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Port details
seqan-apps Official bioinformatic applications based on the SeqAn library
2.4.0_6 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
2.4.0Version of this port present on the latest quarterly branch.
Maintainer: h2+fbsdports@fsfe.org search for ports maintained by this maintainer
Port Added: 2016-05-10 00:52:12
Last Update: 2019-04-12 07:36:31
SVN Revision: 498698
License: BSD3CLAUSE LGPL3 GPLv3
SeqAn is an open source C++ library of efficient algorithms
and data structures for the analysis of sequences with the
focus on biological data.

This port contains applications built on SeqAn and developed
within the SeqAn project. Among them are famous read mappers
like RazerS and Yara, as well as many other tools. Some
applications are packaged separately and the library
can be found at biology/seqan.

WWW: http://www.seqan.de/
SVNWeb : Homepage
    Pseudo-pkg-plist information, but much better, from make generate-plist
    Expand this list (165 items)
  1. /usr/local/share/licenses/seqan-apps-2.4.0_6/catalog.mk
  2. /usr/local/share/licenses/seqan-apps-2.4.0_6/LICENSE
  3. /usr/local/share/licenses/seqan-apps-2.4.0_6/BSD3CLAUSE
  4. /usr/local/share/licenses/seqan-apps-2.4.0_6/LGPL3
  5. /usr/local/share/licenses/seqan-apps-2.4.0_6/GPLv3
  6. bin/alf
  7. bin/bam2roi
  8. bin/bed_sort.sh
  9. bin/bisar
  10. bin/casbar
  11. bin/compute_gain
  12. bin/dfi
  13. bin/fiona
  14. bin/four2three
  15. bin/fx_bam_coverage
  16. bin/gff_sort.sh
  17. bin/gustaf
  18. bin/gustaf_mate_joining
  19. bin/insegt
  20. bin/mason_frag_sequencing
  21. bin/mason_genome
  22. bin/mason_materializer
  23. bin/mason_methylation
  24. bin/mason_simulator
  25. bin/mason_splicing
  26. bin/mason_variator
  27. bin/micro_razers
  28. bin/pair_align
  29. bin/param_chooser
  30. bin/plot.awk
  31. bin/ps2pswLinks.gawk
  32. bin/rabema_build_gold_standard
  33. bin/rabema_evaluate
  34. bin/rabema_prepare_sam
  35. bin/razers
  36. bin/razers3
  37. bin/rep_sep
  38. bin/roi_feature_projection
  39. bin/roi_plot_9.sh
  40. bin/roi_plot_thumbnails
  41. bin/roi_sort.sh
  42. bin/s4_join
  43. bin/s4_search
  44. bin/sak
  45. bin/sam2matrix
  46. bin/samcat
  47. bin/seqan_tcoffee
  48. bin/seqcons2
  49. bin/sgip
  50. bin/snp_store
  51. bin/splazers
  52. bin/stellar
  53. bin/tree_recon
  54. bin/yara_indexer
  55. bin/yara_mapper
  56. man/man1/sak.1.gz
  57. share/doc/alf/LICENSE
  58. share/doc/alf/README
  59. share/doc/alf/example/small.fasta
  60. share/doc/bs_tools/LICENSE
  61. share/doc/bs_tools/README
  62. share/doc/dfi/LICENSE
  63. share/doc/dfi/README
  64. share/doc/dfi/example/fasta1.fa
  65. share/doc/dfi/example/fasta2.fa
  66. share/doc/fiona/LICENSE
  67. share/doc/fiona/README
  68. share/doc/fiona/example/reads.fa
  69. share/doc/fx_tools/LICENSE
  70. share/doc/fx_tools/README
  71. share/doc/gustaf/LICENSE
  72. share/doc/gustaf/README
  73. share/doc/gustaf/example/adeno.fa
  74. share/doc/gustaf/example/adeno_modified.fa
  75. share/doc/gustaf/example/adeno_modified_reads.fa
  76. share/doc/gustaf/example/stellar.gff
  77. share/doc/insegt/LICENSE
  78. share/doc/insegt/README
  79. share/doc/insegt/example/annoOutput.gff
  80. share/doc/insegt/example/annotations.gff
  81. share/doc/insegt/example/readOutput.gff
