Ac trnanalysis (bioconda#15458)

Package uploads complete: [ci skip]
 - biocontainers/trnanalysis:0.1.0--py36h637b7d7_0
 - linux-64/trnanalysis-0.1.0-py36h637b7d7_0.tar.bz2
 - osx-64/trnanalysis-0.1.0-py36h1702cab_0.tar.bz2

Co-authored-by: Elmar Pruesse <epruesse@users.noreply.github.com>

recipes/trnanalysis/LICENSE

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+MIT License
+
+Copyright (c) 2019 Adam Cribbs
+
+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.

recipes/trnanalysis/build.sh

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+#!/bin/bash
+
+# export required env variables
+export C_INCLUDE_PATH=$PREFIX/include
+
+# linking htslib, see:
+# http://pysam.readthedocs.org/en/latest/installation.html#external
+# https://github.com/pysam-developers/pysam/blob/v0.9.0/setup.py#L79
+export CFLAGS="-I$PREFIX/include -DHAVE_LIBDEFLATE"
+export CPPFLAGS="-I$PREFIX/include -DHAVE_LIBDEFLATE"
+export LDFLAGS="-L$PREFIX/lib"
+
+export HTSLIB_LIBRARY_DIR=$PREFIX/lib
+export HTSLIB_INCLUDE_DIR=$PREFIX/include
+
+# remove install_requires (no longer required with conda package)
+sed -i'' -e '/REPO_REQUIREMENT/,/pass/d' setup.py
+sed -i'' -e '/# dependencies/,/dependency_links=dependency_links,/d' setup.py
+
+# https://bioconda.github.io/linting.html#setup-py-install-args
+$PYTHON setup.py install --single-version-externally-managed --record=record.txt
+

recipes/trnanalysis/meta.yaml

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+{% set version = "0.1.0" %}
+
+package:
+  name: trnanalysis
+  version: {{ version }}
+
+source:
+  url: https://files.pythonhosted.org/packages/0a/3b/8a9b6112ebc02babf5a104f88eff7686724da83a882c17a044c8f8a60297/tRNAnalysis-0.1.0.tar.gz
+  sha256: cd931079bcd617b0b9a54d072978c4ab38a432e580cff591fef6a4704ab11e80
+
+build:
+  skip: True # [not py==36]
+  number: 0
+  entry_points:
+    - trnanalysis = trnanalysis.entry:main
+
+requirements:
+  build:
+    - {{ compiler('c') }}
+    - {{ compiler('cxx') }}
+  host:
+    - python
+    - mysqlclient
+    - cgat-apps
+    - numpy
+    - pandas
+    - pysam
+    - ez_setup
+    - setuptools
+  run:
+    - python
+    - mysqlclient
+    - cgat-apps
+    - subread
+    - sortedcontainers
+    - seqtk
+    - trnascan-se
+    - configparser
+    - cgatcore
+    - ez_setup
+    - numpy
+    - pandas
+    - pysam
+    - ruffus
+    - multiqc
+    - seaborn
+    - bowtie
+    - fastqc
+    - fastq-screen
+    - r-base
+    - bioconductor-deseq2
+    - bioconductor-org.hs.eg.db
+    - r-dplyr
+    - r-dt
+    - r-fastqcr
+    - r-ggplot2
+    - r-ggpubr
+    - r-ggrepel
+    - r-ggthemes
+    - r-gridbase
+    - r-htmltools
+    - r-knitr
+    - r-optparse
+    - r-pheatmap
+    - r-plotly
+    - r-rcolorbrewer
+    - r-reshape2
+    - r-scales
+    - r-stringr
+    - r-tidyverse
+    - r-yaml
+    - r-codetools
+
+test:
+  imports:
+    - trnanalysis
+  commands:
+    - trnanalysis --help
+
+about:
+  home: https://trnanalysis.readthedocs.io/en/latest/
+  license: MIT
+  license_file: '{{ environ["RECIPE_DIR"] }}/LICENSE'
+  summary: "tRNA analysis pipeline"