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Port details
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 Version 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: 2022-12-19 18:50:00
Commit Hash: c583575
Also Listed In: java python
License: MIT
Description:
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb - no subversion history 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:

Packages (timestamps in pop-ups are UTC):
snpeff
ABIlatestquarterly
FreeBSD:11:aarch64pkg-falloutpkg-fallout
FreeBSD:11:amd645.05.0
FreeBSD:11:armv6pkg-falloutpkg-fallout
FreeBSD:11:i3865.05.0
FreeBSD:11:mipspkg-falloutpkg-fallout
FreeBSD:11:mips64pkg-falloutpkg-fallout
FreeBSD:12:aarch64pkg-falloutpkg-fallout
FreeBSD:12:amd645.15.1
FreeBSD:12:armv6pkg-falloutpkg-fallout
FreeBSD:12:armv7pkg-falloutpkg-fallout
FreeBSD:12:i3865.15.1
FreeBSD:12:mipspkg-falloutpkg-fallout
FreeBSD:12:mips64pkg-falloutpkg-fallout
FreeBSD:12:powerpc64pkg-falloutpkg-fallout
FreeBSD:13:aarch64pkg-falloutpkg-fallout
FreeBSD:13:amd645.15.1
FreeBSD:13:armv6pkg-falloutpkg-fallout
FreeBSD:13:armv7pkg-falloutpkg-fallout
FreeBSD:13:i3865.15.1
FreeBSD:13:mipspkg-falloutpkg-fallout
FreeBSD:13:mips64pkg-falloutpkg-fallout
FreeBSD:13:powerpc64pkg-fallout5.1
FreeBSD:13:riscv64pkg-falloutpkg-fallout
FreeBSD:14:aarch64pkg-falloutpkg-fallout
FreeBSD:14:amd645.1pkg-fallout
FreeBSD:14:armv6pkg-falloutpkg-fallout
FreeBSD:14:armv7pkg-falloutpkg-fallout
FreeBSD:14:i3865.1pkg-fallout
FreeBSD:14:mipspkg-falloutpkg-fallout
FreeBSD:14:mips64pkg-falloutpkg-fallout
FreeBSD:14:powerpc645.1pkg-fallout
FreeBSD:14:riscv64pkg-falloutpkg-fallout
 
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build 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:
Options name:
USES:
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.

Number of commits found: 6

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
5.1
19 Dec 2022 18:50:00
commit hash:c5835753ea70c074f8796aa1df459838ef61c6f7commit hash:c5835753ea70c074f8796aa1df459838ef61c6f7commit hash:c5835753ea70c074f8796aa1df459838ef61c6f7commit hash:c5835753ea70c074f8796aa1df459838ef61c6f7 files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/snpeff: Update to 5.1

Unbreak fetch, which depends on an unversioned distfile
Requested version tags upstream and looking at other build options
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)
5.0
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)
5.0
24 May 2022 20:09:35
commit hash:c7d1c247d8ea8f87edd6a5012702a3cd10d99d49commit hash:c7d1c247d8ea8f87edd6a5012702a3cd10d99d49commit hash:c7d1c247d8ea8f87edd6a5012702a3cd10d99d49commit hash:c7d1c247d8ea8f87edd6a5012702a3cd10d99d49 files touched by this commit
Rene Ladan (rene) search for other commits by this committer
cleanup: remove expired versions of OpenJDK (12 through 16)

Adjust ports depending on expired versions of OpenJDK:
- biology/snpeff: 12+ -> 17+
- devel/RStudio: 12 -> 11
- www/closure-compiler: 13 -> 11+

Allow java/openjdk17 to use java/openjdk17-bootstrap on i386
too, this builds just fine on 13.1-i386

Remove jdk12-doc as it is no longer relevant.

Clean up Java version calculations in bsd.java.mk

Reviewed by: jwb, java (glewis)

Differential Revision: https://reviews.freebsd.org/D35280
5.0
19 Apr 2021 16:41:58
commit hash:3bc87a0f1a1b36d958c9478a0d2feaeebf283dbecommit hash:3bc87a0f1a1b36d958c9478a0d2feaeebf283dbecommit hash:3bc87a0f1a1b36d958c9478a0d2feaeebf283dbecommit hash:3bc87a0f1a1b36d958c9478a0d2feaeebf283dbe files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/snpeff: Improvements to Makefile and patches

Reported by:    Omp
5.0
18 Apr 2021 18:46:29
commit hash:5164d38ee538f6791a25b81f28a27126b90444f7commit hash:5164d38ee538f6791a25b81f28a27126b90444f7commit hash:5164d38ee538f6791a25b81f28a27126b90444f7commit hash:5164d38ee538f6791a25b81f28a27126b90444f7 files touched by this commit
Jason W. Bacon (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: 6