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Port details on branch 2022Q3
sra-tools NCBI's toolkit for handling data in INSDC Sequence Read Archives
3.0.6 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 View this port on Repology. pkg-fallout 3.0.6Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2021-06-22 18:00:14
Last Update: 2023-08-10 17:17:24
Commit Hash: 0f2f80c
Also Listed In: java
License: PD LGPL21+
WWW:
https://github.com/ncbi/sra-tools
Description:
SRA tools is a toolkit for using data in the INSDC Sequence Read Archives. SRAs operated by International Nucleotide Sequence Database Collaboration houses sequence reads and alignments generated by "next-gen" sequencers. SRA tools allows conversion of .sra files, which INSDC SRAs maintain, from/to other formats that the 'next-gen' sequenecers generate including: * csfasta/csqual (ABI SOLiD) * fastq (and fasta for writing) * hdf5 (PacBio, reading only) * qseq (older Illumina) * sam (writing only) / bam (reading only) * sff The toolkit uses NCBI-VDB back-end enabling seamless access to remote SRA data and local SRA files.
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb - no subversion history for this port

Manual pages:
FreshPorts has no man page information for this port.
pkg-plist: as obtained via: make generate-plist
Expand this list (290 items)
Collapse this list.
  1. @ldconfig
  2. /usr/local/share/licenses/sra-tools-3.0.6/catalog.mk
  3. /usr/local/share/licenses/sra-tools-3.0.6/LICENSE
  4. /usr/local/share/licenses/sra-tools-3.0.6/PD
  5. /usr/local/share/licenses/sra-tools-3.0.6/LGPL21+
  6. bin/abi-dump
  7. bin/abi-dump.3
  8. bin/abi-dump.3.0.6
  9. bin/align-info
  10. bin/align-info.3
  11. bin/align-info.3.0.6
  12. bin/cache-mgr
  13. bin/cache-mgr.3
  14. bin/cache-mgr.3.0.6
  15. bin/check-corrupt
  16. bin/check-corrupt.3
  17. bin/check-corrupt.3.0.6
  18. bin/fasterq-dump
  19. bin/fasterq-dump-orig.3.0.6
  20. bin/fasterq-dump.3
  21. bin/fasterq-dump.3.0.6
  22. bin/fastq-dump
  23. bin/fastq-dump-orig.3.0.6
  24. bin/fastq-dump.3
  25. bin/fastq-dump.3.0.6
  26. bin/illumina-dump
  27. bin/illumina-dump.3
  28. bin/illumina-dump.3.0.6
  29. bin/kdbmeta
  30. bin/kdbmeta.3
  31. bin/kdbmeta.3.0.6
  32. bin/ngs-pileup
  33. bin/ngs-pileup.3
  34. bin/ngs-pileup.3.0.6
  35. bin/prefetch
  36. bin/prefetch-orig.3.0.6
  37. bin/prefetch.3
  38. bin/prefetch.3.0.6
  39. bin/rcexplain
  40. bin/rcexplain.3
  41. bin/rcexplain.3.0.6
  42. bin/ref-variation
  43. bin/ref-variation.3
  44. bin/ref-variation.3.0.6
  45. bin/sam-dump
  46. bin/sam-dump-orig.3.0.6
  47. bin/sam-dump.3
  48. bin/sam-dump.3.0.6
  49. bin/sff-dump
  50. bin/sff-dump.3
  51. bin/sff-dump.3.0.6
  52. bin/sra-info
  53. bin/sra-info.3
  54. bin/sra-info.3.0.6
  55. bin/sra-pileup
  56. bin/sra-pileup-orig.3.0.6
  57. bin/sra-pileup.3
  58. bin/sra-pileup.3.0.6
  59. bin/sra-search
  60. bin/sra-search.3
  61. bin/sra-search.3.0.6
  62. bin/sra-stat
  63. bin/sra-stat.3
  64. bin/sra-stat.3.0.6
  65. bin/srapath
  66. bin/srapath-orig.3.0.6
  67. bin/srapath.3
  68. bin/srapath.3.0.6
  69. bin/sratools
  70. bin/sratools.3
  71. bin/sratools.3.0.6
  72. bin/test-sra
  73. bin/test-sra.3
  74. bin/test-sra.3.0.6
  75. bin/var-expand
  76. bin/var-expand.3
  77. bin/var-expand.3.0.6
  78. bin/vdb-config
  79. bin/vdb-config.3
  80. bin/vdb-config.3.0.6
  81. bin/vdb-decrypt
  82. bin/vdb-decrypt.3
  83. bin/vdb-decrypt.3.0.6
  84. bin/vdb-dump
  85. bin/vdb-dump-orig.3.0.6
  86. bin/vdb-dump.3
  87. bin/vdb-dump.3.0.6
  88. bin/vdb-encrypt
