| Port details |
- biostar-tools Meta-port for Biostar Handbook tools
- 1.10.1_2 biology
 =0      1.10.1Version of this port present on the latest quarterly branch. - Maintainer: jwb@FreeBSD.org
- Port Added: 2021-06-18 22:00:16
- Last Update: 2023-04-25 15:17:15
- Commit Hash: feb1fa3
- Also Listed In: python
- License: NA
- Description:
- 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
/usr/ports/sysutils/linux-miniconda-installer/pkg-descr
  ¦  ¦  ¦  ¦  - pkg-plist: as obtained via:
make generate-plist - Dependency lines:
-
- biostar-tools>0:biology/biostar-tools
- To install the port:
- cd /usr/ports/biology/biostar-tools/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/biostar-tools
- pkg install biostar-tools
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.- PKGNAME: biostar-tools
- Flavors: there is no flavor information for this port.
- distinfo:
- TIMESTAMP = 1638373720
Packages (timestamps in pop-ups are UTC):
- Dependencies
- NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
- Build dependencies:
-
- python3.9 : lang/python39
- Test dependencies:
-
- python3.9 : lang/python39
- Runtime dependencies:
-
- wget>0 : ftp/wget
- curl>0 : ftp/curl
- nano>0 : editors/nano
- parallel>0 : sysutils/parallel
- seqkit>0 : biology/seqkit
- csvtk>0 : science/csvtk
- py39-csvkit>0 : textproc/py-csvkit@py39
- miller>0 : textproc/miller
- ncbi-entrez-direct>0 : biology/ncbi-entrez-direct
- readseq>0 : biology/readseq
- snpeff>0 : biology/snpeff
- picard-tools>0 : biology/picard-tools
- bbmap>0 : biology/bbmap
- minimap2>0 : biology/minimap2
- bwa>0 : biology/bwa
- bowtie2>0 : biology/bowtie2
- samtools>0 : biology/samtools
- emboss>0 : biology/emboss
- bedtools>0 : biology/bedtools
- bamtools>0 : biology/bamtools
- py39-cutadapt>0 : biology/py-cutadapt@py39
- seqtk>0 : biology/seqtk
- datamash>0 : textproc/datamash
- bcftools>0 : biology/bcftools
- subread>0 : biology/subread
- hisat2>0 : biology/hisat2
- trimmomatic>0 : biology/trimmomatic
- fastqc>0 : biology/fastqc
- picard-tools>0 : biology/picard-tools
- ncbi-blast+>0 : biology/ncbi-blast+
- cd-hit>0 : biology/cd-hit
- py39-biopython>0 : biology/py-biopython@py39
- py39-pysam>0 : biology/py-pysam@py39
- freebayes>0 : biology/freebayes
- p5-Net-SSLeay>0 : security/p5-Net-SSLeay
- bioawk>0 : biology/bioawk
- vt>0 : biology/vt
- py39-crossmap>0 : biology/py-crossmap@py39
- py39-goatools>0 : biology/py-goatools@py39
- erminej>0 : biology/erminej
- py39-ont-fast5-api>0 : biology/py-ont-fast5-api@py39
- py39-multiqc>0 : biology/py-multiqc@py39
- flash>0 : biology/flash
- bfc : biology/bfc
- Jellyfish>0 : biology/jellyfish
- mafft>0 : biology/mafft
- clustal-omega>0 : biology/clustal-omega
- py39-pywgsim>0 : biology/py-pywgsim@py39
- sam2pairwise>0 : biology/sam2pairwise
- kallisto>0 : biology/kallisto
- bamutil>0 : biology/bamutil
- py39-deepTools>0 : biology/py-deeptools@py39
- igv>0 : biology/igv
- gffread>0 : biology/gffread
- python3.9 : lang/python39
- sra-tools>0 : biology/sra-tools
- There are no ports dependent upon this port
Configuration Options:- No options to configure
- Options name:
- biology_biostar-tools
- USES:
- metaport python
- pkg-message:
- For install:
-
If you need bedGraphToBigWig, run:
cd ${PORTSDIR}/biology/ucsc-userapps && make install clean
- WWW: https://www.biostarhandbook.com
- Master Sites:
- There is no master site for this port.
