Merge pull request #74837 from bcdarwin/biocaml

ocamlPackages_latest.phylogenetics: init at unstable-2019-11-15
This commit is contained in:
Vincent Laporte 2019-12-06 17:53:28 +00:00 committed by GitHub
commit 34084d471e
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8 changed files with 138 additions and 4 deletions

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@ -0,0 +1,30 @@
{ stdenv, buildDunePackage, fetchFromGitHub
, ounit, async, base64, camlzip, cfstream
, core, ppx_jane, ppx_sexp_conv, rresult, uri, xmlm }:
buildDunePackage rec {
pname = "biocaml";
version = "0.10.0";
owner = "biocaml";
minimumOCamlVersion = "4.07";
src = fetchFromGitHub {
inherit owner;
repo = pname;
rev = "v${version}";
sha256 = "0dghqx6jbzihmga8jjwwavs0wqksgcns4z1nmwj0ds9ik3mcra30";
};
buildInputs = [ ppx_jane ppx_sexp_conv ];
checkInputs = [ ounit ];
propagatedBuildInputs = [ async base64 camlzip cfstream core rresult uri xmlm ];
meta = with stdenv.lib; {
description = "Bioinformatics library for Ocaml";
homepage = "http://${owner}.github.io/${pname}";
maintainers = [ maintainers.bcdarwin ];
license = licenses.gpl2;
};
}

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@ -0,0 +1,30 @@
{ stdenv, buildDunePackage, fetchFromGitHub, m4, core_kernel, ounit }:
buildDunePackage rec {
pname = "cfstream";
version = "1.3.0";
minimumOCamlVersion = "4.04.1";
src = fetchFromGitHub {
owner = "biocaml";
repo = pname;
rev = version;
sha256 = "1bpzpci0cx6r3sdk183mm603wgzvvj46nlx0lpx44108anxcxbak";
};
patches = [ ./git_commit.patch ];
buildInputs = [ m4 ];
checkInputs = [ ounit ];
propagatedBuildInputs = [ core_kernel ];
doCheck = true;
meta = with stdenv.lib; {
inherit (src.meta) homepage;
description = "Simple Core-inspired wrapper for standard library Stream module";
maintainers = [ maintainers.bcdarwin ];
license = licenses.lgpl21;
};
}

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@ -0,0 +1,13 @@
diff --git a/lib/jbuild b/lib/jbuild
index fcc5a39..d72d50c 100644
--- a/lib/jbuild
+++ b/lib/jbuild
@@ -10,7 +10,7 @@
(rule (
(targets (GIT_COMMIT))
(deps (../bin/git_commit.sh))
- (action (with-stdout-to ${@} (run ${<})))
+ (action (with-stdout-to ${@} (run echo "None")))
))
(rule (

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@ -0,0 +1,22 @@
{ stdenv, buildDunePackage, fetchFromBitbucket, gnuplot, core }:
buildDunePackage rec {
pname = "gnuplot";
version = "0.5.3";
src = fetchFromBitbucket {
owner = "ogu";
repo = "${pname}-ocaml";
rev = "release-${version}";
sha256 = "00sn9g46pj8pfh7faiyxg3pfhq7w9knafyabjr464bh6qz5kiin3";
};
propagatedBuildInputs = [ core gnuplot ];
meta = with stdenv.lib; {
inherit (src.meta) homepage;
description = "Ocaml bindings to Gnuplot";
maintainers = [ maintainers.bcdarwin ];
license = licenses.lgpl21;
};
}

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@ -1,4 +1,4 @@
{ stdenv, buildDunePackage, fetchFromGitHub, integers, stdlib-shims }:
{ stdenv, buildDunePackage, fetchFromGitHub, stdlib-shims }:
buildDunePackage rec {
pname = "owl-base";

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@ -7,9 +7,8 @@ buildDunePackage rec {
inherit (owl-base) version src meta;
buildInputs = [ eigen ];
checkInputs = [ alcotest ];
propagatedBuildInputs = [ stdio stdlib-shims openblasCompat owl-base ];
propagatedBuildInputs = [ eigen stdio stdlib-shims openblasCompat owl-base ];
# tests not enabled for now due to owlbarn/owl/issues/460
}

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@ -0,0 +1,28 @@
{ stdenv, buildDunePackage, fetchFromGitHub, ppx_deriving
, alcotest, biocaml, gnuplot, lacaml, menhir, owl }:
buildDunePackage rec {
pname = "phylogenetics";
version = "unstable-2019-11-15";
src = fetchFromGitHub {
owner = "biocaml";
repo = pname;
rev = "91c03834db065cf4a86f33affbb9cfd216defc9f";
sha256 = "0i9m0633a6a724as35ix8z3p1gj267cl0hmqrpw4qfq39zxmgnxb";
};
minimumOCamlVersion = "4.08"; # e.g., uses Float.min
checkInputs = [ alcotest ];
propagatedBuildInputs = [ biocaml gnuplot lacaml menhir owl ppx_deriving ];
doCheck = false; # many tests require bppsuite
meta = with stdenv.lib; {
inherit (std.meta) homepage;
description = "Bioinformatics library for Ocaml";
maintainers = [ maintainers.bcdarwin ];
license = licenses.cecill-b;
};
}

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@ -73,6 +73,8 @@ let
bigstringaf = callPackage ../development/ocaml-modules/bigstringaf { };
biocaml = callPackage ../development/ocaml-modules/biocaml { };
bistro = callPackage ../development/ocaml-modules/bistro { };
bitstring = callPackage ../development/ocaml-modules/bitstring { };
@ -138,6 +140,8 @@ let
cairo2 = callPackage ../development/ocaml-modules/cairo2 { };
cfstream = callPackage ../development/ocaml-modules/cfstream { };
charInfo_width = callPackage ../development/ocaml-modules/charInfo_width { };
checkseum = callPackage ../development/ocaml-modules/checkseum { };
@ -293,6 +297,10 @@ let
gmap = callPackage ../development/ocaml-modules/gmap { };
gnuplot = callPackage ../development/ocaml-modules/gnuplot {
inherit (pkgs) gnuplot;
};
herelib = callPackage ../development/ocaml-modules/herelib { };
higlo = callPackage ../development/ocaml-modules/higlo { };
@ -470,7 +478,9 @@ let
metrics-lwt = callPackage ../development/ocaml-modules/metrics/lwt.nix { };
metrics-unix = callPackage ../development/ocaml-modules/metrics/unix.nix { };
metrics-unix = callPackage ../development/ocaml-modules/metrics/unix.nix {
inherit (pkgs) gnuplot;
};
mezzo = callPackage ../development/compilers/mezzo { };
@ -621,6 +631,8 @@ let
pgsolver = callPackage ../development/ocaml-modules/pgsolver { };
phylogenetics = callPackage ../development/ocaml-modules/phylogenetics { };
piqi = callPackage ../development/ocaml-modules/piqi {
base64 = base64_2;
};