  89. bin/vdb-encrypt.3
  90. bin/vdb-encrypt.3.0.6
  91. bin/vdb-validate
  92. bin/vdb-validate.3
  93. bin/vdb-validate.3.0.6
  94. include/ncbi-vdb/NGS.hpp
  95. include/ngs/Alignment.hpp
  96. include/ngs/AlignmentIterator.hpp
  97. include/ngs/ErrorMsg.hpp
  98. include/ngs/Fragment.hpp
  99. include/ngs/FragmentIterator.hpp
  100. include/ngs/Package.hpp
  101. include/ngs/Pileup.hpp
  102. include/ngs/PileupEvent.hpp
  103. include/ngs/PileupEventIterator.hpp
  104. include/ngs/PileupIterator.hpp
  105. include/ngs/Read.hpp
  106. include/ngs/ReadCollection.hpp
  107. include/ngs/ReadGroup.hpp
  108. include/ngs/ReadGroupIterator.hpp
  109. include/ngs/ReadIterator.hpp
  110. include/ngs/Reference.hpp
  111. include/ngs/ReferenceIterator.hpp
  112. include/ngs/ReferenceSequence.hpp
  113. include/ngs/Statistics.hpp
  114. include/ngs/StringRef.hpp
  115. include/ngs/adapter/AlignmentItf.hpp
  116. include/ngs/adapter/ErrorMsg.hpp
  117. include/ngs/adapter/FragmentItf.hpp
  118. include/ngs/adapter/PileupEventItf.hpp
  119. include/ngs/adapter/PileupItf.hpp
  120. include/ngs/adapter/ReadCollectionItf.hpp
  121. include/ngs/adapter/ReadGroupItf.hpp
  122. include/ngs/adapter/ReadItf.hpp
  123. include/ngs/adapter/Refcount.hpp
  124. include/ngs/adapter/ReferenceItf.hpp
  125. include/ngs/adapter/ReferenceSequenceItf.hpp
  126. include/ngs/adapter/StatisticsItf.hpp
  127. include/ngs/adapter/StringItf.hpp
  128. include/ngs/adapter/defs.h
  129. include/ngs/inl/Alignment.hpp
  130. include/ngs/inl/AlignmentIterator.hpp
  131. include/ngs/inl/Fragment.hpp
  132. include/ngs/inl/FragmentIterator.hpp
  133. include/ngs/inl/Package.hpp
  134. include/ngs/inl/Pileup.hpp
  135. include/ngs/inl/PileupEvent.hpp
  136. include/ngs/inl/PileupEventIterator.hpp
  137. include/ngs/inl/PileupIterator.hpp
  138. include/ngs/inl/Read.hpp
  139. include/ngs/inl/ReadCollection.hpp
  140. include/ngs/inl/ReadGroup.hpp
  141. include/ngs/inl/ReadGroupIterator.hpp
  142. include/ngs/inl/ReadIterator.hpp
  143. include/ngs/inl/Reference.hpp
  144. include/ngs/inl/ReferenceIterator.hpp
  145. include/ngs/inl/ReferenceSequence.hpp
  146. include/ngs/inl/Statistics.hpp
  147. include/ngs/inl/StringRef.hpp
  148. include/ngs/itf/AlignmentItf.h
  149. include/ngs/itf/AlignmentItf.hpp
  150. include/ngs/itf/ErrBlock.h
  151. include/ngs/itf/ErrBlock.hpp
  152. include/ngs/itf/ErrorMsg.hpp
  153. include/ngs/itf/FragmentItf.h
  154. include/ngs/itf/FragmentItf.hpp
  155. include/ngs/itf/PackageItf.hpp
  156. include/ngs/itf/PileupEventItf.h
  157. include/ngs/itf/PileupEventItf.hpp
  158. include/ngs/itf/PileupItf.h
  159. include/ngs/itf/PileupItf.hpp
  160. include/ngs/itf/ReadCollectionItf.h
  161. include/ngs/itf/ReadCollectionItf.hpp
  162. include/ngs/itf/ReadGroupItf.h
  163. include/ngs/itf/ReadGroupItf.hpp
  164. include/ngs/itf/ReadItf.h
  165. include/ngs/itf/ReadItf.hpp
  166. include/ngs/itf/Refcount.h
  167. include/ngs/itf/Refcount.hpp
  168. include/ngs/itf/ReferenceItf.h
  169. include/ngs/itf/ReferenceItf.hpp
  170. include/ngs/itf/ReferenceSequenceItf.h
  171. include/ngs/itf/ReferenceSequenceItf.hpp
  172. include/ngs/itf/StatisticsItf.h
  173. include/ngs/itf/StatisticsItf.hpp
  174. include/ngs/itf/StringItf.h
  175. include/ngs/itf/StringItf.hpp
  176. include/ngs/itf/VTable.h
  177. include/ngs/itf/VTable.hpp
  178. include/ngs/itf/defs.h
  179. include/ngs/unix/arm64/atomic32.h
  180. include/ngs/unix/fat86/atomic32.h
  181. include/ngs/unix/i386/atomic32.h
  182. include/ngs/unix/x86_64/atomic32.h
