Date: Fri, 8 Nov 2024 00:44:29 GMT From: "Jason W. Bacon" <jwb@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: 197d365d40dc - main - biology/biostar-tools: Update to 2.0 Message-ID: <202411080044.4A80iTEF080767@gitrepo.freebsd.org>
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The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=197d365d40dcb3c57f17e11d18b96441cf5d68af commit 197d365d40dcb3c57f17e11d18b96441cf5d68af Author: Jason W. Bacon <jwb@FreeBSD.org> AuthorDate: 2024-11-08 00:42:29 +0000 Commit: Jason W. Bacon <jwb@FreeBSD.org> CommitDate: 2024-11-08 00:44:28 +0000 biology/biostar-tools: Update to 2.0 Add ucsc-userapps to metaport. It was previously excluded due to packaging restrictions. --- biology/biostar-tools/Makefile | 8 +++++--- biology/biostar-tools/distinfo | 2 +- biology/biostar-tools/files/biostar-shell.in | 0 biology/biostar-tools/files/pkg-message.in | 13 +++++++++++++ biology/biostar-tools/pkg-descr | 7 ++----- biology/biostar-tools/pkg-message | 11 ----------- 6 files changed, 21 insertions(+), 20 deletions(-) diff --git a/biology/biostar-tools/Makefile b/biology/biostar-tools/Makefile index ae02abc2c890..6002cae2fc71 100644 --- a/biology/biostar-tools/Makefile +++ b/biology/biostar-tools/Makefile @@ -1,6 +1,7 @@ PORTNAME= biostar-tools -PORTVERSION= 1.11 +PORTVERSION= 2.0 CATEGORIES= biology python +MASTER_SITES= # empty MAINTAINER= jwb@FreeBSD.org COMMENT= Meta-port for Biostar Handbook tools @@ -63,7 +64,8 @@ RUN_DEPENDS= wget>0:ftp/wget \ bamutil>0:biology/bamutil \ ${PYTHON_PKGNAMEPREFIX}deepTools>0:biology/py-deeptools@${PY_FLAVOR} \ igv>0:biology/igv \ - gffread>0:biology/gffread + gffread>0:biology/gffread \ + ucsc-userapps>0:biology/ucsc-userapps USES= metaport python @@ -74,7 +76,7 @@ USES= metaport python RUN_DEPENDS+= sra-tools>0:biology/sra-tools .endif -SUB_FILES= biostar-shell +SUB_FILES= biostar-shell pkg-message PLIST_FILES= bin/biostar-shell do-install: diff --git a/biology/biostar-tools/distinfo b/biology/biostar-tools/distinfo index 19b785822b56..4bfd994ffd70 100644 --- a/biology/biostar-tools/distinfo +++ b/biology/biostar-tools/distinfo @@ -1 +1 @@ -TIMESTAMP = 1717414690 +TIMESTAMP = 1731026515 diff --git a/biology/biostar-tools/files/biostar-shell.in b/biology/biostar-tools/files/biostar-shell.in old mode 100755 new mode 100644 diff --git a/biology/biostar-tools/files/pkg-message.in b/biology/biostar-tools/files/pkg-message.in new file mode 100644 index 000000000000..5499288900c9 --- /dev/null +++ b/biology/biostar-tools/files/pkg-message.in @@ -0,0 +1,13 @@ +[ +{ type: install + message: <<EOM + +Biostar-tools 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 +%%PREFIX%%/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. +EOM +} +] diff --git a/biology/biostar-tools/pkg-descr b/biology/biostar-tools/pkg-descr index 41a5f646b935..6cbffce10a0b 100644 --- a/biology/biostar-tools/pkg-descr +++ b/biology/biostar-tools/pkg-descr @@ -1,8 +1,5 @@ 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 +work through the Biostar Handbook. The handbook instructs the reader to install these tools mostly via bioconda, which then requires the user to activate the bioconda @@ -11,7 +8,7 @@ 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 +Biostar-tools 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 diff --git a/biology/biostar-tools/pkg-message b/biology/biostar-tools/pkg-message deleted file mode 100644 index 4adbdc124805..000000000000 --- a/biology/biostar-tools/pkg-message +++ /dev/null @@ -1,11 +0,0 @@ -[ -{ type: install - message: <<EOM - -If you need bedGraphToBigWig, run: - - cd ${PORTSDIR}/biology/ucsc-userapps && make install clean - -EOM -} -]
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