From nobody Wed Jan 10 15:20:37 2024 X-Original-To: dev-commits-ports-all@mlmmj.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mlmmj.nyi.freebsd.org (Postfix) with ESMTP id 4T9BMB3rWnz579YW; Wed, 10 Jan 2024 15:20:38 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4T9BMB0ST4z5001; Wed, 10 Jan 2024 15:20:38 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1704900038; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=6Qp5VUtmqmODRhOG7w57z4xI3IamVEkiVMILZ8lCCCM=; b=dGih5UgA9J7a+k1ENNYaVWovyVWNynww6ylenmc7t6x2NCO9oPjVuswaaZcW+T+SiDuGI1 TyJjI3QDa6ed3dLRVSC7Ncv+BGmD/1crT0t5r9LkA7KZS3hhP6dnRT9NrWTlpet2hs8IZS p6gGC7mFhNdU3wlJ2fOIo3KQAJ4XrO93ZGn+v/C9CgkjrEdCLVrTpgu/IoaRioo6Iiu7Gi KdnKjnSlI68nSdTC5bpYErIeliPQk4oLTlfVdchJvEZ7IFTg0n6uWUtiQ1MqB14LsjEv1s WDQJ7IupsjHMbBbriuD/CA72kebCZVlQzOaB9XS16Kx5VfFxUtksONz2XtAYag== ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1704900038; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=6Qp5VUtmqmODRhOG7w57z4xI3IamVEkiVMILZ8lCCCM=; b=tBiV+J0ZhFKsoL3/bB6C4Q6yQpBVere0YNMOxPTH/NUNZMy6ZLTI3af6VMaZ6iLla/xRCq +ljbLnEnwdSFFRgzBU7mflzmztt8wmGxid+SNsMiP5PExAqDYKEeOJMNlfGrhuDxGfiKhB 01uEkNN/SEQ8905ehM8Dxl07kbkmyindlRWhYzLAA/032b6H5EyvPgtX2nGoNYVPthgjx1 2lKyt8L4u4xiy398AAgjw5Rv6xXNpivPaWpbkEyllNC8iRu0Tshfl7PJUXxugRwGC2DB49 2MyMCrEd1qDn2iG1jwMDipOzkX3G3lgj4gUIZlssz1I3vMcME+FoYMS6KF5V0g== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1704900038; a=rsa-sha256; cv=none; b=L8TUbAD0fQrOoUf3/qF7NMW1bwtoSgP3/xn9TCN2c52By9+8YVyTje34gA1pjnz4TPJ4Bo BXRr0hPdUqVx3+FcZRhlQfJXoGnc8NsFgd5twpnqe5ABV2jP+bR9/u2MX9HU73UprYAlZq 4MHq3ewzs1H7jNgwYjG5n1saUaYI1SkJcffoHQJIW5ZpzDUpF7d8di86oeYhfjMTR1dxJi 9iMW0D8b2ruWjt5FGmWwICJImRyJY4osJLDaKEGqXNWtBeH8jBU8y9s5DwNXeE78fionrN pVhgAg9NzhyYDAqaa+2SkmAHzMThxRbmmFIyeKSYs6iwjTqA8A6VcXv3HMIyfg== Received: from gitrepo.freebsd.org (gitrepo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:5]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 4T9BM95nb1zgm7; Wed, 10 Jan 2024 15:20:37 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.17.1/8.17.1) with ESMTP id 40AFKbsE042876; Wed, 10 Jan 2024 15:20:37 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.17.1/8.17.1/Submit) id 40AFKb9W042873; Wed, 10 Jan 2024 15:20:37 GMT (envelope-from git) Date: Wed, 10 Jan 2024 15:20:37 GMT Message-Id: <202401101520.40AFKb9W042873@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: "Jason W. Bacon" Subject: git: fabf2f6b2fbf - main - biology/py-macs3: Peak caller for TF binding sites List-Id: Commit messages for all branches of the ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-all List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-dev-commits-ports-all@freebsd.org X-BeenThere: dev-commits-ports-all@freebsd.org MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: jwb X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: fabf2f6b2fbf0e0eeabffa05efb9135208244601 Auto-Submitted: auto-generated The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=fabf2f6b2fbf0e0eeabffa05efb9135208244601 commit fabf2f6b2fbf0e0eeabffa05efb9135208244601 Author: Jason W. Bacon AuthorDate: 2024-01-10 15:19:56 +0000 