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authorJustin Bedo <cu@cua0.org>2019-01-11 08:05:02 +1100
committerJustin Bedo <cu@cua0.org>2019-01-11 08:05:02 +1100
commitbc35eb11bd28b3d3cab659112f8b0d42b7c30204 (patch)
tree22c1803667e00eca03f997950831ae5d1b53cf2e
parent28196d5d4e4144e9c64c758b0de9678493d91490 (diff)
cnvkit: use nixpkgs python modules
-rw-r--r--tools/cnvkit-app.nix48
1 files changed, 3 insertions, 45 deletions
diff --git a/tools/cnvkit-app.nix b/tools/cnvkit-app.nix
index d44c508..dc9f023 100644
--- a/tools/cnvkit-app.nix
+++ b/tools/cnvkit-app.nix
@@ -7,6 +7,9 @@
, biopython
, six
, numpy
+, pillow
+, pysam
+, future
, scipy
, pandas
, matplotlib
@@ -31,51 +34,6 @@ let pyfaidx = buildPythonPackage rec {
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";