From 801fad7b6c5b2a7c5f9adc0480e0465f02a5cba2 Mon Sep 17 00:00:00 2001 From: Anupam Gautam Date: Mon, 25 Nov 2024 23:09:10 +0100 Subject: [PATCH] GenEra Conda Recipes Submission (#51721) * Committer: Anupam Gautam TIPP_plastid is a User-Friendly Tool for De Novo Assembly of Organellar Genomes with HiFi Data * Update recipes/tipp/build.sh Co-authored-by: Martin Grigorov * Update recipes/tipp/build.sh Co-authored-by: Martin Grigorov * Update recipes/tipp/build.sh Co-authored-by: Martin Grigorov * Update recipes/tipp/build.sh Co-authored-by: Martin Grigorov * Update recipes/tipp/build.sh Co-authored-by: Martin Grigorov * Update recipes/tipp/meta.yaml Co-authored-by: Martin Grigorov * Committer: Anupam Gautam suggestion incorporated * Committer: Anupam Gautam updated meta and build. * GenEra conda recipes * removed genera files * GenEra conda recipe * cleaning * update * python updated * changes added * added test and abSENSE release * added test and abSENSE release * update * update * Update recipes/genera/meta.yaml Co-authored-by: Mervin Fansler * Update recipes/genera/meta.yaml Co-authored-by: Mervin Fansler * Update meta.yaml * Solved abSENSE License issue * resolved absense issue * Update recipes/genera/meta.yaml Co-authored-by: Mervin Fansler * Update meta.yaml --------- Co-authored-by: Anupam Gautam Co-authored-by: Martin Grigorov Co-authored-by: Alicia A. Evans <108547992+aliciaaevans@users.noreply.github.com> Co-authored-by: richard-burhans Co-authored-by: Mervin Fansler Co-authored-by: Anupam Gautam --- recipes/genera/build.sh | 24 +++++++++++++++++++++ recipes/genera/meta.yaml | 45 ++++++++++++++++++++++++++++++++++++++++ 2 files changed, 69 insertions(+) create mode 100644 recipes/genera/build.sh create mode 100644 recipes/genera/meta.yaml diff --git a/recipes/genera/build.sh b/recipes/genera/build.sh new file mode 100644 index 0000000000000..6703c9eb54fa6 --- /dev/null +++ b/recipes/genera/build.sh @@ -0,0 +1,24 @@ +#!/bin/bash + +# Exit on any error +set -ex + +# Ensure all main scripts are executable +chmod +x genEra Erassignment hmmEra tree2ncbitax FASTSTEP3R test_installation.sh + +# Define the Conda binary path +CONDABIN="${PREFIX}/bin" + +# Ensure the directory exists +mkdir -p "$CONDABIN" + + +# Move executables to the Conda binary directory +mv genEra "$CONDABIN" +mv Erassignment "$CONDABIN" +mv hmmEra "$CONDABIN" +mv tree2ncbitax "$CONDABIN" +mv FASTSTEP3R "$CONDABIN" +mv test_installation.sh "$CONDABIN" + +echo "Installation complete. Executables have been moved to ${CONDABIN}." diff --git a/recipes/genera/meta.yaml b/recipes/genera/meta.yaml new file mode 100644 index 0000000000000..1937ba150929c --- /dev/null +++ b/recipes/genera/meta.yaml @@ -0,0 +1,45 @@ +{% set version = '1.4.2' %} + +package: + name: genera + version: {{ version|replace('-', '_') }} + +source: + - url: https://github.com/josuebarrera/GenEra/archive/refs/tags/v{{ version }}.tar.gz + sha256: acc49698b68151550b825c73f1f03dd268da2c73ecc7ac4c55eccb8bec5b1a54 + +build: + number: 0 + noarch: generic + run_exports: + - {{ pin_subpackage('genera', max_pin="x.x") }} + +requirements: + host: + - python >=3.8,<3.9 + run: + - python >=3.8,<3.9 + - diamond >=2.1.10 + - mmseqs2 =14.7e284 + - foldseek =3.915ef7d + - scipy =1.7.3 + - r-seqinr =4.2_16 + - r-optparse =1.7.3 + - r-bio3d =2.4_3 + - r-tidyverse =1.3.2 + - r-phytools >=0.6_99 + - orthofinder =2.5.5 + - ncbitax2lin >=2.3.2 + - absense >=1.0.1 + +test: + commands: + - genEra -h + - hmmEra -h + - test_installation.sh -h + +about: + home: https://github.com/josuebarrera/GenEra + license: "GPL-3.0-or-later" + license_family: GPL3 + summary: "Uncovering gene-family founder events during major evolutionary transitions in animals, plants and fungi using GenEra"