2019-07-05 00:29:51 +00:00
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{stdenv, fetchurl, unzip, which, python, perl}:
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2018-08-16 07:23:14 +00:00
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stdenv.mkDerivation rec {
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2019-08-15 12:41:18 +00:00
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pname = "hisat2";
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2018-08-16 07:23:14 +00:00
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version = "2.1.0";
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src = fetchurl {
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url = "ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/downloads/hisat2-${version}-source.zip";
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sha256 = "10g73sdf6vqqfhhd92hliw7bbpkb8v4pp5012r5l21zws7p7d8l9";
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};
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2019-07-05 00:29:51 +00:00
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nativeBuildInputs = [ unzip which ];
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buildInputs = [ python perl ];
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2018-08-16 07:23:14 +00:00
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installPhase = ''
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mkdir -p $out/bin
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cp hisat2 \
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hisat2-inspect-l \
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hisat2-build-s \
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hisat2-align-l \
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hisat2-inspect \
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hisat2-align-s \
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hisat2-inspect-s \
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hisat2-build-l \
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hisat2-build \
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extract_exons.py \
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extract_splice_sites.py \
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hisat2_extract_exons.py \
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hisat2_extract_snps_haplotypes_UCSC.py \
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hisat2_extract_snps_haplotypes_VCF.py \
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hisat2_extract_splice_sites.py \
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hisat2_simulate_reads.py \
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hisatgenotype_build_genome.py \
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hisatgenotype_extract_reads.py \
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hisatgenotype_extract_vars.py \
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hisatgenotype_hla_cyp.py \
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hisatgenotype_locus.py \
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hisatgenotype.py \
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$out/bin
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'';
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meta = with stdenv.lib; {
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description = "Graph based aligner";
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license = licenses.gpl3;
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homepage = https://ccb.jhu.edu/software/hisat2/index.shtml;
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maintainers = with maintainers; [ jbedo ];
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platforms = [ "x86_64-linux" "i686-linux" ];
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};
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}
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