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biology/biostar-tools: Update to 2.0

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Add ucsc-userapps to metaport.
It was previously excluded due to packaging restrictions.
This commit is contained in:
Jason W. Bacon 2024-11-07 18:42:29 -06:00
parent ea3326c72b
commit 197d365d40
6 changed files with 21 additions and 20 deletions
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8
biology/biostar-tools/Makefile
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@ -1,6 +1,7 @@
PORTNAME= biostar-tools PORTNAME= biostar-tools
PORTVERSION= 1.11 PORTVERSION= 2.0
CATEGORIES= biology python CATEGORIES= biology python
MASTER_SITES= # empty
MAINTAINER= jwb@FreeBSD.org MAINTAINER= jwb@FreeBSD.org
COMMENT= Meta-port for Biostar Handbook tools COMMENT= Meta-port for Biostar Handbook tools
@ -63,7 +64,8 @@ RUN_DEPENDS= wget>0:ftp/wget \
bamutil>0:biology/bamutil \ bamutil>0:biology/bamutil \
${PYTHON_PKGNAMEPREFIX}deepTools>0:biology/py-deeptools@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}deepTools>0:biology/py-deeptools@${PY_FLAVOR} \
igv>0:biology/igv \ igv>0:biology/igv \
gffread>0:biology/gffread gffread>0:biology/gffread \
ucsc-userapps>0:biology/ucsc-userapps
USES= metaport python USES= metaport python
@ -74,7 +76,7 @@ USES= metaport python
RUN_DEPENDS+= sra-tools>0:biology/sra-tools RUN_DEPENDS+= sra-tools>0:biology/sra-tools
.endif .endif
SUB_FILES= biostar-shell SUB_FILES= biostar-shell pkg-message
PLIST_FILES= bin/biostar-shell PLIST_FILES= bin/biostar-shell
do-install: do-install:

2
biology/biostar-tools/distinfo
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@ -1 +1 @@
TIMESTAMP = 1717414690 TIMESTAMP = 1731026515

0
biology/biostar-tools/files/biostar-shell.in Executable file → Normal file
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13
biology/biostar-tools/files/pkg-message.in Normal file
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@ -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
}
]

7
biology/biostar-tools/pkg-descr
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@ -1,8 +1,5 @@
Biostar-Tools is a metaport for installing all the tools necessary to Biostar-Tools is a metaport for installing all the tools necessary to
work through the Biostar Handbook, except for bedGrapToBigWig, which work through the Biostar Handbook.
has license restrictions. If you need bedGraphToBigWig, run
cd /usr/ports/biology/ucsc-userapps && make install clean
The handbook instructs the reader to install these tools mostly via The handbook instructs the reader to install these tools mostly via
bioconda, which then requires the user to activate the bioconda 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 /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 default PATH (normally /usr/local/bin) so they just work without any
special environment. Emboss commands are installed to special environment. Emboss commands are installed to
/usr/local/emboss/bin due to conflicts with other packages. Run /usr/local/emboss/bin due to conflicts with other packages. Run

11
biology/biostar-tools/pkg-message
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@ -1,11 +0,0 @@
[
{ type: install
message: <<EOM
If you need bedGraphToBigWig, run:
cd ${PORTSDIR}/biology/ucsc-userapps && make install clean
EOM
}
]