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Port details
seqan-apps Official Bioinformatic applications based on the SeqAn library
2.2.0_8 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
Maintainer: h2+fbsdports@fsfe.org search for ports maintained by this maintainer
Port Added: 10 May 2016 00:52:12
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 : PortsMon
    Pseudo-pkg-plist information, but much better, from make generate-plist
    Expand this list (165 items)
  1. /usr/local/share/licenses/seqan-apps-2.2.0_8/catalog.mk
  2. /usr/local/share/licenses/seqan-apps-2.2.0_8/LICENSE
  3. /usr/local/share/licenses/seqan-apps-2.2.0_8/BSD3CLAUSE
  4. /usr/local/share/licenses/seqan-apps-2.2.0_8/LGPL3
  5. /usr/local/share/licenses/seqan-apps-2.2.0_8/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. share/doc/alf/LICENSE
  57. share/doc/alf/README
  58. share/doc/alf/example/small.fasta
  59. share/doc/bs_tools/LICENSE
  60. share/doc/bs_tools/README
  61. share/doc/dfi/LICENSE
  62. share/doc/dfi/README
  63. share/doc/dfi/example/fasta1.fa
  64. share/doc/dfi/example/fasta2.fa
  65. share/doc/fiona/LICENSE
  66. share/doc/fiona/README
  67. share/doc/fiona/example/reads.fa
  68. share/doc/fx_tools/LICENSE
  69. share/doc/fx_tools/README
  70. share/doc/gustaf/LICENSE
  71. share/doc/gustaf/README
  72. share/doc/gustaf/example/adeno.fa
  73. share/doc/gustaf/example/adeno_modified.fa
  74. share/doc/gustaf/example/adeno_modified_reads.fa
  75. share/doc/gustaf/example/stellar.gff
  76. share/doc/insegt/LICENSE
  77. share/doc/insegt/README
  78. share/doc/insegt/example/annoOutput.gff
  79. share/doc/insegt/example/annotations.gff
  80. share/doc/insegt/example/readOutput.gff
  81. share/doc/insegt/example/tupleOutput.gff
  82. share/doc/mason2/LICENSE
  83. share/doc/mason2/README
  84. share/doc/mason2/README.mason_frag_sequencing
  85. share/doc/mason2/README.mason_genome
  86. share/doc/mason2/README.mason_materializer
  87. share/doc/mason2/README.mason_methylation
  88. share/doc/mason2/README.mason_simulator
  89. share/doc/mason2/README.mason_splicing
  90. share/doc/mason2/README.mason_variator
  91. share/doc/mason2/example/adeno_virus.fa
  92. share/doc/micro_razers/LICENSE
  93. share/doc/micro_razers/README
  94. share/doc/micro_razers/example/genome.fa
  95. share/doc/micro_razers/example/reads.fa
  96. share/doc/micro_razers/example/reads.fa.result
  97. share/doc/ngs_roi/LICENSE
  98. share/doc/ngs_roi/R/ngsroi_0.1.tar.gz
  99. share/doc/ngs_roi/R/ngsroi_0.1.zip
  100. share/doc/ngs_roi/README
  101. share/doc/ngs_roi/example/dmel.bed
  102. share/doc/ngs_roi/example/dmel.gtf
  103. share/doc/ngs_roi/example/example.bam
  104. share/doc/pair_align/LICENSE
  105. share/doc/pair_align/README
  106. share/doc/param_chooser/LICENSE
  107. share/doc/param_chooser/README
  108. share/doc/rabema/LICENSE
  109. share/doc/rabema/README
  110. share/doc/razers/LICENSE
  111. share/doc/razers/README
  112. share/doc/razers/example/genome.fa
  113. share/doc/razers/example/reads.fa
  114. share/doc/razers/example/reads2.fa
  115. share/doc/razers3/LICENSE
  116. share/doc/razers3/README
  117. share/doc/razers3/example/genome.fa
  118. share/doc/razers3/example/reads.fa
  119. share/doc/razers3/example/reads2.fa
  120. share/doc/rep_sep/LICENSE
  121. share/doc/rep_sep/README
  122. share/doc/sak/LICENSE
  123. share/doc/sak/README
  124. share/doc/sak/README.sak.txt
  125. share/doc/sak/man/sak.1
  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.

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

PKGNAME: seqan-apps

distinfo:

TIMESTAMP = 1473848209
SHA256 (seqan-seqan-seqan-v2.2.0_GH0.tar.gz) = 6add074932c2723ef1fb658c88f906bdd6ced1fc34cb16a7410251ffc4cb8cc8
SIZE (seqan-seqan-seqan-v2.2.0_GH0.tar.gz) = 110936119


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
  4. gcc6 : lang/gcc6
  5. as : devel/binutils
Runtime dependencies:
  1. gcc6 : lang/gcc6
There are no ports dependent upon this port

Configuration Options
     No options to configure

USES:
cmake:outsource

Master Sites:
  1. https://codeload.github.com/seqan/seqan/tar.gz/seqan-v2.2.0?dummy=/

Number of commits found: 15

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
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: 15

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