cnvkit: init

1 files changed, 102 insertions, 0 deletions

diff --git a/tools/cnvkit-app.nix b/tools/cnvkit-app.nix
new file mode 100644
index 0000000..d44c508
--- /dev/null
+++ b/tools/cnvkit-app.nix
@@ -0,0 +1,102 @@
+{ lib
+, fetchurl
+, rPackages
+, rWrapper
+, buildPythonPackage
+, fetchPypi
+, biopython
+, six
+, numpy
+, scipy
+, pandas
+, matplotlib
+, reportlab
+, zlib
+, bzip2
+, htslib
+, libjpeg
+, pkgconfig
+, futures
+}:
+
+let pyfaidx = buildPythonPackage rec {
+      pname = "pyfaidx";
+      version = "0.5.3.1";
+
+      src = fetchPypi {
+        inherit pname version;
+        sha256 = "0mjbksbj9hh2cf0yjr951cjahhn0lg7p71kd3kvbnscqyxa44kfr";
+      };
+
+      propagatedBuildInputs = [ six ];
+    };
+
+    pysam = buildPythonPackage rec {
+      pname = "pysam";
+      version = "0.14";
+
+      src = fetchPypi {
+        inherit pname version;
+        sha256 = "11snrwl5pn6knarf0c7zcpkhc7rijb6cfpw8sl3pdvnynj1fmj69";
+      };
+
+      buildInputs = [ zlib ];
+
+      preConfigure = ''
+        export HTSLIB_MODE="external"
+        export HTSLIB_LIBRARY_DIR=${htslib}/lib
+        export HTSLIB_INCLUDE_DIR=${htslib}/include
+      '';
+
+    };
+
+    future = buildPythonPackage rec {
+      pname = "future";
+      version = "0.16.0";
+
+      doCheck = false;
+
+      src = fetchPypi {
+        inherit pname version;
+        sha256 = "1nzy1k4m9966sikp0qka7lirh8sqrsyainyf8rk97db7nwdfv773";
+      };
+    };
+
+    pillow = buildPythonPackage rec {
+      pname = "Pillow";
+      version = "5.0.0";
+
+      doCheck = false;
+
+      src = fetchPypi {
+        inherit pname version;
+        sha256 = "1fz1n1cq65dqdbiwy1cn8l21amqbzq18rdmmcr670ks24dn9vwhj";
+      };
+
+      buildInputs = [ zlib libjpeg pkgconfig ];
+    };
+
+    cghFLasso = rPackages.buildRPackage rec {
+      name = "cghFLasso-${version}";
+      version = "0.2-1";
+      src = fetchurl {
+        url = "https://cran.r-project.org/src/contrib/Archive/cghFLasso/cghFLasso_${version}.tar.gz";
+        sha256 = "0b1hnjf9g0v47hbz0dy9m6jhcl1ky20yyhhmm8myng2sndcpjsbf";
+      };
+    };
+
+    cnvR = rWrapper.override {
+      packages = with rPackages; [ DNAcopy cghFLasso ];
+    };
+
+in buildPythonPackage rec {
+  pname = "CNVkit";
+  version = "0.9.5";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1sa70bmnxj1lzp33pbj3axk6n77czswwj9cirimxh2qrn84i7vs3";
+  };
+
+  propagatedBuildInputs = [ biopython numpy scipy pandas matplotlib reportlab pyfaidx pysam futures future pillow cnvR ];
+}