prepare release

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.

VERSION

@@ -1 +1 @@
-0.4.2
+0.4.3

devel/conda/build.sh

@@ -0,0 +1,4 @@
+# configure, make, and install
+configure --prefix=$PREFIX --with-zlib=$PREFIX
+make -j${CPU_COUNT}
+make install

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. 

devel/developer_guidelines.txt → 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/
+https://packaging.python.org/tutorials/packaging-projects/