add sipros

recipes/sipros/LICENSE

@@ -0,0 +1,24 @@
+MIT License
+
+Copyright (c) 2023 Phase Technician XYZ
+
+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.
+
+Code written for the MSToolkit uses the Apache License, Version 2.0. All 3rd 
+party software included in the MSToolkit library retains its original license.

recipes/sipros/Raxport.sh

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+#!/usr/bin/env bash
+SOURCE="${BASH_SOURCE[0]}"
+while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink
+   DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
+   SOURCE="$(readlink "$SOURCE")"
+   [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located
+done
+DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
+mono "$DIR/Raxport.exe" "$@"

recipes/sipros/build.sh

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+#!/bin/bash
+set -e
+
+mkdir -p "$PREFIX/bin"
+chmod u+x bin/*
+cp -r bin/* "$PREFIX/bin"
+
+cp -r EnsembleScripts "$PREFIX"
+cp -r V4Scripts "$PREFIX"
+
+cp -r configTemplates "$PREFIX"
+
+cp $RECIPE_DIR/Raxport.sh "$PREFIX/bin/Raxport"
+chmod +x "$PREFIX/bin/Raxport"

recipes/sipros/meta.yaml

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+{% set name = "sipros" %}
+{% set version = "4.01" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: https://github.com/thepanlab/Sipros4/releases/download/{{ version }}/siprosRelease.zip
+  sha256: 10030671b94a8a2ab354396178f35c30a8e8e0c633864533690c1ff285906c9c
+
+build:
+  noarch: generic
+  number: 0
+  skip: False
+  run_exports:
+    - {{ pin_subpackage('sipros', max_pin="x") }}
+
+requirements:
+  run:
+    - bioconductor-biostrings =2.70.1
+    - mono
+    - numpy =1.16
+    - python =2.7
+    - r-base >=4.3,<4.4.0a0
+    - r-stringr =1.5
+    - r-tidyr =1.3
+    - scikit-learn =0.20.3
+
+test:
+  commands:
+    - configGenerator -h
+    - SiprosEnsembleOMP --help
+    - SiprosV4OMP --help
+    - Raxport -h
+    - python $CONDA_PREFIX/EnsembleScripts/sipros_psm_tabulating.py -v
+    - python $CONDA_PREFIX/V4Scripts/sipros_peptides_filtering.py -v
+
+about:
+  home: https://github.com/thepanlab/Sipros4
+  license: MIT
+  # currently include in the recipe folder because from the release (https://github.com/thepanlab/Sipros4/issues/3)
+  license_file: LICENSE
+  summary: "Tools for stable isotopic mass spectrometry-based metaproteomics"
+  description: |
+      "Tools for stable isotopic mass spectrometry-based metaproteomics research developed by Sipros team. These include Raxport, SiprosV4, SiprosEnsemble and some python / R scripts."
+
+extra:
+  recipe-maintainers:
+    - bernt-matthias
+    - yi-xiong
+  identifiers:
+    - biotools:sipros
+    - doi:10.1186/s40168-024-01866-1