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Port details
biostar-tools Meta-port for Biostar Handbook tools
2.0 biology on this many watch lists=2 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 1.11Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2021-06-18 22:00:16
Last Update: 2024-11-08 00:44:28
Commit Hash: 197d365
People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
Also Listed In: python
License: NA
WWW:
https://www.biostarhandbook.com
Description:
Biostar-Tools is a metaport for installing all the tools necessary to 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 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 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 "biostar-shell" to add the emboss commands to your PATH, and simply exit the shell to return your PATH to normal.
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb - no subversion history for this port

Manual pages:
FreshPorts has no man page information for this port.
pkg-plist: as obtained via: make generate-plist
Expand this list (4 items)
Collapse this list.
  1. bin/biostar-shell
  2. /usr/local/share/licenses/biostar-tools-2.0/catalog.mk
  3. /usr/local/share/licenses/biostar-tools-2.0/LICENSE
  4. /usr/local/share/licenses/biostar-tools-2.0/NA
Collapse this list.
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 = 1731026515
Packages (timestamps in pop-ups are UTC):
biostar-tools
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest2.02.0------
FreeBSD:13:quarterly2.02.0------
FreeBSD:14:latest2.02.0------
FreeBSD:14:quarterly2.02.0------
FreeBSD:15:latest--n/a-n/a---
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. python3.11 : lang/python311
Test dependencies:
  1. python3.11 : lang/python311
Runtime dependencies:
  1. wget>0 : ftp/wget
  2. curl>0 : ftp/curl
  3. nano>0 : editors/nano
  4. parallel>0 : sysutils/parallel
  5. seqkit>0 : biology/seqkit
  6. csvtk>0 : science/csvtk
  7. py311-csvkit>0 : textproc/py-csvkit@py311
  8. miller>0 : textproc/miller
  9. ncbi-entrez-direct>0 : biology/ncbi-entrez-direct
  10. readseq>0 : biology/readseq
  11. snpeff>0 : biology/snpeff
  12. picard-tools>0 : biology/picard-tools
  13. bbmap>0 : biology/bbmap
  14. minimap2>0 : biology/minimap2
  15. bwa>0 : biology/bwa
  16. bowtie2>0 : biology/bowtie2
  17. samtools>0 : biology/samtools
  18. emboss>0 : biology/emboss
  19. bedtools>0 : biology/bedtools
  20. bamtools>0 : biology/bamtools
  21. py311-cutadapt>0 : biology/py-cutadapt@py311
  22. seqtk>0 : biology/seqtk
  23. datamash>0 : textproc/datamash
  24. bcftools>0 : biology/bcftools
  25. subread>0 : biology/subread
  26. hisat2>0 : biology/hisat2
  27. trimmomatic>0 : biology/trimmomatic
  28. fastqc>0 : biology/fastqc
  29. picard-tools>0 : biology/picard-tools
  30. ncbi-blast+>0 : biology/ncbi-blast+
  31. cd-hit>0 : biology/cd-hit
  32. py311-biopython>0 : biology/py-biopython@py311
  33. py311-pysam>0 : biology/py-pysam@py311
  34. freebayes>0 : biology/freebayes
  35. p5-Net-SSLeay>0 : security/p5-Net-SSLeay
  36. bioawk>0 : biology/bioawk
  37. vt>0 : biology/vt
  38. py311-crossmap>0 : biology/py-crossmap@py311
  39. py311-goatools>0 : biology/py-goatools@py311
  40. erminej>0 : biology/erminej
  41. py311-ont-fast5-api>0 : biology/py-ont-fast5-api@py311
  42. py311-multiqc>0 : biology/py-multiqc@py311
  43. flash>0 : biology/flash
  44. bfc : biology/bfc
  45. Jellyfish>0 : biology/jellyfish
  46. mafft>0 : biology/mafft
  47. clustal-omega>0 : biology/clustal-omega
  48. sam2pairwise>0 : biology/sam2pairwise
  49. kallisto>0 : biology/kallisto
  50. bamutil>0 : biology/bamutil
  51. py311-deepTools>0 : biology/py-deeptools@py311
  52. igv>0 : biology/igv
  53. gffread>0 : biology/gffread
  54. ucsc-userapps>0 : biology/ucsc-userapps
  55. python3.11 : lang/python311
  56. 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:
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 "biostar-shell" to add the emboss commands to your PATH, and simply exit the shell to return your PATH to normal.
Master Sites:
  1. There is no master site for this port.

