Scanpy scripts

recipes/scanpy-scripts/build.sh

@@ -0,0 +1,5 @@
+#!/usr/bin/env bash
+
+mkdir -p $PREFIX/bin
+cp *.py $PREFIX/bin
+cp *.sh $PREFIX/bin

recipes/scanpy-scripts/meta.yaml

@@ -0,0 +1,48 @@
+{% set version = '0.0.2' %}
+
+package:
+  name: scanpy-scripts
+  version: {{ version }}
+
+source:
+  url: https://github.com/ebi-gene-expression-group/scanpy-scripts/archive/v{{ version }}.tar.gz
+  sha256: 4d9d3193857e5f801540236db547aa91db6c1db47c43943915f130c4fa8a31b2
+
+build:
+  number: 0
+  skip: True # [not py36]
+
+requirements:
+    host:
+        - python>=3.6
+    run:
+        - python>=3.6
+        - pandas>=0.22
+        - matplotlib>=3.0.0
+        - scanpy>=1.3.2
+
+test:
+    commands:
+        - scanpy-read-10x.py --help
+        - scanpy-filter-cells.py --help
+        - scanpy-filter-genes.py --help
+        - scanpy-normalise-data.py --help
+        - scanpy-find-variable-genes.py --help
+        - scanpy-scale-data.py --help
+        - scanpy-run-pca.py --help
+        - scanpy-neighbours.py --help
+        - scanpy-run-umap.py --help
+        - scanpy-run-tsne.py --help
+        - scanpy-find-cluster.py --help
+        - scanpy-find-markers.py --help
+        - which scanpy-scripts-post-install-tests.sh
+
+about:
+    home: https://github.com/ebi-gene-expression-group/scanpy-scripts
+    dev_url: https://github.com/ebi-gene-expression-group/scanpy-scripts
+    license: GPL-3
+    summary: A set of wrappers for individual components of the scanpy package.
+             Functions in python packages are hard to call when building workflows
+             outside of python, so this package adds a set of simple wrappers with
+             robust argument parsing.
+    license_family: GPL

recipes/scanpy-scripts/post-link.sh

@@ -0,0 +1,4 @@
+#!/usr/bin/env bash
+
+echo 'Post install test script "scanpy-scripts-post-install-tests.sh" requires'
+echo 'conda package "bats-core".'