Merge pull request #74837 from bcdarwin/biocaml
ocamlPackages_latest.phylogenetics: init at unstable-2019-11-15
This commit is contained in:
commit
34084d471e
30
pkgs/development/ocaml-modules/biocaml/default.nix
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30
pkgs/development/ocaml-modules/biocaml/default.nix
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@ -0,0 +1,30 @@
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{ stdenv, buildDunePackage, fetchFromGitHub
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, ounit, async, base64, camlzip, cfstream
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, core, ppx_jane, ppx_sexp_conv, rresult, uri, xmlm }:
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buildDunePackage rec {
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pname = "biocaml";
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version = "0.10.0";
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owner = "biocaml";
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minimumOCamlVersion = "4.07";
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src = fetchFromGitHub {
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inherit owner;
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repo = pname;
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rev = "v${version}";
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sha256 = "0dghqx6jbzihmga8jjwwavs0wqksgcns4z1nmwj0ds9ik3mcra30";
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};
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buildInputs = [ ppx_jane ppx_sexp_conv ];
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checkInputs = [ ounit ];
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propagatedBuildInputs = [ async base64 camlzip cfstream core rresult uri xmlm ];
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meta = with stdenv.lib; {
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description = "Bioinformatics library for Ocaml";
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homepage = "http://${owner}.github.io/${pname}";
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maintainers = [ maintainers.bcdarwin ];
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license = licenses.gpl2;
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};
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}
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30
pkgs/development/ocaml-modules/cfstream/default.nix
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30
pkgs/development/ocaml-modules/cfstream/default.nix
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@ -0,0 +1,30 @@
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{ stdenv, buildDunePackage, fetchFromGitHub, m4, core_kernel, ounit }:
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buildDunePackage rec {
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pname = "cfstream";
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version = "1.3.0";
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minimumOCamlVersion = "4.04.1";
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src = fetchFromGitHub {
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owner = "biocaml";
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repo = pname;
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rev = version;
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sha256 = "1bpzpci0cx6r3sdk183mm603wgzvvj46nlx0lpx44108anxcxbak";
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};
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patches = [ ./git_commit.patch ];
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buildInputs = [ m4 ];
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checkInputs = [ ounit ];
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propagatedBuildInputs = [ core_kernel ];
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doCheck = true;
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meta = with stdenv.lib; {
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inherit (src.meta) homepage;
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description = "Simple Core-inspired wrapper for standard library Stream module";
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maintainers = [ maintainers.bcdarwin ];
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license = licenses.lgpl21;
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};
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}
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13
pkgs/development/ocaml-modules/cfstream/git_commit.patch
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13
pkgs/development/ocaml-modules/cfstream/git_commit.patch
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@ -0,0 +1,13 @@
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diff --git a/lib/jbuild b/lib/jbuild
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index fcc5a39..d72d50c 100644
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--- a/lib/jbuild
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+++ b/lib/jbuild
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@@ -10,7 +10,7 @@
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(rule (
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(targets (GIT_COMMIT))
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(deps (../bin/git_commit.sh))
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- (action (with-stdout-to ${@} (run ${<})))
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+ (action (with-stdout-to ${@} (run echo "None")))
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))
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(rule (
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22
pkgs/development/ocaml-modules/gnuplot/default.nix
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22
pkgs/development/ocaml-modules/gnuplot/default.nix
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@ -0,0 +1,22 @@
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{ stdenv, buildDunePackage, fetchFromBitbucket, gnuplot, core }:
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buildDunePackage rec {
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pname = "gnuplot";
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version = "0.5.3";
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src = fetchFromBitbucket {
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owner = "ogu";
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repo = "${pname}-ocaml";
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rev = "release-${version}";
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sha256 = "00sn9g46pj8pfh7faiyxg3pfhq7w9knafyabjr464bh6qz5kiin3";
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};
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propagatedBuildInputs = [ core gnuplot ];
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meta = with stdenv.lib; {
