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Port details on branch 2022Q3
seqan-apps Official bioinformatic applications based on the SeqAn library
2.4.0_11 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 2.4.0_11Version 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: 2023-08-06 21:53:04
Commit Hash: 6d55871
License: BSD3CLAUSE LGPL3 GPLv3
WWW:
https://www.seqan.de/
Description:
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.
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb

Manual pages:
FreshPorts has no man page information for this port.
pkg-plist: as obtained via: make generate-plist
Expand this list (168 items)
Collapse this list.
  1. /usr/local/share/licenses/seqan-apps-2.4.0_11/catalog.mk
  2. /usr/local/share/licenses/seqan-apps-2.4.0_11/LICENSE
  3. /usr/local/share/licenses/seqan-apps-2.4.0_11/BSD3CLAUSE
  4. /usr/local/share/licenses/seqan-apps-2.4.0_11/LGPL3
  5. /usr/local/share/licenses/seqan-apps-2.4.0_11/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/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. @owner
  167. @group
  168. @mode
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, run one of these commands:
  • pkg install biology/seqan-apps
  • pkg install seqan-apps
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: seqan-apps
Flavors: 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
Packages (timestamps in pop-ups are UTC):
seqan-apps
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest2.4.0_112.4.0_11-2.4.0_112.4.0_11-2.4.0_9-
FreeBSD:13:quarterly2.4.0_112.4.0_11-2.4.0_112.4.0_112.4.0_112.4.0_112.4.0_11
FreeBSD:14:latest2.4.0_112.4.0_11-2.4.0_112.4.0_112.4.0_11-2.4.0_11
FreeBSD:14:quarterly2.4.0_112.4.0_11-2.4.0_112.4.0_112.4.0_112.4.0_112.4.0_11
FreeBSD:15:latest2.4.0_112.4.0_11n/a2.4.0_11n/a2.4.0_112.4.0_112.4.0_11
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. boost-libs>0 : devel/boost-libs
  2. cmake : devel/cmake-core
  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_11: ====> 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
Options name:
biology_seqan-apps
USES:
cmake compiler:c++14-lang
FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (1 items)
Collapse this list.
  1. https://codeload.github.com/seqan/seqan/tar.gz/seqan-v2.4.0?dummy=/
Collapse this list.

There are no commits on branch 2022Q3 for this port
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