  183. include/ngs/win/atomic32.h
  184. include/ngs/win/stdbool.h
  185. jar/ngs-doc.jar
  186. jar/ngs-examples.jar
  187. jar/ngs-java.jar
  188. jar/ngs-src.jar
  189. lib64/libncbi-ngs-c++-static.a
  190. lib64/libncbi-ngs-c++.a
  191. lib64/libncbi-ngs-c++.a.3
  192. lib64/libncbi-ngs-c++.a.3.0.6
  193. lib64/libncbi-ngs-static.a
  194. lib64/libncbi-ngs.a
  195. lib64/libncbi-ngs.a.3
  196. lib64/libncbi-ngs.a.3.0.6
  197. lib64/libncbi-ngs.so
  198. lib64/libncbi-ngs.so.3
  199. lib64/libncbi-ngs.so.3.0.6
  200. lib64/libngs-c++-static.a
  201. lib64/libngs-c++.a
  202. lib64/libngs-c++.a.3
  203. lib64/libngs-c++.a.3.0.6
  204. lib64/libngs-c++.so
  205. lib64/libngs-c++.so.3
  206. lib64/libngs-c++.so.3.0.6
  207. share/examples/sra-tools/AlignSliceTest.cpp
  208. share/examples/sra-tools/AlignTest.cpp
  209. share/examples/sra-tools/DumpReferenceFASTA.cpp
  210. share/examples/sra-tools/FragTest.cpp
  211. share/examples/sra-tools/Makefile
  212. share/examples/sra-tools/PileupTest.cpp
  213. share/examples/sra-tools/README.txt
  214. share/examples/sra-tools/RefTest.cpp
  215. share/examples/sra-tools/expected.txt
  216. share/examples/sra-tools/java/Makefile
  217. share/examples/sra-tools/java/README.txt
  218. share/examples/sra-tools/java/examples/AlignSliceTest.java
  219. share/examples/sra-tools/java/examples/AlignTest.java
  220. share/examples/sra-tools/java/examples/DumpReferenceFASTA.java
  221. share/examples/sra-tools/java/examples/FragTest.java
  222. share/examples/sra-tools/java/examples/PileupTest.java
  223. share/examples/sra-tools/java/examples/ReadGroupTest.java
  224. share/examples/sra-tools/java/examples/RefTest.java
  225. share/examples/sra-tools/java/expected.txt
  226. share/examples/sra-tools/python/AlignSliceTest.py
  227. share/examples/sra-tools/python/AlignTest.py
  228. share/examples/sra-tools/python/FragTest.py
  229. share/examples/sra-tools/python/Makefile
  230. share/examples/sra-tools/python/PileupTest.py
  231. share/examples/sra-tools/python/README.txt
  232. share/examples/sra-tools/python/RefTest.py
  233. share/examples/sra-tools/python/expected.txt
  234. share/javadoc/ngs-doc/allclasses-index.html
  235. share/javadoc/ngs-doc/allpackages-index.html
  236. share/javadoc/ngs-doc/constant-values.html
  237. share/javadoc/ngs-doc/element-list
  238. share/javadoc/ngs-doc/gov/nih/nlm/ncbi/ngs/LibDependencies.html
  239. share/javadoc/ngs-doc/gov/nih/nlm/ncbi/ngs/NGS.html
  240. share/javadoc/ngs-doc/gov/nih/nlm/ncbi/ngs/package-summary.html
  241. share/javadoc/ngs-doc/gov/nih/nlm/ncbi/ngs/package-tree.html
  242. share/javadoc/ngs-doc/help-doc.html
  243. share/javadoc/ngs-doc/index-all.html
  244. share/javadoc/ngs-doc/index.html
  245. share/javadoc/ngs-doc/jquery-ui.overrides.css
  246. share/javadoc/ngs-doc/legal/ADDITIONAL_LICENSE_INFO
  247. share/javadoc/ngs-doc/legal/ASSEMBLY_EXCEPTION
  248. share/javadoc/ngs-doc/legal/LICENSE
  249. share/javadoc/ngs-doc/legal/jquery.md
  250. share/javadoc/ngs-doc/legal/jqueryUI.md
  251. share/javadoc/ngs-doc/member-search-index.js
  252. share/javadoc/ngs-doc/module-search-index.js
  253. share/javadoc/ngs-doc/ngs/Alignment.html
  254. share/javadoc/ngs-doc/ngs/AlignmentIterator.html
  255. share/javadoc/ngs-doc/ngs/ErrorMsg.html
  256. share/javadoc/ngs-doc/ngs/Fragment.html
  257. share/javadoc/ngs-doc/ngs/FragmentIterator.html
  258. share/javadoc/ngs-doc/ngs/Package.html
  259. share/javadoc/ngs-doc/ngs/Pileup.html
  260. share/javadoc/ngs-doc/ngs/PileupEvent.html
