New recipe: Slamdunk (#10199)

* Slamdunk recipe setup. * No fixed java version. * Java-jdk -> Openjdk. * PREFIX removed from recipe. * wget dependency added. * conda build checking. * path extensions. * Only py2.7 requirement. * Win skip removed. * lka * lkal * pip install switch * samtools dependencies added * senf * senf1 * recent * satool * sha * shaupdate * freaky * testy * testz * Slamdunk v0.3.1 bioconda build 0. * SHA256 updated. * Skipping py3 build. Using pip. * Python3 builds not skipped - otherwise package will not be built at all. * OSX build deactivated. * Skip py3k. OSX activated. * OSX deactivated for good. * .buildkite restored. Skip merged into one-liner.
bioconda · Aug 3, 2018 · ccd9911 · ccd9911
1 parent 64fbc1f
commit ccd9911
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diff --git a/recipes/slamdunk/build.sh b/recipes/slamdunk/build.sh
@@ -0,0 +1,7 @@
+#!/bin/bash
+
+if [[ $OSTYPE == darwin* ]]; then
+     export LDFLAGS="${LDFLAGS} -headerpad_max_install_names"
+fi
+
+python -m pip install --no-deps --ignore-installed .
diff --git a/recipes/slamdunk/meta.yaml b/recipes/slamdunk/meta.yaml
@@ -0,0 +1,82 @@
+{% set version = "0.3.1" %}
+{% set sha256 = "2cc5d561ef2c3014595b646858ae2fa76c3d3972a2b624dd5d01eb82ac239c28" %}
+
+package:
+  name: slamdunk
+  version: {{ version }}
+
+source:
+  sha256: '{{sha256}}'
+  url: "https://github.com/t-neumann/slamdunk/archive/v0.3.1.tar.gz"
+
+build:
+  entry_points:
+    - slamdunk=slamdunk.slamdunk:run
+    - alleyoop=slamdunk.alleyoop:run
+    - splash=slamdunk.splash:run
+  number: 0
+  skip: True # [py3k or osx]
+
+requirements:
+  build:
+    - {{ compiler('cxx') }}
+    - cmake
+    - wget
+
+  host:
+    - python
+    - setuptools
+    - joblib >=0.9.4
+    - pybedtools >=0.6.4
+    - intervaltree >=2.1.0
+    - pandas >=0.13.1
+    - biopython >=1.63
+    - pysam >=0.8.3
+    - cython >=0.20.1
+    - zlib
+    - openjdk
+    - r-base
+    - ncurses
+    - zlib
+    - bzip2
+    - curl
+    - xz
+    - libdeflate
+  run:
+    - python
+    - joblib >=0.9.4
+    - pybedtools >=0.6.4
+    - intervaltree >=2.1.0
+    - pandas >=0.13.1
+    - biopython >=1.63
+    - pysam >=0.8.3
+    - cython >=0.20.1
+    - zlib
+    - openjdk
+    - r-base
+    - ncurses
+    - zlib
+    - bzip2
+    - curl
+    - xz
+    - libdeflate
+
+test:
+  imports:
+    - slamdunk
+    - slamdunk.contrib
+    - slamdunk.dunks
+    - slamdunk.plot
+    - slamdunk.slamseq
+    - slamdunk.test
+    - slamdunk.utils
+  commands:
+    - slamdunk --help
+    - alleyoop --help
+    - splash --help
+
+about:
+  home: "http://t-neumann.github.io/slamdunk"
+  license: GNU Affero General Public License v3 (AGPLv3)
+  license_file: LICENSE
+  summary: "SlamDunk is a novel, fully automated software tool for automated, robust, scalable and reproducible SLAMseq data analysis."