  82. share/doc/insegt/example/tupleOutput.gff
  83. share/doc/mason2/LICENSE
  84. share/doc/mason2/README
  85. share/doc/mason2/README.mason_frag_sequencing
  86. share/doc/mason2/README.mason_genome
  87. share/doc/mason2/README.mason_materializer
  88. share/doc/mason2/README.mason_methylation
  89. share/doc/mason2/README.mason_simulator
  90. share/doc/mason2/README.mason_splicing
  91. share/doc/mason2/README.mason_variator
  92. share/doc/mason2/example/adeno_virus.fa
  93. share/doc/micro_razers/LICENSE
  94. share/doc/micro_razers/README
  95. share/doc/micro_razers/example/genome.fa
  96. share/doc/micro_razers/example/reads.fa
  97. share/doc/micro_razers/example/reads.fa.result
  98. share/doc/ngs_roi/LICENSE
  99. share/doc/ngs_roi/R/ngsroi_0.1.tar.gz
  100. share/doc/ngs_roi/R/ngsroi_0.1.zip
  101. share/doc/ngs_roi/README
  102. share/doc/ngs_roi/example/dmel.bed
  103. share/doc/ngs_roi/example/dmel.gtf
  104. share/doc/ngs_roi/example/example.bam
  105. share/doc/pair_align/LICENSE
  106. share/doc/pair_align/README
  107. share/doc/param_chooser/LICENSE
  108. share/doc/param_chooser/README
  109. share/doc/rabema/LICENSE
  110. share/doc/rabema/README
  111. share/doc/razers/LICENSE
  112. share/doc/razers/README
  113. share/doc/razers/example/genome.fa
  114. share/doc/razers/example/reads.fa
  115. share/doc/razers/example/reads2.fa
  116. share/doc/razers3/LICENSE
  117. share/doc/razers3/README
  118. share/doc/razers3/example/genome.fa
  119. share/doc/razers3/example/reads.fa
  120. share/doc/razers3/example/reads2.fa
  121. share/doc/rep_sep/LICENSE
  122. share/doc/rep_sep/README
  123. share/doc/sak/LICENSE
  124. share/doc/sak/README
  125. share/doc/sak/README.sak.txt
  126. share/doc/sam2matrix/LICENSE
  127. share/doc/sam2matrix/README
  128. share/doc/samcat/LICENSE
  129. share/doc/samcat/README
  130. share/doc/searchjoin/LICENSE
  131. share/doc/searchjoin/README
  132. share/doc/seqan_tcoffee/LICENSE
  133. share/doc/seqan_tcoffee/README
  134. share/doc/seqan_tcoffee/example/seq.fa
  135. share/doc/seqcons2/LICENSE
  136. share/doc/seqcons2/README
  137. share/doc/sgip/LICENSE
  138. share/doc/sgip/README
  139. share/doc/sgip/example/iso_m2D_m196.A01
  140. share/doc/sgip/example/iso_r01_m200.A00
  141. share/doc/sgip/example/iso_r01_m200.A01
  142. share/doc/sgip/example/iso_r01_m200.B00
  143. share/doc/sgip/example/iso_r01_m200.B01
  144. share/doc/sgip/example/latin-4
  145. share/doc/sgip/example/lattice-4
  146. share/doc/sgip/example/sts-7
  147. share/doc/snp_store/LICENSE
  148. share/doc/snp_store/README
  149. share/doc/snp_store/example/exampleGenome.fa
  150. share/doc/snp_store/example/exampleReads.gff
  151. share/doc/splazers/LICENSE
  152. share/doc/splazers/README
  153. share/doc/splazers/example/genome.fa
  154. share/doc/splazers/example/reads.fa
  155. share/doc/splazers/example/reads.fa.result
  156. share/doc/stellar/LICENSE
  157. share/doc/stellar/README
  158. share/doc/stellar/example/NC_001474.fasta
  159. share/doc/stellar/example/NC_001477.fasta
  160. share/doc/stellar/example/reads.fasta
  161. share/doc/tree_recon/LICENSE
  162. share/doc/tree_recon/README
  163. share/doc/tree_recon/example/example.dist
  164. share/doc/yara/LICENSE
  165. share/doc/yara/README.rst
  166. Collapse this list.
Dependency lines:
  • seqan-apps>0:biology/seqan-apps