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inherit (src.meta) homepage;
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description = "Ocaml bindings to Gnuplot";
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maintainers = [ maintainers.bcdarwin ];
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license = licenses.lgpl21;
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};
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}
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@ -1,4 +1,4 @@
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{ stdenv, buildDunePackage, fetchFromGitHub, integers, stdlib-shims }:
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{ stdenv, buildDunePackage, fetchFromGitHub, stdlib-shims }:
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buildDunePackage rec {
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pname = "owl-base";
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@ -7,9 +7,8 @@ buildDunePackage rec {
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inherit (owl-base) version src meta;
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buildInputs = [ eigen ];
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checkInputs = [ alcotest ];
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propagatedBuildInputs = [ stdio stdlib-shims openblasCompat owl-base ];
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propagatedBuildInputs = [ eigen stdio stdlib-shims openblasCompat owl-base ];
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# tests not enabled for now due to owlbarn/owl/issues/460
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}
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28
pkgs/development/ocaml-modules/phylogenetics/default.nix
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28
pkgs/development/ocaml-modules/phylogenetics/default.nix
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@ -0,0 +1,28 @@
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{ stdenv, buildDunePackage, fetchFromGitHub, ppx_deriving
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, alcotest, biocaml, gnuplot, lacaml, menhir, owl }:
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buildDunePackage rec {
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pname = "phylogenetics";
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version = "unstable-2019-11-15";
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src = fetchFromGitHub {
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owner = "biocaml";
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repo = pname;
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rev = "91c03834db065cf4a86f33affbb9cfd216defc9f";
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sha256 = "0i9m0633a6a724as35ix8z3p1gj267cl0hmqrpw4qfq39zxmgnxb";
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};
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minimumOCamlVersion = "4.08"; # e.g., uses Float.min
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checkInputs = [ alcotest ];
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propagatedBuildInputs = [ biocaml gnuplot lacaml menhir owl ppx_deriving ];
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doCheck = false; # many tests require bppsuite
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meta = with stdenv.lib; {
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inherit (std.meta) homepage;
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description = "Bioinformatics library for Ocaml";
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maintainers = [ maintainers.bcdarwin ];
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license = licenses.cecill-b;
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};
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}
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@ -73,6 +73,8 @@ let
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bigstringaf = callPackage ../development/ocaml-modules/bigstringaf { };
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biocaml = callPackage ../development/ocaml-modules/biocaml { };
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bistro = callPackage ../development/ocaml-modules/bistro { };
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bitstring = callPackage ../development/ocaml-modules/bitstring { };
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@ -138,6 +140,8 @@ let
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cairo2 = callPackage ../development/ocaml-modules/cairo2 { };
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cfstream = callPackage ../development/ocaml-modules/cfstream { };
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charInfo_width = callPackage ../development/ocaml-modules/charInfo_width { };
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checkseum = callPackage ../development/ocaml-modules/checkseum { };
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@ -293,6 +297,10 @@ let
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gmap = callPackage ../development/ocaml-modules/gmap { };
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gnuplot = callPackage ../development/ocaml-modules/gnuplot {
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inherit (pkgs) gnuplot;
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};
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herelib = callPackage ../development/ocaml-modules/herelib { };
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higlo = callPackage ../development/ocaml-modules/higlo { };
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@ -470,7 +478,9 @@ let
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metrics-lwt = callPackage ../development/ocaml-modules/metrics/lwt.nix { };
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metrics-unix = callPackage ../development/ocaml-modules/metrics/unix.nix { };
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metrics-unix = callPackage ../development/ocaml-modules/metrics/unix.nix {
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inherit (pkgs) gnuplot;
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};
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mezzo = callPackage ../development/compilers/mezzo { };
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@ -621,6 +631,8 @@ let
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pgsolver = callPackage ../development/ocaml-modules/pgsolver { };
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phylogenetics = callPackage ../development/ocaml-modules/phylogenetics { };
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piqi = callPackage ../development/ocaml-modules/piqi {
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base64 = base64_2;
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};
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