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Port details
biostar-tools Meta-port for Biostar Handbook tools
1.9.0 biology on this many watch lists=0 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 1.7.0Version 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: 2021-10-14 11:53:52
Commit Hash: 9d1d409
Also Listed In: python
License: BSD2CLAUSE
Description:
SVNWeb : git : Homepage
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-1.9.0/catalog.mk
  3. /usr/local/share/licenses/biostar-tools-1.9.0/LICENSE
  4. /usr/local/share/licenses/biostar-tools-1.9.0/BSD2CLAUSE
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
PKGNAME: biostar-tools
Flavors: there is no flavor information for this port.
distinfo:
Packages (timestamps in pop-ups are UTC):
biostar-tools
ABIlatestquarterly
FreeBSD:11:aarch64--
FreeBSD:11:amd641.7.01.1.0
FreeBSD:11:armv6--
FreeBSD:11:i386--
FreeBSD:11:mips--
FreeBSD:11:mips64--
FreeBSD:12:aarch64--
FreeBSD:12:amd641.9.01.7.0
FreeBSD:12:armv6--
FreeBSD:12:armv7--
FreeBSD:12:i386--
FreeBSD:12:mips--
FreeBSD:12:mips64--
FreeBSD:12:powerpc64--
FreeBSD:13:aarch64--
FreeBSD:13:amd641.9.01.7.0
FreeBSD:13:armv6--
FreeBSD:13:armv7--
FreeBSD:13:i386--
FreeBSD:13:mips--
FreeBSD:13:mips64--
FreeBSD:13:powerpc64--
FreeBSD:14:aarch64--
FreeBSD:14:amd641.9.0-
FreeBSD:14:armv6--
FreeBSD:14:armv7--
FreeBSD:14:i386--
FreeBSD:14:mips--
FreeBSD:14:mips64--
FreeBSD:14:powerpc64--
 

Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. python3.8 : lang/python38
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. py38-csvkit>0 : textproc/py-csvkit@py38
  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. py38-cutadapt>0 : biology/py-cutadapt@py38
  22. seqtk>0 : biology/seqtk
  23. datamash>0 : textproc/datamash
  24. bcftools>0 : biology/bcftools
  25. sra-tools>0 : biology/sra-tools
  26. subread>0 : biology/subread
  27. hisat2>0 : biology/hisat2
  28. trimmomatic>0 : biology/trimmomatic
  29. fastqc>0 : biology/fastqc
  30. picard-tools>0 : biology/picard-tools
  31. ncbi-blast+>0 : biology/ncbi-blast+
  32. cd-hit>0 : biology/cd-hit
  33. py38-biopython>0 : biology/py-biopython@py38
  34. py38-pysam>0 : biology/py-pysam@py38
  35. freebayes>0 : biology/freebayes
  36. p5-Net-SSLeay>0 : security/p5-Net-SSLeay
  37. bioawk>0 : biology/bioawk
  38. vt>0 : biology/vt
  39. py38-crossmap>0 : biology/py-crossmap@py38
  40. py38-goatools>0 : biology/py-goatools@py38
  41. erminej>0 : biology/erminej
  42. py38-ont-fast5-api>0 : biology/py-ont-fast5-api@py38
  43. py38-multiqc>0 : biology/py-multiqc@py38
  44. flash>0 : biology/flash
  45. bfc : biology/bfc
  46. Jellyfish>0 : biology/jellyfish
  47. mafft>0 : biology/mafft
  48. clustal-omega>0 : biology/clustal-omega
  49. py38-pywgsim>0 : biology/py-pywgsim@py38
  50. sam2pairwise>0 : biology/sam2pairwise
  51. kallisto>0 : biology/kallisto
  52. bamutil>0 : biology/bamutil
  53. py38-deepTools>0 : biology/py-deeptools@py38
  54. python3.8 : lang/python38
There are no ports dependent upon this port

Configuration Options:
Options name:

USES:

pkg-message:
If installing:
Master Sites:
  1. There is no master site for this port.

Number of commits found: 13

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
14 Oct 2021 11:53:52
 files touched by this commit commit hash:9d1d409f4253410995aba30263251bb1e44f62dc  1.9.0
jwb search for other commits by this committer
biology/biostar-tools: Add py-deeptools to metaport deps
12 Oct 2021 16:43:08
 files touched by this commit commit hash:2e8996e43d715a60fb52850286a25796fc0b9b4c  1.8.0
jwb search for other commits by this committer
biology/biostar-tools: Add biology/bamutil to metaport deps
27 Sep 2021 12:14:45
 files touched by this commit commit hash:96d32d811873af3c99e0e6380de7f6dba3603399  1.7.0
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
07 Sep 2021 20:41:10
 files touched by this commit commit hash:c73e3a89ec729d2d53d2b124839f39497d4d1b69  1.6.0
jwb search for other commits by this committer
biology/biostar-tools: Add biology/sam2pairwise to run deps

Displays pairwise alignments in a SAM file
06 Sep 2021 14:27:20
 files touched by this commit commit hash:0ec8be4158cacaa92d45914082789d936e8e678b  1.5.0
jwb search for other commits by this committer
biology/biostar-tools: Add mafft, clustal-omega, pywgsim deps

Short-read alignment related tools
24 Aug 2021 16:46:30
 files touched by this commit commit hash:1e0d8ce2079e3b116932d1450f249092abc40a3a  1.4.0
jwb search for other commits by this committer
biostar-tools: Update to 1.4.0

Add multiqc, flash, bfc, and jellyfish to metaport deps
13 Aug 2021 14:16:27
 files touched by this commit commit hash:361278dd7c6792f2ef8cb628d385dc8ea287076a  1.3.0
jwb search for other commits by this committer
biostar-tools: Correct category for py-ont-fast5-api
13 Aug 2021 13:37:48
 files touched by this commit commit hash:3ed2dd540f07e1493b6f3532f65ae3548b9ad8cb  1.3.0
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
09 Jul 2021 12:35:55
 files touched by this commit commit hash:abcde308144327fccd7d6f6ad0b6f70448b0f275  1.2.0
jwb search for other commits by this committer
biology/biostar-tools: Add erminej run depend to metaport
02 Jul 2021 17:03:10
 files touched by this commit commit hash:8b48d38ecee37869f24ce0cb1c7ec43037d9d479  1.1.0
jwb search for other commits by this committer
biology/biostar-tools: Add biology/py-goatools to metaport depends
28 Jun 2021 00:01:32
 files touched by this commit commit hash:97f088e8685297c2dd9e1f39986ca45445a52fc1  0.9.0
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
22 Jun 2021 18:00:23
 files touched by this commit commit hash:1885ed0eb12466cc4aa8ced3c0f8645f4f8a1cf6  0.9.0
jwb search for other commits by this committer
biostar-tools: Add sra-tools dependency to metaport
18 Jun 2021 21:56:23
 files touched by this commit commit hash:6df92a09ad7a75d3533ac3510cba668c74689255  0.9.0
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: 13