To install the port: cd /usr/ports/biology/seqan-apps/ && make install clean
To add the package: pkg install seqan-apps

PKGNAME: seqan-apps

There is no flavor information for this port.

distinfo:

TIMESTAMP = 1517833288
SHA256 (seqan-seqan-seqan-v2.4.0_GH0.tar.gz) = d7084d17729214003e84818e0280a16f223c8f1c6a30eeef040c27e0c0047bd7
SIZE (seqan-seqan-seqan-v2.4.0_GH0.tar.gz) = 109626901


NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.

Build dependencies:
  1. boost-libs>0 : devel/boost-libs
  2. cmake : devel/cmake
  3. ninja : devel/ninja
There are no ports dependent upon this port

Configuration Options
===> The following configuration options are available for seqan-apps-2.4.0_6:
====> Options available for the radio ARCH: you can only select none or one of them
     SSE4=off: Use SSE4 and POPCNT instructions
     AVX2=off: Use SSE4, AVX2 and POPCNT instructions
     NATIVE=off: Use all available instruction sets (-march=native)
===> Use 'make config' to modify these settings

USES:
cmake compiler:openmp

Master Sites:
  1. https://codeload.github.com/seqan/seqan/tar.gz/seqan-v2.4.0?dummy=/

Number of commits found: 27

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
12 Apr 2019 06:36:31
Original commit files touched by this commit  2.4.0_6
Revision:498698
jbeich search for other commits by this committer
devel/boost-*: update to 1.70.0

Changes:	http://www.boost.org/users/history/version_1_70_0.html
PR:		235956
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D19303
25 Dec 2018 20:25:40
Original commit files touched by this commit  2.4.0_5
Revision:488341
tcberner search for other commits by this committer
Change cmake default behaviour to outsource.

Ports that build out of source now simply can use "USES=cmake"
instead of "USES=cmake:outsource". Ports that fail to build
out of source now need to specify "USES=cmake:insource".

I tried to only set insource where explictely needed.

PR:		232038
Exp-run by:	antoine
12 Dec 2018 01:35:36
Original commit files touched by this commit  2.4.0_5
Revision:487272
gerald search for other commits by this committer
Bump PORTREVISION for ports depending on the canonical version of GCC
defined via Mk/bsd.default-versions.mk which has moved from GCC 7.4 t
GCC 8.2 under most circumstances.

This includes ports
 - with USE_GCC=yes or USE_GCC=any,
 - with USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and
 - with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang,
   c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, as a double check, everything INDEX-11 showed depending on lang/gcc7.

PR:		231590
12 Dec 2018 00:15:50
Original commit files touched by this commit  2.4.0_4
Revision:487266
jbeich search for other commits by this committer
devel/boost-*: update to 1.69.0

Changes:	http://www.boost.org/users/history/version_1_69_0.html
PR:		232525
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D17645
09 Nov 2018 21:37:01
Original commit files touched by this commit  2.4.0_3
Revision:484547
swills search for other commits by this committer
biology/seqan-apps: fix build with GCC-based architectures

PR:		232045
Submitted by:	Piotr Kubaj <pkubaj@anongoth.pl>
Approved by:	maintainer timeout (h2+fbsdports@fsfe.org >1 month)
09 Aug 2018 06:58:31
Original commit files touched by this commit  2.4.0_3
Revision:476723
jbeich search for other commits by this committer
devel/boost-*: update to 1.68.0

- Switch to C++14 for libboost_system to support C++14 consumers

Changes:	http://www.boost.org/users/history/version_1_68_0.html
PR:		229569
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D16165
29 Jul 2018 22:18:46
Original commit files touched by this commit  2.4.0_2
Revision:475857
gerald search for other commits by this committer
Bump PORTREVISION for ports depending on the canonical version of GCC
in the ports tree (via Mk/bsd.default-versions.mk and lang/gcc) which
has now moved from GCC 6 to GCC 7 by default.

