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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
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:

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
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

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
}
]