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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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#!/bin/sh | ||
set -x -e | ||
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#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="${PREFIX}/lib" | ||
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# General info | ||
LTR_FINDER_DIR=${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" | ||
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# Create folders | ||
mkdir -p ${PREFIX}/bin | ||
mkdir -p ${LTR_FINDER_DIR} | ||
cp -r * ${LTR_FINDER_DIR} | ||
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cd source | ||
make CC=$CC CXX=$CXX | ||
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#set C scripts | ||
for name in ${C_PRG} ; do | ||
cp ${C_PRG} ${PREFIX}/bin/ | ||
done | ||
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# set perl scripts | ||
# Set env variables for config parameters needed in RepModelConfig.pm | ||
cat <<END >>${PREFIX}/bin/${PERL_PRG} | ||
#!/bin/bash | ||
NAME=\$(basename \$0) | ||
perl ${LTR_FINDER_DIR}/\${NAME} \$@ | ||
END | ||
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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 |
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{% set name = "ltr_finder" %} | ||
{% set version = "1.07" %} | ||
{% set sha256 = "060ee6b533636a39f6833829c487713d1b85a53245029edcd51e26b21d4d0b0c" %} | ||
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package: | ||
name: "{{ name|lower }}" | ||
version: "{{ version }}" | ||
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source: | ||
url: https://github.com/NBISweden/LTR_Finder/archive/v{{ version }}.tar.gz | ||
sha256: {{ sha256 }} | ||
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build: | ||
number: 0 | ||
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requirements: | ||
build: | ||
- {{ compiler('cxx') }} | ||
- llvm-openmp # [osx] | ||
run: | ||
- perl | ||
- perl-gd | ||
- llvm-openmp # [osx] | ||
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test: | ||
commands: | ||
- ltr_finder 2>&1 | grep -i usage | ||
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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/ |
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#!/bin/sh | ||
set -x -e | ||
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# run the test example | ||
ltr_finder ${PREFIX}/share/LTR_Finder/source/test/3ds_72.fa -P 3ds_72 -w2 -f /dev/stderr 2>&1 |