This includes ports
 - featuring USE_GCC=yes or USE_GCC=any,
 - featuring USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and those
 - with USES=compiler specifying one of openmp, nestedfct, c11, c++0x,
   c++11-lib, c++11-lang, c++14-lang, c++17-lang, or gcc-c++11-lib.

PR:		222542
18 Jun 2018 19:14:48
Original commit files touched by this commit  2.4.0_1
Revision:472707
linimon search for other commits by this committer
Mark as broken on powerpc64 pending fix for PR 199603.

Approved by:	portmgr (tier-2 blanket)
18 Apr 2018 13:57:43
Original commit files touched by this commit  2.4.0_1
Revision:467711
jbeich search for other commits by this committer
devel/boost-*: update to 1.67.0

Changes:	http://www.boost.org/users/history/version_1_67_0.html
PR:		227427
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D15030
10 Mar 2018 06:21:37
Original commit files touched by this commit  2.4.0
Revision:464043
yuri search for other commits by this committer
biology/seqan-apps, biology/seqan: Update to 2.4.0

Port changes for biology/seqan-apps:
* Changed to DISTVERSION
* Updated COMMENT
* Added USES=compiler:openmp
* Removed BROKEN_xx (upstream now claims support for these architectures)
* Removed USE_GCC
* Added SSE4/AVX2/NATIVE SIMD options

Port changes for biology/seqan:
* Changed to DISTVERSION
* Added NO_ARCH
* Added PORTDOCS=*
* Updated do-install

PR:		225682
Submitted by:	Hannes Hauswedell <h2+fbsdports@fsfe.org> (maintainer)
Approved by:	tcberner (mentor, implicit)
18 Jan 2018 04:11:03
Original commit files touched by this commit  2.2.0_9
Revision:459315
jbeich search for other commits by this committer
devel/boost-*: update to 1.66.0

Changes:	http://www.boost.org/users/history/version_1_66_0.html
PR:		223922
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D13279
11 Dec 2017 07:18:48
Original commit files touched by this commit  2.2.0_8
Revision:455927
linimon search for other commits by this committer
Mark several ports newly broken on arm.

While here, pet portlint.

Approved by:	portmgr (tier-2 blanket)
25 Sep 2017 00:08:17
Original commit files touched by this commit  2.2.0_8
Revision:450560
jbeich search for other commits by this committer
devel/boost-*: update to 1.65.1

Changes:	http://www.boost.org/users/history/version_1_65_1.html
PR:		218835
Approved by:	maintainer timeout (1.65.1: 2 weeks; 1.65.0: 1 month)
Tested by:	jhibbits (on powerpc64, earlier version)
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D11582
25 Sep 2017 00:05:06
Original commit files touched by this commit  2.2.0_7
Revision:450557
jbeich search for other commits by this committer
devel/boost-*: enable C++11 features

PR:		218835
Obtained from:	https://github.com/DragonFlyBSD/DeltaPorts/pull/690
Approved by:	maintainer timeout (2 months)
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D11582
10 Sep 2017 20:55:39
Original commit files touched by this commit  2.2.0_6
Revision:449591
gerald search for other commits by this committer
Bump PORTREVISION for ports depending on the canonical version of GCC
(via Mk/bsd.default-versions.mk and lang/gcc) which has moved from
GCC 5.4 to GCC 6.4 under most circumstances.

This includes ports
 - with USE_GCC=yes or USE_GCC=any,
 - with USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and
 - with USES=compiler specifying openmp, nestedfct, c++11-lib, c++11-lang,
   c++14-lang, c++0x, c11, or gcc-c++11-lib.

PR:		219275
21 May 2017 23:37:34
Original commit files touched by this commit  2.2.0_4
Revision:441431
linimon search for other commits by this committer
It is possible that r441426 will fix the build problem on armv6.  Give
it a try.

