Add recipe for HELIANO, a tool for the detection of helitrons in diverse genomes

recipes/heliano/build.sh

@@ -0,0 +1,46 @@
+#!/bin/bash
+#Based on https://github.com/TobyBaril/EarlGrey/blob/main/configure
+set -x
+
+# Define paths
+PACKAGE_HOME=${PREFIX}/share/${PKG_NAME}-${PKG_VERSION}-${PKG_BUILDNUM}
+
+# create directories
+mkdir -p ${PREFIX}/bin
+mkdir -p ${PACKAGE_HOME}
+
+# put package in share directory
+cp -rf * ${PACKAGE_HOME}/
+
+# fix file paths
+BCHECK=${PACKAGE_HOME}/heliano_bcheck.R
+FISHER=${PACKAGE_HOME}/heliano_fisher.R
+HMMmodel=${PACKAGE_HOME}/RepHel.hmm
+Headermodel=${PACKAGE_HOME}/tclcv.txt
+SPLIT=${PACKAGE_HOME}/SplitJoint.R
+SORT=${PACKAGE_HOME}/Sort.sh
+myPYTHON_PATH=`which python3`
+
+sed -i.bak "s|_INTERPRETERPYTHON_PATH_|${myPYTHON_PATH}|" ${PACKAGE_HOME}/heliano.py
+sed -i.bak "s|_HMM_|${HMMmodel}|" ${PACKAGE_HOME}/heliano.py
+sed -i.bak "s|_HEADER_|${Headermodel}|" ${PACKAGE_HOME}/heliano.py
+sed -i.bak "s|_FISHER_|${FISHER}|" ${PACKAGE_HOME}/heliano.py
+sed -i.bak "s|_BOUNDARY_|${BCHECK}|" ${PACKAGE_HOME}/heliano.py
+sed -i.bak "s|_SPLIT_JOINT_|${SPLIT}|" ${PACKAGE_HOME}/heliano.py
+sed -i.bak "s|_SORTPRO_|${SORT}|" ${PACKAGE_HOME}/heliano.py
+
+# set permissions to files
+cp ${PACKAGE_HOME}/heliano.py ${PACKAGE_HOME}/heliano
+cp ${PACKAGE_HOME}/heliano_cons.py ${PACKAGE_HOME}/heliano_cons
+chmod +x ${PACKAGE_HOME}/heliano
+chmod +x ${PACKAGE_HOME}/heliano_cons
+
+# test for conda
+df -h
+
+# put files in the executable bin
+cd ${PREFIX}/bin
+ln -sf ${PACKAGE_HOME}/heliano
+ln -sf ${PACKAGE_HOME}/heliano_cons
+
+echo "Succeed! Please find programs in bin/ directory."

recipes/heliano/meta.yaml

@@ -0,0 +1,55 @@
+{% set name = "heliano" %}
+{% set version = "1.2.0" %}
+{% set sha256 = "65db4bb60701219ebb512f53ef95a8afa51135bb0492caf68f19e6d9ba2b5179" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: https://github.com/Zhenlisme/heliano/archive/refs/tags/v{{ version }}.tar.gz
+  sha256: {{ sha256 }}
+
+build:
+  number: 0
+  run_exports:
+    - {{ pin_subpackage('heliano', max_pin='x') }}
+  noarch: generic
+
+requirements:
+  run:
+    - python =3.9
+    - r-base
+    - biopython
+    - pybedtools
+    - r-bedtoolsr
+    - r-seqinr
+    - bedtools
+    - dialign2
+    - mafft
+    - cd-hit 
+    - blast
+    - emboss
+    - hmmer
+    - genometools-genometools
+    - rnabob
+
+test:
+  commands:
+    - df -h
+    - heliano -h
+
+about:
+  home: "https://github.com/Zhenlisme/heliano"
+  dev_url: "https://github.com/Zhenlisme/heliano"
+  license: GPL-3
+  summary: "HELIANO: A fast and accurate tool for detection of Helitron-like elements"
+  description: |
+    Helitron-like elements (HLE1 and HLE2) are DNA transposons. 
+    They have been found in diverse species and seem to play significant roles in the evolution of host genomes. 
+    Although known for over twenty years, Helitron sequences are still challenging to identify. 
+    Here, we propose HELIANO (Helitron-like elements annotator) as an efficient solution for detecting Helitron-like elements.
+
+extra:
+  identifiers:
+    - doi:10.1093/nar/gkae679