/devel/pypi/upload_pypi.sh similarity index 100% rename from devel/upload_pypi.sh rename to devel/pypi/upload_pypi.sh