Commit: Jason W. Bacon CommitDate: 2024-01-10 15:19:56 +0000 biology/py-macs3: Peak caller for TF binding sites MACS (Model-based Analysis of ChIP-Seq) is a tool for identifying transcription factor (TF) binding sites. Such sites are generated by CHiP-Seq (CHromatin immuno-Precipitation sequencing) and ATAC-Seq (Assay for Transposase Accessible Chromatin Sequencing). MACS identifies "peaks" in the genome sequence, which are areas enriched in bound TFs or accessible chromatin. --- biology/Makefile | 1 + biology/py-macs3/Makefile | 49 ++++++++++++++++++++++ biology/py-macs3/distinfo | 3 ++ .../py-macs3/files/patch-MACS3_fermi-lite_ksw.c | 11 +++++ biology/py-macs3/files/patch-pyproject.toml | 6 +++ biology/py-macs3/files/patch-requirements.txt | 8 ++++ biology/py-macs3/files/patch-setup.py | 20 +++++++++ biology/py-macs3/pkg-descr | 6 +++ 8 files changed, 104 insertions(+) diff --git a/biology/Makefile b/biology/Makefile index 6f35c5481dc7..11fc752f7b4c 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -179,6 +179,7 @@ SUBDIR += py-libsedml SUBDIR += py-loompy SUBDIR += py-macs2 + SUBDIR += py-macs3 SUBDIR += py-mrcfile SUBDIR += py-multiqc SUBDIR += py-ont-fast5-api diff --git a/biology/py-macs3/Makefile b/biology/py-macs3/Makefile new file mode 100644 index 000000000000..d2cad2892df4 --- /dev/null +++ b/biology/py-macs3/Makefile @@ -0,0 +1,49 @@ +PORTNAME= MACS3 +DISTVERSIONPREFIX= v +DISTVERSION= 3.0.0 +CATEGORIES= biology python +PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Peak caller aimed at transcription factor binding sites +WWW= https://github.com/taoliu/MACS + +LICENSE= BSD3CLAUSE +LICENSE_FILE= ${WRKSRC}/LICENSE + +BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}wheel>0:devel/py-wheel@${PY_FLAVOR} \ + ${PYNUMPY} \ + simde>0:devel/simde \ + ${PYTHON_PKGNAMEPREFIX}cykhash>0:devel/py-cykhash@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}hmmlearn>0:math/py-hmmlearn@${PY_FLAVOR} +RUN_DEPENDS= ${PYNUMPY} \ + ${PYTHON_PKGNAMEPREFIX}cykhash>0:devel/py-cykhash@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}hmmlearn>0:math/py-hmmlearn@${PY_FLAVOR} +TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}pytest>0:devel/py-pytest@${PY_FLAVOR} \ + bash:shells/bash + +USES= localbase perl5 python shebangfix +USE_GITHUB= yes +USE_PERL5= test +USE_PYTHON= autoplist concurrent cython pep517 + +GH_ACCOUNT= macs3-project +GH_PROJECT= MACS +SHEBANG_FILES= test/cmdlinetest* test/prockreport test/*.py test/pyprofile* + +.include + +.if ${OPSYS} == FreeBSD && ${OSVERSION} < 1302509 +IGNORE= does not run properly on FreeBSD 13.2 and earlier due to use of dynamically loaded libc by py-threadpoolctl. Please upgrade to a newer FreeBSD or use py-macs2 instead. See PR 276231 +.endif + +post-stage: + ${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/MACS3/*/*.so + +# FIXME: Some tests fail due to a py-threadpoolctl issue +# https://github.com/joblib/threadpoolctl/pull/148 +do-test: deinstall install + @${RM} -rf ${WRKSRC}/temp + @cd ${WRKSRC}/test && ./cmdlinetest tag + +.include diff --git a/biology/py-macs3/distinfo b/biology/py-macs3/distinfo new file