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author | Matthew Bauer <mjbauer95@gmail.com> | 2018-09-10 15:11:58 -0500 |
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committer | GitHub <noreply@github.com> | 2018-09-10 15:11:58 -0500 |
commit | 40d19d8e7cb5b6322ff7e4090eb3d858c044f5e5 (patch) | |
tree | 41389acdb3405defd52cf98d23cac8fd992fdc5a /pkgs/applications/science/biology | |
parent | 579e206bdb000f0828c2da0d90c5147b41c115fc (diff) | |
parent | 9bd7a4f5208cfa92c0ae8cca1ae6f69f0f8f242d (diff) | |
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Merge pull request #45102 from jbedo/hisat2
hisat2: init 2.1.0
Diffstat (limited to 'pkgs/applications/science/biology')
-rw-r--r-- | pkgs/applications/science/biology/hisat2/default.nix | 49 |
1 files changed, 49 insertions, 0 deletions
diff --git a/pkgs/applications/science/biology/hisat2/default.nix b/pkgs/applications/science/biology/hisat2/default.nix new file mode 100644 index 00000000000..9ccf54a8113 --- /dev/null +++ b/pkgs/applications/science/biology/hisat2/default.nix @@ -0,0 +1,49 @@ +{stdenv, fetchurl, unzip, which, python}: + +stdenv.mkDerivation rec { + name = "hisat2-${version}"; + version = "2.1.0"; + + src = fetchurl { + url = "ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/downloads/hisat2-${version}-source.zip"; + sha256 = "10g73sdf6vqqfhhd92hliw7bbpkb8v4pp5012r5l21zws7p7d8l9"; + }; + + buildInputs = [ unzip which python ]; + + installPhase = '' + mkdir -p $out/bin + cp hisat2 \ + hisat2-inspect-l \ + hisat2-build-s \ + hisat2-align-l \ + hisat2-inspect \ + hisat2-align-s \ + hisat2-inspect-s \ + hisat2-build-l \ + hisat2-build \ + extract_exons.py \ + extract_splice_sites.py \ + hisat2_extract_exons.py \ + hisat2_extract_snps_haplotypes_UCSC.py \ + hisat2_extract_snps_haplotypes_VCF.py \ + hisat2_extract_splice_sites.py \ + hisat2_simulate_reads.py \ + hisatgenotype_build_genome.py \ + hisatgenotype_extract_reads.py \ + hisatgenotype_extract_vars.py \ + hisatgenotype_hla_cyp.py \ + hisatgenotype_locus.py \ + hisatgenotype.py \ + $out/bin + ''; + + meta = with stdenv.lib; { + description = "Graph based aligner"; + license = licenses.gpl3; + homepage = https://ccb.jhu.edu/software/hisat2/index.shtml; + maintainers = with maintainers; [ jbedo ]; + platforms = [ "x86_64-linux" "i686-linux" ]; + }; + +} |