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Port details
snpeff Genetic variant annotation and effect prediction toolbox
5.0 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 5.0Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2021-04-18 18:48:08
Last Update: 2021-04-19 16:41:58
Commit Hash: 3bc87a0
Also Listed In: java python
License: MIT
Description:
SVNWeb : git : Homepage
pkg-plist: as obtained via: make generate-plist
Expand this list (81 items)
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  1. /usr/local/share/licenses/snpeff-5.0/catalog.mk
  2. /usr/local/share/licenses/snpeff-5.0/LICENSE
  3. /usr/local/share/licenses/snpeff-5.0/MIT
  4. bin/snpEff
  5. bin/snpSift
  6. libexec/snpeff/1kg.sh
  7. libexec/snpeff/annotate_demo.sh
  8. libexec/snpeff/annotate_demo_GATK.sh
  9. libexec/snpeff/bedEffOnePerLine.pl
  10. libexec/snpeff/buildDbNcbi.sh
  11. libexec/snpeff/cgShore.pl
  12. libexec/snpeff/cgShore.sh
  13. libexec/snpeff/countColumns.py
  14. libexec/snpeff/db.pl
  15. libexec/snpeff/extractSequences.pl
  16. libexec/snpeff/fasta2tab.pl
  17. libexec/snpeff/fastaSample.pl
  18. libexec/snpeff/fastaSplit.pl
  19. libexec/snpeff/fastqSplit.pl
  20. libexec/snpeff/filterBy.py
  21. libexec/snpeff/gffRemovePhase.pl
  22. libexec/snpeff/gsa/bayesFactor_correction_scoreCount.r
  23. libexec/snpeff/gsa/bayesFactor_correction_scoreCount.sh
  24. libexec/snpeff/gsa/bayesFactor_correction_scoreCount_max10.sh
  25. libexec/snpeff/gsa/checkGeneNames.py
  26. libexec/snpeff/gsa/create_sets.bds
  27. libexec/snpeff/gsa/geneSetOverlap.py
  28. libexec/snpeff/gsa/geneSetOverlap.sort.txt
  29. libexec/snpeff/gsa/geneSetsGtex.py
  30. libexec/snpeff/gsa/pvalue_correction_scoreCount.r
  31. libexec/snpeff/gsa/pvalue_correction_scoreCount.sh
  32. libexec/snpeff/gsa/pvalue_correction_scoreCount_min10.sh
  33. libexec/snpeff/isutf8.py
  34. libexec/snpeff/join.pl
  35. libexec/snpeff/joinSnpEff.pl
  36. libexec/snpeff/make_and_commit_docs.sh
  37. libexec/snpeff/make_dbNSFP.sh
  38. libexec/snpeff/nextProt_filter.pl
  39. libexec/snpeff/ped2vcf.py
  40. libexec/snpeff/plot.pl
  41. libexec/snpeff/plotHistogram.pl
  42. libexec/snpeff/plotLabel.pl
  43. libexec/snpeff/plotMA.pl
  44. libexec/snpeff/plotQQ.pl
  45. libexec/snpeff/plotQQsubsample.pl
  46. libexec/snpeff/plotSmoothScatter.pl
  47. libexec/snpeff/plotXY.pl
  48. libexec/snpeff/queue.pl
  49. libexec/snpeff/sam2fastq.pl
  50. libexec/snpeff/sample.pl
  51. libexec/snpeff/snpEff
  52. libexec/snpeff/snpEff.bak
  53. libexec/snpeff/snpEff.orig
  54. libexec/snpeff/snpSift
  55. libexec/snpeff/snpSift.orig
  56. libexec/snpeff/snpSift_filter_sample_to_number.pl
  57. libexec/snpeff/sortLine.py
  58. libexec/snpeff/splitChr.pl
  59. libexec/snpeff/statsNum.pl
  60. libexec/snpeff/swapCols.pl
  61. libexec/snpeff/transpose.pl
  62. libexec/snpeff/txt2fa.pl
  63. libexec/snpeff/txt2vcf.py
  64. libexec/snpeff/uniqCount.pl
  65. libexec/snpeff/uniqCut.pl
  66. libexec/snpeff/vcfAnnFirst.py
  67. libexec/snpeff/vcfBareBones.pl
  68. libexec/snpeff/vcfEffHighest.ORI.py
  69. libexec/snpeff/vcfEffOnePerLine.pl
  70. libexec/snpeff/vcfFilterSamples.pl
  71. libexec/snpeff/vcfInfoOnePerLine.pl
  72. libexec/snpeff/vcfOnlyAlts.pl
  73. libexec/snpeff/vcfReduceGenotypes.pl
  74. libexec/snpeff/vcfRefCorrect.py
  75. libexec/snpeff/wigSplit.pl
  76. share/java/classes/snpeff/SnpSift.jar
  77. share/java/classes/snpeff/snpEff.config
  78. share/java/classes/snpeff/snpEff.jar
  79. @owner
  80. @group
  81. @mode
Collapse this list.
Dependency lines:
  • snpeff>0:biology/snpeff
To install the port: cd /usr/ports/biology/snpeff/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/snpeff
  • pkg install snpeff
PKGNAME: snpeff
Flavors: there is no flavor information for this port.
distinfo:
Packages (timestamps in pop-ups are UTC):
snpeff
ABIlatestquarterly
FreeBSD:11:aarch64--
FreeBSD:11:amd645.05.0
FreeBSD:11:armv6--
FreeBSD:11:i3865.05.0
FreeBSD:11:mips--
FreeBSD:11:mips64--
FreeBSD:12:aarch64-5.0
FreeBSD:12:amd645.05.0
FreeBSD:12:armv6--
FreeBSD:12:armv7--
FreeBSD:12:i3865.05.0
FreeBSD:12:mips--
FreeBSD:12:mips64--
FreeBSD:12:powerpc64--
FreeBSD:13:aarch64-5.0
FreeBSD:13:amd645.05.0
FreeBSD:13:armv6--
FreeBSD:13:armv7--
FreeBSD:13:i3865.05.0
FreeBSD:13:mips--
FreeBSD:13:mips64--
FreeBSD:13:powerpc64-5.0
FreeBSD:14:aarch645.0-
FreeBSD:14:amd645.0-
FreeBSD:14:armv6--
FreeBSD:14:armv7--
FreeBSD:14:i3865.0-
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. bash : shells/bash
  2. java : java/openjdk12
  3. python3.8 : lang/python38
This port is required by:
for Run
  1. biology/biostar-tools

Configuration Options:
Options name:

USES:

FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (1 items)
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  1. https://snpeff.blob.core.windows.net/versions/
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Number of commits found: 2

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
19 Apr 2021 16:41:58
 files touched by this commit commit hash:3bc87a0f1a1b36d958c9478a0d2feaeebf283dbe  5.0
jwb search for other commits by this committer
biology/snpeff: Improvements to Makefile and patches

Reported by:    Omp
18 Apr 2021 18:46:29
 files touched by this commit commit hash:5164d38ee538f6791a25b81f28a27126b90444f7  5.0
jwb search for other commits by this committer
biology/snpeff: Genetic variant annotation and effect prediction toolbox

Genetic variant annotation and functional effect prediction toolbox. It
annotates and predicts the effects of genetic variants on genes and proteins
(such as amino acid changes).

Number of commits found: 2