Merge pull request #11 from pdimens/condatest

merge conda testing branch into main

.misc/build.sh

@@ -0,0 +1,22 @@
+#! usr/bin/env bash
+
+# for installing conda package
+mkdir -p $PREFIX/bin
+mkdir -p $PREFIX/bin/lepmap3
+mkdir -p $PREFIX/bin/lepanchor
+# LepWrap executable
+chmod +x LepWrap
+cp LepWrap $PREFIX/bin/
+# associated scripts
+chmod +x scripts/*
+cp scripts/* $PREFIX/bin/
+# LepMap3 modules and scripts
+cp software/LepMap3/*.class $PREFIX/bin/lepmap3
+cp software/LepMap3/scripts/* $PREFIX/bin
+# LepAnchor modules and scripts
+cp software/LepAnchor/*.class $PREFIX/bin/lepanchor
+cp software/LepAnchor/scripts/* $PREFIX/bin
+cp software/LepAnchor/deps/ucsc_binaries/* $PREFIX/bin
+cp software/LepAnchor/deps/*.pl software/LepAnchor/deps/Red software/LepAnchor/deps/all_lastz.ctl software/LepAnchor/deps/scoreMatrix.q software/LepAnchor/deps/step* $PREFIX/bin
+# Snakemake rules
+cp rules/LepAnchor/*.smk rules/LepMap3/*.smk $PREFIX/bin

.misc/install.sh

@@ -0,0 +1,28 @@
+#! /usr/bin/env bash
+
+if [ -z "$CONDA_PREFIX" ]; then
+    echo "No active conda environment detected, will not install dependencies unless in an active environment"
+    exit 1
+fi
+
+# install LepWrap into conda PATH
+mkdir -p $CONDA_PREFIX/bin
+mkdir -p $CONDA_PREFIX/bin/lepmap3
+mkdir -p $CONDA_PREFIX/bin/lepanchor
+# LepWrap executable
+cp LepWrap $CONDA_PREFIX/bin/
+chmod +x $CONDA_PREFIX/bin/LepWrap
+# associated scripts
+chmod +x scripts/*
+cp scripts/* $CONDA_PREFIX/bin/
+# LepMap3 modules and scripts
+cp software/LepMap3/*.class $CONDA_PREFIX/bin/lepmap3
+cp software/LepMap3/scripts/* $CONDA_PREFIX/bin
+# LepAnchor modules and scripts
+cp software/LepAnchor/*.class $CONDA_PREFIX/bin/lepanchor
+cp software/LepAnchor/scripts/* $CONDA_PREFIX/bin
+ln -s $CONDA_PREFIX/bin/lepmap3/*.class $CONDA_PREFIX/bin/lepanchor/*.class $CONDA_PREFIX/bin/ 
+cp software/LepAnchor/deps/ucsc_binaries/* $CONDA_PREFIX/bin
+cp software/LepAnchor/deps/*.pl software/LepAnchor/deps/Red software/LepAnchor/deps/all_lastz.ctl software/LepAnchor/deps/scoreMatrix.q software/LepAnchor/deps/step* $CONDA_PREFIX/bin
+# Snakemake rules
+cp rules/LepAnchor/*.smk rules/LepMap3/*.smk $CONDA_PREFIX/bin

.misc/meta.yml

@@ -0,0 +1,49 @@
+{% set version = "3.6.2" %}
+{% set sha256 = "0f0998ecd50b586d69b50e53d9a0b3d5aa3afa70bd96fe85c2fa3ba02e58278b" %}
+
+package:
+  name: lepwrap
+  version: '{{ version }}'
+
+source:
+  url: https://github.com/pdimens/LepWrap/archive/refs/tags/{{ version }}.tar.gz
+  sha256: {{ sha256 }}
+
+build:
+  number: 3
+  noarch: generic
+
+requirements:
+  build:
+  host:
+  run:
+    - bzip2
+    - font-ttf-dejavu-sans-mono
+    - font-ttf-ubuntu
+    - pygraphviz
+    - graphviz
+    - imagemagick
+    - openjdk
+    - pandoc
+    - python >=3.9
+    - r-base >=4
+    - r-dplyr
+    - r-tidyr
+    - r-stringr
+    - r-ggplot2
+    - r-readr
+    - sed
+    - snakemake >=6.4
+
+test:
+  commands:
+    - "java --version"
+    - "R --version"
+about:
+  home: "https://github.com/pdimens/LepWrap/"
+  license: "The GNU General Public License v3.0 (GPL3)"
+  summary: "The Snakemake pipeline to use Lep-Map3 to create linkage maps and LepAnchor for anchoring+orienting genome assemblies."
+
+extra:
+  container:
+    extended-base: True