  261. share/javadoc/ngs-doc/ngs/PileupEventIterator.html
  262. share/javadoc/ngs-doc/ngs/PileupIterator.html
  263. share/javadoc/ngs-doc/ngs/Read.html
  264. share/javadoc/ngs-doc/ngs/ReadCollection.html
  265. share/javadoc/ngs-doc/ngs/ReadGroup.html
  266. share/javadoc/ngs-doc/ngs/ReadGroupIterator.html
  267. share/javadoc/ngs-doc/ngs/ReadIterator.html
  268. share/javadoc/ngs-doc/ngs/Reference.html
  269. share/javadoc/ngs-doc/ngs/ReferenceIterator.html
  270. share/javadoc/ngs-doc/ngs/ReferenceSequence.html
  271. share/javadoc/ngs-doc/ngs/Statistics.html
  272. share/javadoc/ngs-doc/ngs/package-summary.html
  273. share/javadoc/ngs-doc/ngs/package-tree.html
  274. share/javadoc/ngs-doc/overview-summary.html
  275. share/javadoc/ngs-doc/overview-tree.html
  276. share/javadoc/ngs-doc/package-search-index.js
  277. share/javadoc/ngs-doc/resources/glass.png
  278. share/javadoc/ngs-doc/resources/x.png
  279. share/javadoc/ngs-doc/script-dir/jquery-3.6.1.min.js
  280. share/javadoc/ngs-doc/script-dir/jquery-ui.min.css
  281. share/javadoc/ngs-doc/script-dir/jquery-ui.min.js
  282. share/javadoc/ngs-doc/script.js
  283. share/javadoc/ngs-doc/search.js
  284. share/javadoc/ngs-doc/serialized-form.html
  285. share/javadoc/ngs-doc/stylesheet.css
  286. share/javadoc/ngs-doc/tag-search-index.js
  287. share/javadoc/ngs-doc/type-search-index.js
  288. @owner
  289. @group
  290. @mode
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Dependency lines:
  • sra-tools>0:biology/sra-tools
To install the port:
cd /usr/ports/biology/sra-tools/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/sra-tools
  • pkg install sra-tools
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: sra-tools
Flavors: there is no flavor information for this port.
ONLY_FOR_ARCHS: aarch64 amd64
distinfo:
TIMESTAMP = 1691599515 SHA256 (ncbi-sra-tools-3.0.6_GH0.tar.gz) = 9fecfd819ee9beaf8a1d3e4b76a5d49e747bc064525b40416e0730a168986348 SIZE (ncbi-sra-tools-3.0.6_GH0.tar.gz) = 44957431

Expand this list (2 items)

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SHA256 (ncbi-ncbi-vdb-3.0.6_GH0.tar.gz) = 4b6f93336bf8664fdcc151d41ea0793f0b0f88cfcb7c2aa049f162a72f905223 SIZE (ncbi-ncbi-vdb-3.0.6_GH0.tar.gz) = 18972238

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Packages (timestamps in pop-ups are UTC):
sra-tools
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest3.0.63.0.6------
FreeBSD:13:quarterly3.0.63.0.6------
FreeBSD:14:latest3.0.63.0.6------
FreeBSD:14:quarterly3.0.63.0.6------
FreeBSD:15:latest3.0.63.0.6n/a-n/a---
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. bash : shells/bash
  2. java : java/openjdk17
  3. bison : devel/bison
  4. cmake : devel/cmake-core
  5. ninja : devel/ninja
Runtime dependencies:
  1. java : java/openjdk17
Library dependencies:
  1. libxml2.so : textproc/libxml2
  2. libhdf5.so : science/hdf5
  3. libepoll-shim.so : devel/libepoll-shim
  4. libzstd.so : archivers/zstd
This port is required by:
for Run
  1. biology/atac-seq
  2. biology/biostar-tools
  3. biology/chip-seq
  4. biology/rna-seq

Configuration Options:
===> The following configuration options are available for sra-tools-3.0.6: EXAMPLES=on: Build and/or install examples ===> Use 'make config' to modify these settings
Options name:
biology_sra-tools
USES:
bison cmake shebangfix
FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (1 items)
Collapse this list.
  1. https://codeload.github.com/ncbi/sra-tools/tar.gz/3.0.6?dummy=/
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There are no commits on branch 2022Q3 for this port