|
| Commit History - (may be incomplete: for full details, see links to repositories near top of page) |
| Commit | Credits | Log message |
|---|
1.10.1_2
25 Apr 2023 15:17:15
 |
Christian Weisgerber (naddy) |
audio/opus: bump consumers after update to 1.4 |
1.10.1_1
23 Apr 2023 09:09:58
|
Gerald Pfeifer (gerald) |
*: Bump PORTREVISIONs for math/mpc update to 1.3.1 |
07 Sep 2022 21:58:51
|
Stefan Eßer (se) |
Remove WWW entries moved into port Makefiles
Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.
This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.
Approved by: portmgr (tcberner) |
1.10.1
07 Sep 2022 21:10:59
|
Stefan Eßer (se) |
Add WWW entries to port Makefiles
It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.
Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.
There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.
(Only the first 15 lines of the commit message are shown above  ) |
1.10.1
01 Dec 2021 15:49:28
|
Jason W. Bacon (jwb) |
biology/biostar-tools: Allow package build on non-amd64 systems
Only sra-tools is still non-portable, but it will take some time to
add support for other architectures. In the meantime, allow aarch64
and powerpc64 users to have a biostar-tools package. |
1.10.0
10 Nov 2021 20:52:01
|
Jason W. Bacon (jwb) |
biostar-tools: Add gffread to metaport deps |
1.9.1
30 Oct 2021 15:27:03
|
Jason W. Bacon (jwb) |
biology/biostar-tools: Add biology/igv to metaport deps |
1.9.0
14 Oct 2021 11:53:52
|
Jason W. Bacon (jwb) |
biology/biostar-tools: Add py-deeptools to metaport deps |
1.8.0
12 Oct 2021 16:43:08
|
Jason W. Bacon (jwb) |
biology/biostar-tools: Add biology/bamutil to metaport deps |
1.7.0
27 Sep 2021 12:14:45
|
Jason W. Bacon (jwb) |
biology/biostar-tools: Add biology/kallisto run depend to metaport
Also clean up other deps for consistency |
1.6.0
07 Sep 2021 20:41:10
|
Jason W. Bacon (jwb) |
biology/biostar-tools: Add biology/sam2pairwise to run deps
Displays pairwise alignments in a SAM file |
1.5.0
06 Sep 2021 14:27:20
|
Jason W. Bacon (jwb) |
biology/biostar-tools: Add mafft, clustal-omega, pywgsim deps
Short-read alignment related tools |
1.4.0
24 Aug 2021 16:46:30
|
Jason W. Bacon (jwb) |
biostar-tools: Update to 1.4.0
Add multiqc, flash, bfc, and jellyfish to metaport deps |
1.3.0
13 Aug 2021 14:16:27
|
Jason W. Bacon (jwb) |
biostar-tools: Correct category for py-ont-fast5-api |
1.3.0
13 Aug 2021 13:37:48
|
Jason W. Bacon (jwb) |
biostar-tools: Add new deps to metaport
csvkit, miller: Tools for working with comma-separated data
py-ont-fast5-api: Library and tools for Oxford Nanopore fast5 files |
1.2.0
09 Jul 2021 12:35:55
|
Jason W. Bacon (jwb) |
biology/biostar-tools: Add erminej run depend to metaport |
1.1.0
02 Jul 2021 17:03:10
|
Jason W. Bacon (jwb) |
biology/biostar-tools: Add biology/py-goatools to metaport depends |
0.9.0
28 Jun 2021 00:01:32
|
Jason W. Bacon (jwb) |
biology/biostar-tools: Remove falsehood in pkg-message
We now use native sra-tools, not linux-sra-tools |
0.9.0
22 Jun 2021 18:00:23
|
Jason W. Bacon (jwb) |
biostar-tools: Add sra-tools dependency to metaport |
0.9.0
18 Jun 2021 21:56:23
|
Jason W. Bacon (jwb) |
biology/biostar-tools: Meta-port for Biostar Handbook tools
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 |
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