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[ci skip] Merge PR 20006
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Merge PR #20006, commits were: 
 * add another test
 * cp compiled c progras
 * fix global variable usage
 * fix and add test
 * first try add recipe ltr_finder
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Juke34 authored Jan 28, 2020
1 parent d1e6454 commit 6f401d0
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44 changes: 44 additions & 0 deletions recipes/ltr_finder/build.sh
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#!/bin/sh
set -x -e

#import
export CFLAGS="-I$PREFIX/include"
export CPPFLAGS="-I$PREFIX/include"
export CXXFLAGS="-I$PREFIX/include"
export LDFLAGS="-L$PREFIX/lib"
export CPATH=${PREFIX}/include
export C_INCLUDE_PATH=${C_INCLUDE_PATH}:${PREFIX}/include
export LIBRARY_PATH="${PREFIX}/lib"
export LD_LIBRARY_PATH="${PREFIX}/lib"

# General info
LTR_FINDER_DIR=${PREFIX}/share/LTR_Finder
PERL_PRG="genome_plot.pl"
PERL_OTHER_PRG="check_result.pl down_tRNA.pl filter_rt.pl genome_plot2.pl genome_plot_svg.pl"
C_PRG="ltr_finder psearch"

# Create folders
mkdir -p ${PREFIX}/bin
mkdir -p ${LTR_FINDER_DIR}
cp -r * ${LTR_FINDER_DIR}

cd source
make CC=$CC CXX=$CXX

#set C scripts
for name in ${C_PRG} ; do
cp ${C_PRG} ${PREFIX}/bin/
done

# set perl scripts
# Set env variables for config parameters needed in RepModelConfig.pm
cat <<END >>${PREFIX}/bin/${PERL_PRG}
#!/bin/bash
NAME=\$(basename \$0)
perl ${LTR_FINDER_DIR}/\${NAME} \$@
END

chmod a+x ${PREFIX}/bin/${PERL_PRG}
for name in ${PERL_OTHER_PRG} ; do
ln -s ${PREFIX}/bin/${PERL_PRG} ${PREFIX}/bin/$(basename $name)
done
34 changes: 34 additions & 0 deletions recipes/ltr_finder/meta.yaml
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{% set name = "ltr_finder" %}
{% set version = "1.07" %}
{% set sha256 = "060ee6b533636a39f6833829c487713d1b85a53245029edcd51e26b21d4d0b0c" %}

package:
name: "{{ name|lower }}"
version: "{{ version }}"

source:
url: https://github.com/NBISweden/LTR_Finder/archive/v{{ version }}.tar.gz
sha256: {{ sha256 }}

build:
number: 0

requirements:
build:
- {{ compiler('cxx') }}
- llvm-openmp # [osx]
run:
- perl
- perl-gd
- llvm-openmp # [osx]

test:
commands:
- ltr_finder 2>&1 | grep -i usage

about:
home: https://github.com/NBISweden/LTR_Finder/
license: MIT
license_file: LICENSE
summary: LTR_Finder is an efficient program for finding full-length LTR retrotranspsons in genome sequences.
dev_url: https://github.com/NBISweden/LTR_Finder/
5 changes: 5 additions & 0 deletions recipes/ltr_finder/run_test.sh
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#!/bin/sh
set -x -e

# run the test example
ltr_finder ${PREFIX}/share/LTR_Finder/source/test/3ds_72.fa -P 3ds_72 -w2 -f /dev/stderr 2>&1

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