mode 100644 index 000000000000..757e9bbaf640 --- /dev/null +++ b/biology/py-macs3/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1703890666 +SHA256 (macs3-project-MACS-v3.0.0_GH0.tar.gz) = faa7ec2ea1f47b8c4cd747f00f2754d0e40051fe44d81d229d0111e3dad34a1d +SIZE (macs3-project-MACS-v3.0.0_GH0.tar.gz) = 197389439 diff --git a/biology/py-macs3/files/patch-MACS3_fermi-lite_ksw.c b/biology/py-macs3/files/patch-MACS3_fermi-lite_ksw.c new file mode 100644 index 000000000000..d66d83f33606 --- /dev/null +++ b/biology/py-macs3/files/patch-MACS3_fermi-lite_ksw.c @@ -0,0 +1,11 @@ +--- MACS3/fermi-lite/ksw.c.orig 2023-11-15 16:09:23 UTC ++++ MACS3/fermi-lite/ksw.c +@@ -28,7 +28,7 @@ + + /* I modified this according to https://github.com/lh3/bwa/pull/283/*/ + #ifdef USE_SIMDE +-#include "lib/x86/sse2.h" ++#include + #else + #include + #endif diff --git a/biology/py-macs3/files/patch-pyproject.toml b/biology/py-macs3/files/patch-pyproject.toml new file mode 100644 index 000000000000..cf54cae8892f --- /dev/null +++ b/biology/py-macs3/files/patch-pyproject.toml @@ -0,0 +1,6 @@ +--- pyproject.toml.orig 2024-01-06 15:00:01 UTC ++++ pyproject.toml +@@ -1,2 +1,2 @@ + [build-system] +-requires=['setuptools>=60.0', 'numpy>=1.19', 'cykhash>=2.0,<3.0', 'Cython~=3.0', 'hmmlearn>=0.3'] ++requires=['setuptools>=60.0', 'numpy>=1.19', 'cykhash>=2.0,<3.0', 'Cython>=0', 'hmmlearn>=0.3'] diff --git a/biology/py-macs3/files/patch-requirements.txt b/biology/py-macs3/files/patch-requirements.txt new file mode 100644 index 000000000000..0c8106f79680 --- /dev/null +++ b/biology/py-macs3/files/patch-requirements.txt @@ -0,0 +1,8 @@ +--- requirements.txt.orig 2024-01-06 14:55:53 UTC ++++ requirements.txt +@@ -1,4 +1,4 @@ +-Cython~=3.0 ++Cython>=0 + numpy>=1.19 + hmmlearn>=0.3 + cykhash>=2.0,<3.0 diff --git a/biology/py-macs3/files/patch-setup.py b/biology/py-macs3/files/patch-setup.py new file mode 100644 index 000000000000..58dde13ba2c2 --- /dev/null +++ b/biology/py-macs3/files/patch-setup.py @@ -0,0 +1,20 @@ +--- setup.py.orig 2023-11-15 16:09:23 UTC ++++ setup.py +@@ -40,7 +40,7 @@ classifiers =[\ + install_requires = [ "numpy>=1.19", + "hmmlearn>=0.3", + "cykhash>=2.0,<3.0", +- "Cython~=3.0" ] ++ "Cython>=0" ] + + tests_requires = [ 'pytest' ] + +@@ -70,7 +70,7 @@ def main(): + + if not clang: + try: +- gcc_version_check = subprocess.check_output( ["gcc", "--version"], universal_newlines=True) ++ gcc_version_check = subprocess.check_output( ["cc", "--version"], universal_newlines=True) + if gcc_version_check.find("clang") != -1: + clang = True + else: diff --git a/biology/py-macs3/pkg-descr b/biology/py-macs3/pkg-descr new file mode 100644 index 000000000000..7e901a88e5ea --- /dev/null +++ b/biology/py-macs3/pkg-descr @@ -0,0 +1,6 @@ +MACS (Model-based Analysis of ChIP-Seq) is a tool for identifying +transcription factor (TF) binding sites. Such sites are generated +by CHiP-Seq (CHromatin immuno-Precipitation sequencing) and ATAC-Seq +(Assay for Transposase Accessible Chromatin Sequencing). MACS +identifies "peaks" in the genome sequence, which are areas enriched +in bound TFs or accessible chromatin.