diff options
author | Mx Kookie <kookie@spacekookie.de> | 2020-10-31 19:35:09 +0100 |
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committer | Mx Kookie <kookie@spacekookie.de> | 2020-10-31 19:35:09 +0100 |
commit | c4625b175f8200f643fd6e11010932ea44c78433 (patch) | |
tree | bce3f89888c8ac3991fa5569a878a9eab6801ccc /infra/libkookie/nixpkgs/pkgs/applications/science/biology/tebreak/default.nix | |
parent | 49f735974dd103039ddc4cb576bb76555164a9e7 (diff) | |
parent | d661aa56a8843e991261510c1bb28fdc2f6975ae (diff) |
Add 'infra/libkookie/' from commit 'd661aa56a8843e991261510c1bb28fdc2f6975ae'
git-subtree-dir: infra/libkookie
git-subtree-mainline: 49f735974dd103039ddc4cb576bb76555164a9e7
git-subtree-split: d661aa56a8843e991261510c1bb28fdc2f6975ae
Diffstat (limited to 'infra/libkookie/nixpkgs/pkgs/applications/science/biology/tebreak/default.nix')
-rw-r--r-- | infra/libkookie/nixpkgs/pkgs/applications/science/biology/tebreak/default.nix | 42 |
1 files changed, 42 insertions, 0 deletions
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/biology/tebreak/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/biology/tebreak/default.nix new file mode 100644 index 000000000000..07669d097a44 --- /dev/null +++ b/infra/libkookie/nixpkgs/pkgs/applications/science/biology/tebreak/default.nix @@ -0,0 +1,42 @@ +{ stdenv, fetchFromGitHub, last, exonerate, minia, python3Packages, bwa +, samtools, findutils }: + +python3Packages.buildPythonApplication rec { + pname = "tebreak"; + version = "1.1"; + + src = fetchFromGitHub { + owner = "adamewing"; + repo = "tebreak"; + rev = version; + sha256 = "13mgh775d8hkl340923lfwwm4r5ps70girn8d6wgfxzwzxylz8iz"; + }; + + nativeBuildInputs = [ findutils python3Packages.cython ]; + propagatedBuildInputs = with python3Packages; [ + pysam + scipy + bx-python + scikit-bio + ]; + + preConfigure = '' + # patch the paths to all required software + for f in $(find . -type f) ; do + sed -i "s|'bwa'|'${bwa}/bin/bwa'|" $f + sed -i "s|'minia'|'${minia}/bin/minia'|" $f + sed -i "s|'exonerate'|'${exonerate}/bin/exonerate'|" $f + sed -i "s|'samtools'|'${samtools}/bin/samtools'|" $f + sed -i "s|'lastal'|'${last}/bin/lastal'|" $f + sed -i "s|'lastdb'|'${last}/bin/lastdb'|" $f + done + ''; + + meta = with stdenv.lib; { + description = "Find and characterise transposable element insertions"; + homepage = "https://github.com/adamewing/tebreak"; + license = licenses.mit; + maintainers = with maintainers; [ jbedo ]; + platforms = platforms.x86_64; + }; +} |