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Port details on branch 2022Q3
snpeff Genetic variant annotation and effect prediction toolbox
5.1 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 5.1Version 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: 2023-11-06 10:03:47
Commit Hash: 06df180
Also Listed In: java python
License: MIT
WWW:
https://snpeff.sourceforge.net/
Description:
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). Features: Supports over 38,000 genomes Standard ANN annotation format Cancer variants analysis GATK compatible (-o gatk) HGVS notation Sequence Ontology standardized terms
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 (81 items)
Collapse this list.
  1. /usr/local/share/licenses/snpeff-5.1/catalog.mk
  2. /usr/local/share/licenses/snpeff-5.1/LICENSE
  3. /usr/local/share/licenses/snpeff-5.1/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
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: snpeff
Flavors: there is no flavor information for this port.
distinfo:
TIMESTAMP = 1671473460 SHA256 (snpeff-5.1/snpEff_latest_core.zip) = 919e0595c08e86d1dd82279723c83cb872070244ee4ce0cb3167bde2b272893b SIZE (snpeff-5.1/snpEff_latest_core.zip) = 67191760
Packages (timestamps in pop-ups are UTC):
snpeff
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest5.15.1--5.1---
FreeBSD:13:quarterly5.15.1--5.1-5.15.1
FreeBSD:14:latest5.15.1--5.1--5.1
FreeBSD:14:quarterly5.15.1--5.1-5.15.1
FreeBSD:15:latest5.15.1n/a-n/a-5.1-
FreeBSD:15:quarterly--n/a-n/a---
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. python3.9 : lang/python39
Test dependencies:
  1. python3.9 : lang/python39
Runtime dependencies:
  1. bash : shells/bash
  2. java : java/openjdk17
  3. python3.9 : lang/python39
This port is required by:
for Run
  1. biology/biostar-tools
Configuration Options:
No options to configure
Options name:
biology_snpeff
USES:
python shebangfix zip
FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (1 items)
Collapse this list.
  1. https://snpeff.blob.core.windows.net/versions/
Collapse this list.

There are no commits on branch 2022Q3 for this port
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