From 6a1ce54871ef03235b5756a8d4ac90154c73b384 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Rolf=20Schr=C3=B6der?= Date: Tue, 24 Sep 2024 05:50:16 +0200 Subject: [PATCH 1/5] nextflow: 22.10.6 -> 24.04.4 + remove buildFHSEnv `nextflow` is no build by compiling from source instead of using the downloaded release file. This improves the overall accesibility (`version` will be shown on https://search.nixos.org/packages?query=nextflow) and allows to add & run tests more easily. --- .../interpreters/nextflow/default.nix | 107 +- .../interpreters/nextflow/deps.json | 2026 +++++++++++++++++ 2 files changed, 2093 insertions(+), 40 deletions(-) create mode 100644 pkgs/development/interpreters/nextflow/deps.json diff --git a/pkgs/development/interpreters/nextflow/default.nix b/pkgs/development/interpreters/nextflow/default.nix index 0408bf243121..187d1253e2c6 100644 --- a/pkgs/development/interpreters/nextflow/default.nix +++ b/pkgs/development/interpreters/nextflow/default.nix @@ -1,52 +1,85 @@ -{ lib -, stdenv -, fetchurl -, makeWrapper -, openjdk17 -, wget -, which -, gnused -, gawk -, coreutils -, buildFHSEnv +{ + lib, + stdenv, + fetchFromGitHub, + makeWrapper, + openjdk, + gradle, + wget, + which, + gnused, + gawk, + coreutils, + bash, }: - -let - nextflow = -stdenv.mkDerivation rec { +stdenv.mkDerivation (finalAttrs: { pname = "nextflow"; - version = "22.10.6"; + # 24.08.0-edge is compatible with Java 21. The current (as of 2024-09-19) + # nextflow release (24.04.4) does not yet support java21, but java19. The + # latter is not in nixpkgs(-unstable) anymore. + version = "24.08.0-edge"; - src = fetchurl { - url = "https://github.com/nextflow-io/nextflow/releases/download/v${version}/nextflow-${version}-all"; - hash = "sha256-zeYsKxWRnzr0W6CD+yjoAXwCN/AbN5P4HhH1oftnrjY="; + src = fetchFromGitHub { + owner = "nextflow-io"; + repo = "nextflow"; + rev = "6e866ae81ff3bf8a9729e9dbaa9dd89afcb81a4b"; + hash = "sha256-SA27cuP3iO5kD6u0uTeEaydyqbyJzOkVtPrb++m3Tv0="; }; nativeBuildInputs = [ makeWrapper - openjdk17 - wget - which - gnused - gawk - coreutils + gradle ]; - dontUnpack = true; + postPatch = '' + # Nextflow invokes the constant "/bin/bash" (not as a shebang) at + # several locations so we fix that globally. However, when running inside + # a container, we actually *want* "/bin/bash". Thus the global fix needs + # to be reverted for this specific use case. + substituteInPlace modules/nextflow/src/main/groovy/nextflow/executor/BashWrapperBuilder.groovy \ + --replace-fail "['/bin/bash'," "['${bash}/bin/bash'," \ + --replace-fail "if( containerBuilder ) {" "if( containerBuilder ) { + launcher = launcher.replaceFirst(\"/nix/store/.*/bin/bash\", \"/bin/bash\")" + ''; + + mitmCache = gradle.fetchDeps { + inherit (finalAttrs) pname; + data = ./deps.json; + }; + __darwinAllowLocalNetworking = true; + + # During the build, some additional dependencies are downloaded ("detached + # configuration"). We thus need to run a full build on instead of the default + # one. + # See https://github.com/NixOS/nixpkgs/pull/339197#discussion_r1747749061 + gradleUpdateTask = "pack"; + # See Makefile (`make pack`) + preBuild = '' + export BUILD_PACK=1 + ''; + gradleBuildTask = "pack"; installPhase = '' runHook preInstall mkdir -p $out/bin - install -Dm755 $src $out/bin/nextflow + install -Dm755 build/releases/nextflow-${finalAttrs.version}-dist $out/bin/nextflow runHook postInstall ''; postFixup = '' wrapProgram $out/bin/nextflow \ - --prefix PATH : ${lib.makeBinPath nativeBuildInputs} \ - --set JAVA_HOME ${openjdk17.home} + --prefix PATH : ${ + lib.makeBinPath [ + coreutils + gawk + gnused + wget + which + ] + } \ + --set JAVA_HOME ${openjdk.home} ''; meta = with lib; { @@ -61,17 +94,11 @@ stdenv.mkDerivation rec { homepage = "https://www.nextflow.io/"; changelog = "https://github.com/nextflow-io/nextflow/releases"; license = licenses.asl20; - maintainers = with maintainers; [ Etjean edmundmiller ]; + maintainers = with maintainers; [ + Etjean + edmundmiller + ]; mainProgram = "nextflow"; platforms = platforms.unix; }; -}; -in -if stdenv.hostPlatform.isLinux then - buildFHSEnv - { - name = "nextflow"; - targetPkgs = pkgs: [ nextflow ]; - runScript = "nextflow"; - } -else nextflow +}) diff --git a/pkgs/development/interpreters/nextflow/deps.json b/pkgs/development/interpreters/nextflow/deps.json new file mode 100644 index 000000000000..19a8de2470e6 --- /dev/null +++ b/pkgs/development/interpreters/nextflow/deps.json @@ -0,0 +1,2026 @@ +{ + "!comment": "This is a nixpkgs Gradle dependency lockfile. 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"sha256-LjtN7MZPXCoqoG6E2VFOiksp+0ycX6Zh/p0rMtqmBEQ=" + }, + "io/seqera#wave-utils/0.12.1": { + "jar": "sha256-9X38gNB1Pdv8DZvmstNxHQj/I+kIuI9Bpa3x/2rvoO0=", + "module": "sha256-Ukgc/tr5Tu5LwCKmOOHy7cD8KpXkVr6ILyyIRK6gwIQ=", + "pom": "sha256-Fr4n54p6eWDDLO/FJ3O+0fpT7Td0xmhR735eH462g8E=" + }, + "org/apache/groovy#groovy-bom/4.0.21-patch.2": { + "module": "sha256-A38EDWOFyVE2tpRetXMsRbObHavHanSG0Z+Ea6iUErk=", + "pom": "sha256-DbAn/Ue8d61Hro5LY/gnyZwbDF0bcPTxtdeuSnPDXKk=" + }, + "org/apache/groovy#groovy-console/4.0.21-patch.2": { + "jar": "sha256-5u2tAQZfe46pmvWkePVNScU3uw5u8uFCNdaVeELM5Aw=", + "module": "sha256-Xj/ZsAfVMWDtV72+R3RRdrVKmffOH/1ynAlwj2NwMzU=", + "pom": "sha256-C/44K5FvC04qagEWksqaa2QSKoDucSJGeI7b9O8dal8=" + } + } +} From e7dac85a8173ded92b679c21c43ee051d3eac028 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Rolf=20Schr=C3=B6der?= Date: Tue, 24 Sep 2024 05:51:46 +0200 Subject: [PATCH 2/5] nextflow: add a passthru.tests.version --- pkgs/development/interpreters/nextflow/default.nix | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/pkgs/development/interpreters/nextflow/default.nix b/pkgs/development/interpreters/nextflow/default.nix index 187d1253e2c6..3b2a41919a06 100644 --- a/pkgs/development/interpreters/nextflow/default.nix +++ b/pkgs/development/interpreters/nextflow/default.nix @@ -11,6 +11,7 @@ gawk, coreutils, bash, + testers, }: stdenv.mkDerivation (finalAttrs: { pname = "nextflow"; @@ -82,6 +83,13 @@ stdenv.mkDerivation (finalAttrs: { --set JAVA_HOME ${openjdk.home} ''; + # versionCheckHook doesn't work as of 2024-09-23. + # See https://github.com/NixOS/nixpkgs/pull/339197#issuecomment-2363495060 + passthru.tests.version = testers.testVersion { + package = finalAttrs.finalPackage; + command = "env HOME=$TMPDIR nextflow -version"; + }; + meta = with lib; { description = "DSL for data-driven computational pipelines"; longDescription = '' From 8d15ee11acca4b076a427362ea3f3097a4f2b6c0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Rolf=20Schr=C3=B6der?= Date: Tue, 24 Sep 2024 05:57:38 +0200 Subject: [PATCH 3/5] tests/nextflow: init --- nixos/tests/all-tests.nix | 1 + nixos/tests/nextflow.nix | 60 +++++++++++++++++++ .../interpreters/nextflow/default.nix | 2 + 3 files changed, 63 insertions(+) create mode 100644 nixos/tests/nextflow.nix diff --git a/nixos/tests/all-tests.nix b/nixos/tests/all-tests.nix index 15efe3a06b56..5bdd0a1a7aa1 100644 --- a/nixos/tests/all-tests.nix +++ b/nixos/tests/all-tests.nix @@ -658,6 +658,7 @@ in { # TODO: put in networking.nix after the test becomes more complete networkingProxy = handleTest ./networking-proxy.nix {}; nextcloud = handleTest ./nextcloud {}; + nextflow = handleTest ./nextflow.nix {}; nextjs-ollama-llm-ui = runTest ./web-apps/nextjs-ollama-llm-ui.nix; nexus = handleTest ./nexus.nix {}; # TODO: Test nfsv3 + Kerberos diff --git a/nixos/tests/nextflow.nix b/nixos/tests/nextflow.nix new file mode 100644 index 000000000000..b4aad98483b9 --- /dev/null +++ b/nixos/tests/nextflow.nix @@ -0,0 +1,60 @@ +import ./make-test-python.nix ( + { pkgs, ... }: + let + bash = pkgs.dockerTools.pullImage { + imageName = "quay.io/nextflow/bash"; + imageDigest = "sha256:bea0e244b7c5367b2b0de687e7d28f692013aa18970941c7dd184450125163ac"; + sha256 = "161s9f24njjx87qrwq0c9nmnwvyc6iblcxka7hirw78lm7i9x4w5"; + finalImageName = "quay.io/nextflow/bash"; + }; + + hello = pkgs.stdenv.mkDerivation { + name = "nextflow-hello"; + src = pkgs.fetchFromGitHub { + owner = "nextflow-io"; + repo = "hello"; + rev = "afff16a9b45c8e8a4f5a3743780ac13a541762f8"; + hash = "sha256-c8FirHc+J5Y439g0BdHxRtXVrOAzIrGEKA0m1mp9b/U="; + }; + installPhase = '' + cp -r $src $out + ''; + }; + run-nextflow-pipeline = pkgs.writeShellApplication { + name = "run-nextflow-pipeline"; + runtimeInputs = [ pkgs.nextflow ]; + text = '' + export NXF_OFFLINE=true + for b in false true; do + echo "docker.enabled = $b" > nextflow.config + cat nextflow.config + nextflow run -ansi-log false ${hello} + done + ''; + }; + in + { + name = "nextflow"; + + nodes.machine = + { ... }: + { + environment.systemPackages = [ + run-nextflow-pipeline + pkgs.nextflow + ]; + virtualisation = { + docker.enable = true; + }; + }; + + testScript = + { nodes, ... }: + '' + start_all() + machine.wait_for_unit("docker.service") + machine.succeed("docker load < ${bash}") + machine.succeed("run-nextflow-pipeline >&2") + ''; + } +) diff --git a/pkgs/development/interpreters/nextflow/default.nix b/pkgs/development/interpreters/nextflow/default.nix index 3b2a41919a06..e76265f63d35 100644 --- a/pkgs/development/interpreters/nextflow/default.nix +++ b/pkgs/development/interpreters/nextflow/default.nix @@ -12,6 +12,7 @@ coreutils, bash, testers, + nixosTests, }: stdenv.mkDerivation (finalAttrs: { pname = "nextflow"; @@ -83,6 +84,7 @@ stdenv.mkDerivation (finalAttrs: { --set JAVA_HOME ${openjdk.home} ''; + passthru.tests.default = nixosTests.nextflow; # versionCheckHook doesn't work as of 2024-09-23. # See https://github.com/NixOS/nixpkgs/pull/339197#issuecomment-2363495060 passthru.tests.version = testers.testVersion { From 9cd78fd3a60041b96330d69d13eafc5f8407acd0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Rolf=20Schr=C3=B6der?= Date: Mon, 30 Sep 2024 11:15:23 +0200 Subject: [PATCH 4/5] tests/nextflow: restrict to x86_64-linux The docker image hash seems to differ on different systems. See https://github.com/NixOS/nixpkgs/pull/339197#discussion_r1779927407 --- nixos/tests/all-tests.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nixos/tests/all-tests.nix b/nixos/tests/all-tests.nix index 5bdd0a1a7aa1..a300220c4b1f 100644 --- a/nixos/tests/all-tests.nix +++ b/nixos/tests/all-tests.nix @@ -658,7 +658,7 @@ in { # TODO: put in networking.nix after the test becomes more complete networkingProxy = handleTest ./networking-proxy.nix {}; nextcloud = handleTest ./nextcloud {}; - nextflow = handleTest ./nextflow.nix {}; + nextflow = handleTestOn ["x86_64-linux"] ./nextflow.nix {}; nextjs-ollama-llm-ui = runTest ./web-apps/nextjs-ollama-llm-ui.nix; nexus = handleTest ./nexus.nix {}; # TODO: Test nfsv3 + Kerberos From f481bad1e7ca8d42da9eef06af203e3af7d5ed61 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Rolf=20Schr=C3=B6der?= Date: Tue, 1 Oct 2024 08:34:26 +0200 Subject: [PATCH 5/5] nextflow: fix build on darwin --- pkgs/development/interpreters/nextflow/default.nix | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/pkgs/development/interpreters/nextflow/default.nix b/pkgs/development/interpreters/nextflow/default.nix index e76265f63d35..fca7a4854453 100644 --- a/pkgs/development/interpreters/nextflow/default.nix +++ b/pkgs/development/interpreters/nextflow/default.nix @@ -55,8 +55,10 @@ stdenv.mkDerivation (finalAttrs: { # one. # See https://github.com/NixOS/nixpkgs/pull/339197#discussion_r1747749061 gradleUpdateTask = "pack"; - # See Makefile (`make pack`) + # The installer attempts to copy a final JAR to $HOME/.nextflow/... + gradleFlags = ["-Duser.home=\$TMPDIR"]; preBuild = '' + # See Makefile (`make pack`) export BUILD_PACK=1 ''; gradleBuildTask = "pack";