Approved by:	portmgr (tier-2 blanket)
02 May 2017 06:48:11
Original commit files touched by this commit  2.2.0_4
Revision:439934
jbeich search for other commits by this committer
devel/boost-*: update to 1.64.0

Changes:	http://www.boost.org/users/history/version_1_64_0.html
PR:		218835
Approved by:	office (bapt)
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D10472
01 May 2017 19:24:01
Original commit files touched by this commit  2.2.0_3
Revision:439905
linimon search for other commits by this committer
Provide error messages for some ports failing on aarch64, and, in a
few cases, other tier-2 archs.

While here, pet portlint.

Approved by:	portmgr (tier-2 blanket)
01 Apr 2017 15:23:32
Original commit files touched by this commit  2.2.0_3
Revision:437439
gerald search for other commits by this committer
Bump PORTREVISIONs for ports depending on the canonical version of GCC and
lang/gcc which have moved from GCC 4.9.4 to GCC 5.4 (at least under some
circumstances such as versions of FreeBSD or platforms).

This includes ports
 - with USE_GCC=yes or USE_GCC=any,
 - with USES=fortran,
 - using using Mk/bsd.octave.mk which in turn has USES=fortran, and
 - with USES=compiler specifying openmp, nestedfct, c++11-lib, c++14-lang,
   c++11-lang, c++0x, c11, or gcc-c++11-lib.

PR:		216707
26 Feb 2017 15:38:10
Original commit files touched by this commit  2.2.0_2
Revision:434890
linimon search for other commits by this committer
Mark a few more ports that create large logfiles broken on armv6.

Approved by:	portmgr (tier-2 blanket)
09 Jan 2017 13:16:50
Original commit files touched by this commit  2.2.0_2
Revision:430947
amdmi3 search for other commits by this committer
- Remove always-true/false conditions after FreeBSD 9, 10.1, 10.2 EOL

Approved by:	portmgr blanket
06 Jan 2017 08:45:04
Original commit files touched by this commit  2.2.0_2
Revision:430692
jbeich search for other commits by this committer
devel/boost-*: update to 1.63.0

Changes:	http://www.boost.org/users/history/version_1_63_0.html
PR:		215598
Exp-run by:	antoine
Approved by:	office (bapt)
MFH:		2017Q1
25 Nov 2016 21:27:37
Original commit files touched by this commit  2.2.0_1
Revision:427129
gerald search for other commits by this committer
Replace USE_GCC=4.9+ by USE_GCC=yes, now that lang/gcc and the default
version for GCC in the Ports Collection have moved to GCC 4.9.
23 Nov 2016 12:45:47
Original commit files touched by this commit  2.2.0_1
Revision:426908
jbeich search for other commits by this committer
devel/boost-*: update to 1.62.0

- Enable `long double` C99 math usage
- Switch 9.x back to building with GCC

Changes:	http://www.boost.org/users/history/
PR:		199601
Submitted by:	Chen Xu, bapt, amdmi3, truckman (based on)
Reviewed by:	rakuco (kde) (earlier version)
Exp-run by:	antoine (3 tries), truckman (consumers only, earlier versions)
Approved by:	bapt (office)
14 Sep 2016 19:38:58
Original commit files touched by this commit  2.2.0
Revision:422156
pawel search for other commits by this committer
- Update biology/seqan and bilogy/seqan-apps to version 2.2.0 [1]
- Fix spelling in pkg-descr

PR:		212682 [1]
Submitted by:	Hannes Hauswedell (maintainer) [1]
19 May 2016 10:21:25
Original commit files touched by this commit  2.1.1
Revision:415498
amdmi3 search for other commits by this committer
- Fix trailing whitespace in pkg-descrs, categories [a-f]*

Approved by:	portmgr blanket
10 May 2016 00:52:04
Original commit files touched by this commit  2.1.1
Revision:414897
junovitch search for other commits by this committer
New port: biology/seqan-apps

SeqAn is an open source C++ library of efficient algorithms
and data structures for the analysis of sequences with the
focus on biological data.

This port contains applications built on SeqAn and developed
within the SeqAn project. Among them are famous read mappers
like RazerS and Yara, as well as many other tools. Some
applications are packaged seperately and the library
can be found at biology/seqan.

WWW: http://www.seqan.de/

PR:		204127
Submitted by:	Hannes Hauswedell <h2+fbsdports@fsfe.org>

Number of commits found: 27

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