From ec4c5d12631b79ea29a56862f13227e6cfd61dd0 Mon Sep 17 00:00:00 2001
From: Adrian Zimmer <z.adrian1995@gmail.com>
Date: Thu, 28 Apr 2022 11:01:23 +0200
Subject: [PATCH] [ci skip] Merge PR 34476

Merge PR #34476, commits were:
 * Update meta.yaml
 * Re-add openssl pin
 * Add openssl req without pin
 * Remove openssl dependency, move back to nuget instead of github releases
 * Fix file name issue, add openssl runtime dep
 * Fix package build
 * Merge branch 'bioconda:master' into master
 * Merge branch 'bioconda:master' into master
 * Merge branch 'master' of https://github.com/bioconda/bioconda-recipes
 * Merge branch 'master' of https://github.com/bioconda/bioconda-recipes
 * Merge branch 'master' of https://github.com/bioconda/bioconda-recipes
 * Merge branch 'master' of https://github.com/bioconda/bioconda-recipes
 * Merge branch 'master' of https://github.com/bioconda/bioconda-recipes
 * Merge branch 'master' of https://github.com/bioconda/bioconda-recipes
 * Merge branch 'master' of https://github.com/bioconda/bioconda-recipes
 * Merge branch 'master' of https://github.com/bioconda/bioconda-recipes
 * Merge branch 'master' of https://github.com/bioconda/bioconda-recipes
 * Merge branch 'master' of https://github.com/bioconda/bioconda-recipes
 * Merge branch 'master' of https://github.com/bioconda/bioconda-recipes
 * Merge branch 'master' of https://github.com/bioconda/bioconda-recipes
 * Merge branch 'master' of https://github.com/bioconda/bioconda-recipes
 * Merge pull request #1 from bioconda/master

Update Fork
---
 .../proteomiqon-peptidespectrummatching/build.sh  | 10 ++++++++++
 .../proteomiqon-peptidespectrummatching/meta.yaml | 15 +++++++--------
 .../proteomiqon-peptidespectrummatching.sh        |  3 +++
 3 files changed, 20 insertions(+), 8 deletions(-)
 create mode 100644 recipes/proteomiqon-peptidespectrummatching/build.sh
 create mode 100644 recipes/proteomiqon-peptidespectrummatching/proteomiqon-peptidespectrummatching.sh

diff --git a/recipes/proteomiqon-peptidespectrummatching/build.sh b/recipes/proteomiqon-peptidespectrummatching/build.sh
new file mode 100644
index 0000000000000..c62f97ddbb222
--- /dev/null
+++ b/recipes/proteomiqon-peptidespectrummatching/build.sh
@@ -0,0 +1,10 @@
+#!/bin/bash
+unzip $SRC_DIR/$PKG_VERSION
+PREFIX=$(echo "${PREFIX}" | tr '\\' '/')
+DOTNET_ROOT="${PREFIX}/lib/dotnet"
+TOOL_ROOT=$DOTNET_ROOT/tools/PeptideSpectrumMatching
+
+mkdir -p $PREFIX/bin $TOOL_ROOT
+cp -r $SRC_DIR/tools/net5.0/any/* $TOOL_ROOT
+cp "$RECIPE_DIR/proteomiqon-peptidespectrummatching.sh" "$PREFIX/bin/proteomiqon-peptidespectrummatching"
+chmod +x "$PREFIX/bin/proteomiqon-peptidespectrummatching"
diff --git a/recipes/proteomiqon-peptidespectrummatching/meta.yaml b/recipes/proteomiqon-peptidespectrummatching/meta.yaml
index ec32f7aa0d888..a3b852a1b9389 100644
--- a/recipes/proteomiqon-peptidespectrummatching/meta.yaml
+++ b/recipes/proteomiqon-peptidespectrummatching/meta.yaml
@@ -6,20 +6,19 @@ package:
   version: '{{ version }}'
 
 source:
-  url: https://www.nuget.org/api/v2/package/ProteomIQon.PeptideSpectrumMatching/{{ version }}
-  sha256: '{{ sha256 }}'
+  url: https://www.nuget.org/api/v2/package/ProteomIQon.PeptideSpectrumMatching/{{version}}
+  sha256: '{{sha256}}'
 
 build:
   noarch: generic
-  number: 0
-  script:
-    - dotnet tool install --add-source $SRC_DIR --tool-path $PREFIX/bin --version {{ version }} ProteomIQon.PeptideSpectrumMatching
+  number: 1
 
 requirements:
   host:
-    - dotnet-sdk
+    - unzip
   run:
-    - dotnet-runtime
+    - openssl =1.1
+    - dotnet-runtime =5.0
 
 test:
   commands:
@@ -35,4 +34,4 @@ about:
     tolerance (which defines the so called 'search space') and retrieve peptides that are theoretical candidates for a match. For each of the peptide
     candidates we create an theoretical spectrum in silico and compare it to the measured MS/MS scan.
   dev_url: https://github.com/CSBiology/ProteomIQon
-  doc_url: https://csbiology.github.io/ProteomIQon/tools/PeptideSpectrumMatching.html
\ No newline at end of file
+  doc_url: https://csbiology.github.io/ProteomIQon/tools/PeptideSpectrumMatching.html
diff --git a/recipes/proteomiqon-peptidespectrummatching/proteomiqon-peptidespectrummatching.sh b/recipes/proteomiqon-peptidespectrummatching/proteomiqon-peptidespectrummatching.sh
new file mode 100644
index 0000000000000..9ec8b53f48037
--- /dev/null
+++ b/recipes/proteomiqon-peptidespectrummatching/proteomiqon-peptidespectrummatching.sh
@@ -0,0 +1,3 @@
+
+#!/usr/bin/env bash
+dotnet $CONDA_PREFIX/lib/dotnet/tools/PeptideSpectrumMatching/ProteomIQon.PeptideSpectrumMatching.dll "$@"
\ No newline at end of file