Number of commits found: 23

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
2.0
08 Nov 2024 00:44:28
commit hash: 197d365d40dcb3c57f17e11d18b96441cf5d68afcommit hash: 197d365d40dcb3c57f17e11d18b96441cf5d68afcommit hash: 197d365d40dcb3c57f17e11d18b96441cf5d68afcommit hash: 197d365d40dcb3c57f17e11d18b96441cf5d68af files touched by this commit		 Jason W. Bacon (jwb) search for other commits by this committer 
biology/biostar-tools: Update to 2.0

Add ucsc-userapps to metaport.
It was previously excluded due to packaging restrictions.
1.11
03 Jun 2024 11:38:30
commit hash: b8732315154d075cbb8288fd3799961ed0721a1ccommit hash: b8732315154d075cbb8288fd3799961ed0721a1ccommit hash: b8732315154d075cbb8288fd3799961ed0721a1ccommit hash: b8732315154d075cbb8288fd3799961ed0721a1c files touched by this commit		 Jason W. Bacon (jwb) search for other commits by this committer 
biology/biostar-tools: Update to 1.11

Drop abandonware py-pywgsim dep

Reported by:    pkg-fallout
1.10.1_3
16 Feb 2024 13:42:11
commit hash: 306ace396259a771b353a17bffd1e8465c2ac89dcommit hash: 306ace396259a771b353a17bffd1e8465c2ac89dcommit hash: 306ace396259a771b353a17bffd1e8465c2ac89dcommit hash: 306ace396259a771b353a17bffd1e8465c2ac89d files touched by this commit		 Jason W. Bacon (jwb) search for other commits by this committer 
biology/biostar-tools: Update to 1.10.1_3

Add sra-tools to metaport deps on aarch64
Clean up pkg-desc
1.10.1_2
25 Apr 2023 15:17:15
commit hash: feb1fa34f58ea796656b86a81c2a2996b0b03c96commit hash: feb1fa34f58ea796656b86a81c2a2996b0b03c96commit hash: feb1fa34f58ea796656b86a81c2a2996b0b03c96commit hash: feb1fa34f58ea796656b86a81c2a2996b0b03c96 files touched by this commit		 Christian Weisgerber (naddy) search for other commits by this committer 
audio/opus: bump consumers after update to 1.4
1.10.1_1
23 Apr 2023 09:09:58
commit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5bcommit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5bcommit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5bcommit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5b files touched by this commit		 Gerald Pfeifer (gerald) search for other commits by this committer 
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
07 Sep 2022 21:58:51
commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4 files touched by this commit		 Stefan Eßer (se) search for other commits by this committer 
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
commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 files touched by this commit		 Stefan Eßer (se) search for other commits by this committer 
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 View all of this commit message)
1.10.1
01 Dec 2021 15:49:28
commit hash: 70e9e19c3cb7a11ccfef63c91beaf291ea2fb366commit hash: 70e9e19c3cb7a11ccfef63c91beaf291ea2fb366commit hash: 70e9e19c3cb7a11ccfef63c91beaf291ea2fb366commit hash: 70e9e19c3cb7a11ccfef63c91beaf291ea2fb366 files touched by this commit		 Jason W. Bacon (jwb) search for other commits by this committer 
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
commit hash: 17f3e2cbe6f16082e91366537d29d3d53076e295commit hash: 17f3e2cbe6f16082e91366537d29d3d53076e295commit hash: 17f3e2cbe6f16082e91366537d29d3d53076e295commit hash: 17f3e2cbe6f16082e91366537d29d3d53076e295 files touched by this commit		 Jason W. Bacon (jwb) search for other commits by this committer 
biostar-tools: Add gffread to metaport deps
1.9.1
30 Oct 2021 15:27:03
commit hash: 4df7493e10049abc7538f1f5ab1e69f61136a21dcommit hash: 4df7493e10049abc7538f1f5ab1e69f61136a21dcommit hash: 4df7493e10049abc7538f1f5ab1e69f61136a21dcommit hash: 4df7493e10049abc7538f1f5ab1e69f61136a21d files touched by this commit		 Jason W. Bacon (jwb) search for other commits by this committer 
biology/biostar-tools: Add biology/igv to metaport deps
1.9.0
14 Oct 2021 11:53:52
commit hash: 9d1d409f4253410995aba30263251bb1e44f62dccommit hash: 9d1d409f4253410995aba30263251bb1e44f62dccommit hash: 9d1d409f4253410995aba30263251bb1e44f62dccommit hash: 9d1d409f4253410995aba30263251bb1e44f62dc files touched by this commit		 Jason W. Bacon (jwb) search for other commits by this committer 
biology/biostar-tools: Add py-deeptools to metaport deps
1.8.0
12 Oct 2021 16:43:08
commit hash: 2e8996e43d715a60fb52850286a25796fc0b9b4ccommit hash: 2e8996e43d715a60fb52850286a25796fc0b9b4ccommit hash: 2e8996e43d715a60fb52850286a25796fc0b9b4ccommit hash: 2e8996e43d715a60fb52850286a25796fc0b9b4c files touched by this commit		 Jason W. Bacon (jwb) search for other commits by this committer 
biology/biostar-tools: Add biology/bamutil to metaport deps
1.7.0
27 Sep 2021 12:14:45
commit hash: 96d32d811873af3c99e0e6380de7f6dba3603399commit hash: 96d32d811873af3c99e0e6380de7f6dba3603399commit hash: 96d32d811873af3c99e0e6380de7f6dba3603399commit hash: 96d32d811873af3c99e0e6380de7f6dba3603399 files touched by this commit		 Jason W. Bacon (jwb) search for other commits by this committer 
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
commit hash: c73e3a89ec729d2d53d2b124839f39497d4d1b69commit hash: c73e3a89ec729d2d53d2b124839f39497d4d1b69commit hash: c73e3a89ec729d2d53d2b124839f39497d4d1b69commit hash: c73e3a89ec729d2d53d2b124839f39497d4d1b69 files touched by this commit		 Jason W. Bacon (jwb) search for other commits by this committer 
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
commit hash: 0ec8be4158cacaa92d45914082789d936e8e678bcommit hash: 0ec8be4158cacaa92d45914082789d936e8e678bcommit hash: 0ec8be4158cacaa92d45914082789d936e8e678bcommit hash: 0ec8be4158cacaa92d45914082789d936e8e678b files touched by this commit		 Jason W. Bacon (jwb) search for other commits by this committer 
biology/biostar-tools: Add mafft, clustal-omega, pywgsim deps

