From cd2568c7b4a176a1b4c3215a2333b849f033fb23 Mon Sep 17 00:00:00 2001
From: Nathan Edwards <edwardsnj@users.noreply.github.com>
Date: Thu, 23 Jun 2022 12:45:21 -0400
Subject: [PATCH] [ci skip] Merge PR 35412

Merge PR #35412, commits were:
 * Merge branch 'bioconda:master' into scexecute_bioconda_recipe
 * Merge branch 'scexecute_bioconda_recipe' of github.com:HorvathLab/bioconda-recipes into scexecute_bioconda_recipe
 * Remove data subdirectory from conda package
 * Merge branch 'bioconda:master' into scexecute_bioconda_recipe
 * another try...
 * more logging?
 * hope so? or not?
 * hope so?
 * round in circles...
 * again...
 * another attempt...
 * What can I assume about the test command?
 * Why is this failing?
 * tweak test command, third attempt
 * tweak test command, attempt #2
 * tweak test command
 * add summary
 * Merge branch 'scexecute_bioconda_recipe' of github.com:HorvathLab/bioconda-recipes into scexecute_bioconda_recipe
 * Add licence
 * Merge branch 'bioconda:master' into scexecute_bioconda_recipe
 * Initial bioconda recipe for scexecute and screadcounts
---
 recipes/scexecute/build.sh     | 11 ++++++++++
 recipes/scexecute/meta.yaml    | 35 ++++++++++++++++++++++++++++++++
 recipes/screadcounts/build.sh  | 11 ++++++++++
 recipes/screadcounts/meta.yaml | 37 ++++++++++++++++++++++++++++++++++
 4 files changed, 94 insertions(+)
 create mode 100644 recipes/scexecute/build.sh
 create mode 100644 recipes/scexecute/meta.yaml
 create mode 100755 recipes/screadcounts/build.sh
 create mode 100644 recipes/screadcounts/meta.yaml

diff --git a/recipes/scexecute/build.sh b/recipes/scexecute/build.sh
new file mode 100644
index 0000000000000..639c004ba3124
--- /dev/null
+++ b/recipes/scexecute/build.sh
@@ -0,0 +1,11 @@
+#!/bin/bash
+
+TARGET=share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM
+mkdir -p $PREFIX/$TARGET/bin
+mkdir -p $PREFIX/bin
+cp -r * $PREFIX/$TARGET
+rm -rf $PREFIX/$TARGET/data
+chmod -R a+rX $PREFIX/$TARGET
+chmod -R a+rx $PREFIX/$TARGET/bin/*
+cd $PREFIX/bin
+ln -s ../$TARGET/bin/* .
diff --git a/recipes/scexecute/meta.yaml b/recipes/scexecute/meta.yaml
new file mode 100644
index 0000000000000..a4ec512e32d3d
--- /dev/null
+++ b/recipes/scexecute/meta.yaml
@@ -0,0 +1,35 @@
+{% set name = "scexecute" %}
+{% set version = "1.3.1" %}
+{% set md5 = "2be354173821a168e810fecc819bb440" %}
+
+package:
+  name: {{ name }}
+  version: {{ version }}
+
+source:
+  url: https://github.com/HorvathLab/NGS/releases/download/SCExecute-{{ version }}/SCExecute-{{ version }}.Python-3.7.tgz
+  md5: {{ md5 }}
+
+build:
+  noarch: generic
+  number: 0
+
+extra:
+  skip-lints:
+    - should_be_noarch_python
+
+requirements:
+  run:
+    - python >=3.7
+    - pysam
+    - wxpython
+    - samtools
+
+test:
+  commands:
+    - scExecute -h
+
+about:
+  home: https://github.com/HorvathLab/NGS/tree/master/SCExecute#readme
+  summary: "SCExecute generates cell-barcode specific BAM files from aligned, aggregate single-cell sequencing data, executing a user-provided command on each barcode-stratified BAM file."
+  license: MIT
diff --git a/recipes/screadcounts/build.sh b/recipes/screadcounts/build.sh
new file mode 100755
index 0000000000000..c04475a5d398b
--- /dev/null
+++ b/recipes/screadcounts/build.sh
@@ -0,0 +1,11 @@
+#!/bin/bash
+
+TARGET=share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM
+mkdir -p $PREFIX/$TARGET/bin
+mkdir -p $PREFIX/bin
+cp -r * $PREFIX/$TARGET
+rm -rf $PREFIX/$TARGET/data
+chmod -R a+rX $PREFIX/$TARGET
+chmod -R a+rx $PREFIX/$TARGET/bin/
+cd $PREFIX/bin
+ln -s ../$TARGET/bin/* .
diff --git a/recipes/screadcounts/meta.yaml b/recipes/screadcounts/meta.yaml
new file mode 100644
index 0000000000000..eb0ec7af0fce9
--- /dev/null
+++ b/recipes/screadcounts/meta.yaml
@@ -0,0 +1,37 @@
+{% set name = "screadcounts" %}
+{% set version = "1.2.0" %}
+{% set md5 = "83e591cc26df4c14b5a1d0332cfe5349" %}
+
+package:
+  name: {{ name }}
+  version: {{ version }}
+
+source:
+  url: https://github.com/HorvathLab/NGS/releases/download/SCReadCounts-{{ version }}/SCReadCounts-{{ version }}.Python-3.7.tgz
+  md5: {{ md5 }}
+
+build:
+  noarch: generic
+  number: 0
+
+extra:
+  skip-lints:
+    - should_be_noarch_python
+
+requirements:
+  run:
+    - python >=3.7
+    - pysam
+    - wxpython
+    - samtools
+    - numpy
+    - scipy
+
+test:
+  commands:
+    - scReadCounts -h 
+
+about:
+  home: https://github.com/HorvathLab/NGS/tree/master/SCReadCounts#readme
+  summary: "SCReadCounts is a computational tool for a cell-level assessment of the read counts bearing a particular nucleotide at genomic positions of interest from single cell RNA sequencing (scRNA-seq) data."
+  license: MIT