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Port details
fastq-trim Lightening fast sequence read trimmer
0.1.1.4 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: 2022-03-19 12:27:08
Last Update: 2022-09-07 21:58:51
Commit Hash: fb16dfe
License: BSD2CLAUSE
Description:
HomepagecgitgithubgitlabSVNWeb
pkg-plist: as obtained via: make generate-plist
Expand this list (81 items)
Collapse this list.
  1. /usr/local/share/licenses/fastq-trim-0.1.1.4/catalog.mk
  2. /usr/local/share/licenses/fastq-trim-0.1.1.4/LICENSE
  3. /usr/local/share/licenses/fastq-trim-0.1.1.4/BSD2CLAUSE
  4. bin/fastq-scum
  5. bin/fastq-trim
  6. include/fastq-trim-accessors.h
  7. include/fastq-trim-mutators.h
  8. include/fastq-trim-rvs.h
  9. include/fastq-trim.h
  10. lib/libfastq-trim.a
  11. man/man1/fastq-scum.1.gz
  12. man/man1/fastq-trim.1.gz
  13. man/man3/FASTQ_TRIM_ADAPTER1.3.gz
  14. man/man3/FASTQ_TRIM_ADAPTER1_AE.3.gz
  15. man/man3/FASTQ_TRIM_ADAPTER2.3.gz
  16. man/man3/FASTQ_TRIM_ADAPTER2_AE.3.gz
  17. man/man3/FASTQ_TRIM_ADAPTER_MATCH_FUNCTION.3.gz
  18. man/man3/FASTQ_TRIM_INFILE1.3.gz
  19. man/man3/FASTQ_TRIM_INFILE1_AE.3.gz
  20. man/man3/FASTQ_TRIM_INFILE2.3.gz
  21. man/man3/FASTQ_TRIM_INFILE2_AE.3.gz
  22. man/man3/FASTQ_TRIM_INSTREAM1.3.gz
  23. man/man3/FASTQ_TRIM_INSTREAM1_AE.3.gz
  24. man/man3/FASTQ_TRIM_INSTREAM2.3.gz
  25. man/man3/FASTQ_TRIM_INSTREAM2_AE.3.gz
  26. man/man3/FASTQ_TRIM_MAX_MISMATCH_PERCENT.3.gz
  27. man/man3/FASTQ_TRIM_MIN_LENGTH.3.gz
  28. man/man3/FASTQ_TRIM_MIN_MATCH.3.gz
  29. man/man3/FASTQ_TRIM_MIN_QUAL.3.gz
  30. man/man3/FASTQ_TRIM_OUTFILE1.3.gz
  31. man/man3/FASTQ_TRIM_OUTFILE1_AE.3.gz
  32. man/man3/FASTQ_TRIM_OUTFILE2.3.gz
  33. man/man3/FASTQ_TRIM_OUTFILE2_AE.3.gz
  34. man/man3/FASTQ_TRIM_OUTSTREAM1.3.gz
  35. man/man3/FASTQ_TRIM_OUTSTREAM1_AE.3.gz
  36. man/man3/FASTQ_TRIM_OUTSTREAM2.3.gz
  37. man/man3/FASTQ_TRIM_OUTSTREAM2_AE.3.gz
  38. man/man3/FASTQ_TRIM_PHRED_BASE.3.gz
  39. man/man3/FASTQ_TRIM_POLYA_MIN_LEN.3.gz
  40. man/man3/FASTQ_TRIM_VERBOSE.3.gz
  41. man/man3/fastq_trim_set_adapter1.3.gz
  42. man/man3/fastq_trim_set_adapter1_ae.3.gz
  43. man/man3/fastq_trim_set_adapter1_cpy.3.gz
  44. man/man3/fastq_trim_set_adapter2.3.gz
  45. man/man3/fastq_trim_set_adapter2_ae.3.gz
  46. man/man3/fastq_trim_set_adapter2_cpy.3.gz
  47. man/man3/fastq_trim_set_adapter_match_function.3.gz
  48. man/man3/fastq_trim_set_infile1.3.gz
  49. man/man3/fastq_trim_set_infile1_ae.3.gz
  50. man/man3/fastq_trim_set_infile1_cpy.3.gz
  51. man/man3/fastq_trim_set_infile2.3.gz
  52. man/man3/fastq_trim_set_infile2_ae.3.gz
  53. man/man3/fastq_trim_set_infile2_cpy.3.gz
  54. man/man3/fastq_trim_set_instream1.3.gz
  55. man/man3/fastq_trim_set_instream1_ae.3.gz
  56. man/man3/fastq_trim_set_instream1_cpy.3.gz
  57. man/man3/fastq_trim_set_instream2.3.gz
  58. man/man3/fastq_trim_set_instream2_ae.3.gz
  59. man/man3/fastq_trim_set_instream2_cpy.3.gz
  60. man/man3/fastq_trim_set_max_mismatch_percent.3.gz
  61. man/man3/fastq_trim_set_min_length.3.gz
  62. man/man3/fastq_trim_set_min_match.3.gz
  63. man/man3/fastq_trim_set_min_qual.3.gz
  64. man/man3/fastq_trim_set_outfile1.3.gz
  65. man/man3/fastq_trim_set_outfile1_ae.3.gz
  66. man/man3/fastq_trim_set_outfile1_cpy.3.gz
  67. man/man3/fastq_trim_set_outfile2.3.gz
  68. man/man3/fastq_trim_set_outfile2_ae.3.gz
  69. man/man3/fastq_trim_set_outfile2_cpy.3.gz
  70. man/man3/fastq_trim_set_outstream1.3.gz
  71. man/man3/fastq_trim_set_outstream1_ae.3.gz
  72. man/man3/fastq_trim_set_outstream1_cpy.3.gz
  73. man/man3/fastq_trim_set_outstream2.3.gz
  74. man/man3/fastq_trim_set_outstream2_ae.3.gz
  75. man/man3/fastq_trim_set_outstream2_cpy.3.gz
  76. man/man3/fastq_trim_set_phred_base.3.gz
  77. man/man3/fastq_trim_set_polya_min_len.3.gz
  78. man/man3/fastq_trim_set_verbose.3.gz
  79. @owner
  80. @group
  81. @mode
Collapse this list.
Dependency lines:
  • fastq-trim>0:biology/fastq-trim
To install the port:
cd /usr/ports/biology/fastq-trim/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/fastq-trim
  • pkg install fastq-trim
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: fastq-trim
Flavors: there is no flavor information for this port.
distinfo:
Packages (timestamps in pop-ups are UTC):
fastq-trim
ABIlatestquarterly
FreeBSD:11:aarch64--
FreeBSD:11:amd64--
FreeBSD:11:armv6--
FreeBSD:11:i386--
FreeBSD:11:mips--
FreeBSD:11:mips64--
FreeBSD:12:aarch64-0.1.1.4
FreeBSD:12:amd640.1.1.40.1.1.4
FreeBSD:12:armv6--
FreeBSD:12:armv7--
FreeBSD:12:i3860.1.1.40.1.1.4
FreeBSD:12:mips--
FreeBSD:12:mips64--
FreeBSD:12:powerpc64--
FreeBSD:13:aarch640.1.1.40.1.1.4
FreeBSD:13:amd640.1.1.40.1.1.4
FreeBSD:13:armv6-0.1.1.4
FreeBSD:13:armv70.1.1.40.1.1.4
FreeBSD:13:i3860.1.1.40.1.1.4
FreeBSD:13:mips--
FreeBSD:13:mips64--
FreeBSD:13:powerpc64--
FreeBSD:13:riscv64-0.1.1.4
FreeBSD:14:aarch640.1.1.4-
FreeBSD:14:amd640.1.1.4-
FreeBSD:14:armv60.1.1.4-
FreeBSD:14:armv70.1.1.4-
FreeBSD:14:i3860.1.1.4-
FreeBSD:14:mips--
FreeBSD:14:mips64--
FreeBSD:14:powerpc64--
FreeBSD:14:riscv64--
 

Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Library dependencies:
  1. libbiolibc.so : biology/biolibc
  2. libxtend.so : devel/libxtend
There are no ports dependent upon this port

Configuration Options:
Options name:
FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (1 items)
Collapse this list.
  1. https://codeload.github.com/outpaddling/fastq-trim/tar.gz/0.1.1-4-g7e3c5ff?dummy=/
Collapse this list.

Number of commits found: 5

Commit History - (may be incomplete: see SVNWeb link above for full details)
CommitCreditsLog message
07 Sep 2022 21:58:51
commit 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)
0.1.1.4
07 Sep 2022 21:10:59
commit 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)
0.1.1.4
21 Mar 2022 21:19:36
commit hash:19264c9fb1461087c44c483ff401f85d515da0c3commit hash:19264c9fb1461087c44c483ff401f85d515da0c3commit hash:19264c9fb1461087c44c483ff401f85d515da0c3 files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/fastq-trim: Update to 0.1.1.4

Forgot to update fastq-vis -> fastq-scum in docs in previous update
0.1.1.2
21 Mar 2022 20:37:43
commit hash:950fb7be37a071f39e7ddad1dd4e10669635abb9commit hash:950fb7be37a071f39e7ddad1dd4e10669635abb9commit hash:950fb7be37a071f39e7ddad1dd4e10669635abb9 files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/fastq-trim: Update to 0.1.1.2

Replace crash with run with no arguments with help msg
fastq-vis -> fastq-scum (better name for contamination viewer)
0.1.1
19 Mar 2022 12:25:58
commit hash:a47115b9cad4784d5923f6a6e3d0fbef28623e8fcommit hash:a47115b9cad4784d5923f6a6e3d0fbef28623e8fcommit hash:a47115b9cad4784d5923f6a6e3d0fbef28623e8f files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/fastq-trim: Lightening fast sequence read trimmer

Fastq-trim is a lightening fast read trimming tool for QA of
DNA and RNA reads prior to analyses such as RNA-Seq.

Number of commits found: 5