Short-read alignment related tools
1.4.0
24 Aug 2021 16:46:30
commit hash: 1e0d8ce2079e3b116932d1450f249092abc40a3acommit hash: 1e0d8ce2079e3b116932d1450f249092abc40a3acommit hash: 1e0d8ce2079e3b116932d1450f249092abc40a3acommit hash: 1e0d8ce2079e3b116932d1450f249092abc40a3a files touched by this commit		 Jason W. Bacon (jwb) search for other commits by this committer 
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
commit hash: 361278dd7c6792f2ef8cb628d385dc8ea287076acommit hash: 361278dd7c6792f2ef8cb628d385dc8ea287076acommit hash: 361278dd7c6792f2ef8cb628d385dc8ea287076acommit hash: 361278dd7c6792f2ef8cb628d385dc8ea287076a files touched by this commit		 Jason W. Bacon (jwb) search for other commits by this committer 
biostar-tools: Correct category for py-ont-fast5-api
1.3.0
13 Aug 2021 13:37:48
commit hash: 3ed2dd540f07e1493b6f3532f65ae3548b9ad8cbcommit hash: 3ed2dd540f07e1493b6f3532f65ae3548b9ad8cbcommit hash: 3ed2dd540f07e1493b6f3532f65ae3548b9ad8cbcommit hash: 3ed2dd540f07e1493b6f3532f65ae3548b9ad8cb files touched by this commit		 Jason W. Bacon (jwb) search for other commits by this committer 
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
commit hash: abcde308144327fccd7d6f6ad0b6f70448b0f275commit hash: abcde308144327fccd7d6f6ad0b6f70448b0f275commit hash: abcde308144327fccd7d6f6ad0b6f70448b0f275commit hash: abcde308144327fccd7d6f6ad0b6f70448b0f275 files touched by this commit		 Jason W. Bacon (jwb) search for other commits by this committer 
biology/biostar-tools: Add erminej run depend to metaport
1.1.0
02 Jul 2021 17:03:10
commit hash: 8b48d38ecee37869f24ce0cb1c7ec43037d9d479commit hash: 8b48d38ecee37869f24ce0cb1c7ec43037d9d479commit hash: 8b48d38ecee37869f24ce0cb1c7ec43037d9d479commit hash: 8b48d38ecee37869f24ce0cb1c7ec43037d9d479 files touched by this commit		 Jason W. Bacon (jwb) search for other commits by this committer 
biology/biostar-tools: Add biology/py-goatools to metaport depends
0.9.0
28 Jun 2021 00:01:32
commit hash: 97f088e8685297c2dd9e1f39986ca45445a52fc1commit hash: 97f088e8685297c2dd9e1f39986ca45445a52fc1commit hash: 97f088e8685297c2dd9e1f39986ca45445a52fc1commit hash: 97f088e8685297c2dd9e1f39986ca45445a52fc1 files touched by this commit		 Jason W. Bacon (jwb) search for other commits by this committer 
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
commit hash: 1885ed0eb12466cc4aa8ced3c0f8645f4f8a1cf6commit hash: 1885ed0eb12466cc4aa8ced3c0f8645f4f8a1cf6commit hash: 1885ed0eb12466cc4aa8ced3c0f8645f4f8a1cf6commit hash: 1885ed0eb12466cc4aa8ced3c0f8645f4f8a1cf6 files touched by this commit		 Jason W. Bacon (jwb) search for other commits by this committer 
biostar-tools: Add sra-tools dependency to metaport
0.9.0
18 Jun 2021 21:56:23
commit hash: 6df92a09ad7a75d3533ac3510cba668c74689255commit hash: 6df92a09ad7a75d3533ac3510cba668c74689255commit hash: 6df92a09ad7a75d3533ac3510cba668c74689255commit hash: 6df92a09ad7a75d3533ac3510cba668c74689255 files touched by this commit		 Jason W. Bacon (jwb) search for other commits by this committer 
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

Number of commits found: 23
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