From nobody Fri Feb 16 13:44:26 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 4TbtT64Fgxz5BwgS; Fri, 16 Feb 2024 13:44:26 +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 4TbtT63VH1z4cmL; Fri, 16 Feb 2024 13:44:26 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1708091066; 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=hldBa8kYlCLCRMhM1CXsnlija/iZmDgYLlj2hQBspF8=; b=v1ug117gO0IufDe1LcLbWxXIpk62JKqAt1YM7No9dbsBDu8S707k8ZCyrB0/vkJbwpo9+q oZmdOMt1QXWJzgsveqzb3jotJnFGHO1vq5ptVSG2GFIWBtY/v0b6v1Um8yKQhgadmBK6lf hg73YMC8ZnTVNAqxQmU1OCNi84BJS+N3h4+3bA9g3h3VJjdFB8zABd7PwzIqQ/D+vjBDqR UEeq8fz7srmByw3tMwdqI/ikq8+jDkL3nOvENUtHCZdBNGr8eGk35qf8R/3NT5qgYP7N2G qNkqk9WyTLil+OGHBhW4wR9xscgbj+TYP25O63W0qHcnVDuTM83usCCZo4h93A== ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1708091066; 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=hldBa8kYlCLCRMhM1CXsnlija/iZmDgYLlj2hQBspF8=; b=KWPW+aLLq4XMswExvqNQNNyQGiY58FML9lZ5bFXNpakM/++uU2EWIUzSuSLMKs5vfUTxS5 saQONEEVSiUb+QNWMxcqsfQ+zN9p+gEsZbeLu0I59RvC27Vcvn0jKXmazucIsaLeKHowL7 7FQxBXR5hUwgDQUV5iGP9G/fvUJFNB2jlKfA2HdHzXuRxWHGvOZ+xHjxwwvi1TL2qOHjUw Vu/g0ySghB40f8KWlKAIwp8NWY7LBqAIGGCmyVppNns+XdDnsOH0+h5mp/Z7pa1BHh4YDj 0OQlD1WoTGnppTiZBtF3qwR5CHIcu4McPjbjZ+GdJjaFLlDp8y+aZAJ9f4SmSQ== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1708091066; a=rsa-sha256; cv=none; b=FvTMzlpUaSdc+lE4sjnb/CDBSxezIfWP3PIynkOMrkr9f8xNTue7YBwbcb7yq1PD3eO024 gsxNKLf4tMj6pKa/ku0HbgIjRuqIbpZWu/vDOsZgOTK+LkssjLBWLMehv/YUHNMuybzNYb iA/5WP+R02okzBUbPjW3w3YoqS0DwNw/vtyvi+64zpbvucF3r4Q8cMVaMXW1YOf2+LF/Kj Ys018Mv9WOtaxtNn8uPbIRiwTx6RAsE4zRIl1ou815oUowj3ckQcjZfWPJ8LqUq1bkwmtU 9fJLYBnXb2V3NmPMcNTbOZlOQtbRQRNGNOiuE2vpt3Wc4R84FdY96QtWG2yt3Q== 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 4TbtT62WLVzRZc; Fri, 16 Feb 2024 13:44:26 +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 41GDiQtX002852; Fri, 16 Feb 2024 13:44:26 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.17.1/8.17.1/Submit) id 41GDiQkM002849; Fri, 16 Feb 2024 13:44:26 GMT (envelope-from git) Date: Fri, 16 Feb 2024 13:44:26 GMT Message-Id: <202402161344.41GDiQkM002849@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: 306ace396259 - main - biology/biostar-tools: Update to 1.10.1_3 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: 306ace396259a771b353a17bffd1e8465c2ac89d Auto-Submitted: auto-generated The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=306ace396259a771b353a17bffd1e8465c2ac89d commit 306ace396259a771b353a17bffd1e8465c2ac89d Author: Jason W. Bacon AuthorDate: 2024-02-16 13:42:11 +0000 Commit: Jason W. Bacon CommitDate: 2024-02-16 13:42:11 +0000 biology/biostar-tools: Update to 1.10.1_3 Add sra-tools to metaport deps on aarch64 Clean up pkg-desc --- biology/biostar-tools/Makefile | 6 +++--- biology/biostar-tools/distinfo | 2 +- biology/biostar-tools/pkg-descr | 25 ++++++++++++++----------- 3 files changed, 18 insertions(+), 15 deletions(-) diff --git a/biology/biostar-tools/Makefile b/biology/biostar-tools/Makefile index b8cca93134d8..8163303759cf 100644 --- a/biology/biostar-tools/Makefile +++ b/biology/biostar-tools/Makefile @@ -1,6 +1,6 @@ PORTNAME= biostar-tools PORTVERSION= 1.10.1 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= biology python MAINTAINER= jwb@FreeBSD.org @@ -71,8 +71,8 @@ USES= metaport python .include -# Allow pkg build on non-amd64 systems until sra-tools supports them -.if ${ARCH} == amd64 +# sra-tools is only supported on specific architectures +.if ${ARCH} == amd64 || ${ARCH} == aarch64 RUN_DEPENDS+= sra-tools>0:biology/sra-tools .endif diff --git a/biology/biostar-tools/distinfo b/biology/biostar-tools/distinfo index 2d706e980f0b..04755b578d3c 100644 --- a/biology/biostar-tools/distinfo +++ b/biology/biostar-tools/distinfo @@ -1 +1 @@ -TIMESTAMP = 1638373720 +TIMESTAMP = 1708090899 diff --git a/biology/biostar-tools/pkg-descr b/biology/biostar-tools/pkg-descr index eaf4acea11eb..41a5f646b935 100644 --- a/biology/biostar-tools/pkg-descr +++ b/biology/biostar-tools/pkg-descr @@ -1,16 +1,19 @@ -Biostar-Tools is a metaport for installing all the tools necessary to work -through the Biostar Handbook, except for bedGrapToBigWig, which has license -restrictions. If you need bedGraphToBigWig, run +Biostar-Tools is a metaport for installing all the tools necessary to +work through the Biostar Handbook, except for bedGrapToBigWig, which +has license restrictions. If you need bedGraphToBigWig, run cd /usr/ports/biology/ucsc-userapps && make install clean -The handbook instructs the user to install these tools mostly via bioconda, -which then requires the user to activate the bioconda environment each time -they want to use the tools. This meta-package installs all of the tools -except emboss to the default PATH so they just work without any special -environment. Emboss commands are installed to /usr/local/emboss/bin due to -conflicts with other packages. - -You can also install conda packages on FreeBSD. For details, see +The handbook instructs the reader to install these tools mostly via +bioconda, which then requires the user to activate the bioconda +environment each time they want to use the tools. You can also +install conda packages on FreeBSD if you wish. For details, see /usr/ports/sysutils/linux-miniconda-installer/pkg-descr + +This meta-package installs all of the tools except emboss to the +default PATH (normally /usr/local/bin) so they just work without any +special environment. Emboss commands are installed to +/usr/local/emboss/bin due to conflicts with other packages. Run +"biostar-shell" to add the emboss commands to your PATH, and simply +exit the shell to return your PATH to normal.