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Port details
artemis DNA sequence viewer and annotation tool
17.0.1.11 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
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 22 Dec 2001 11:39:40
Also Listed In: java
License: GPLv3
Artemis is a DNA sequence viewer and annotation tool that allows
visualisation of sequence features and the results of analyses within
the context of the sequence, and its six-frame translation.  Artemis is
written in Java, reads EMBL or GENBANK format sequences and feature
tables, and can work on sequences of any size.

ACT (Artemis Comparison Tool) is a DNA sequence comparison viewer based
on Artemis. It can open two or more sequences (and their
annotations/features) together with their comparisons (usually the
result of running blastn or tblastx searches).

WWW: https://www.sanger.ac.uk/science/tools/artemis
SVNWeb : Homepage : PortsMon
    Pseudo-pkg-plist information, but much better, from make generate-plist
    Expand this list (127 items)
  1. /usr/local/share/licenses/artemis-17.0.1.11/catalog.mk
  2. /usr/local/share/licenses/artemis-17.0.1.11/LICENSE
  3. /usr/local/share/licenses/artemis-17.0.1.11/GPLv3
  4. artemis-17.0.1.11/act
  5. artemis-17.0.1.11/art
  6. artemis-17.0.1.11/artemis_sqlmap/Analysis.xml
  7. artemis-17.0.1.11/artemis_sqlmap/AnalysisFeature.xml
  8. artemis-17.0.1.11/artemis_sqlmap/Cv.xml
  9. artemis-17.0.1.11/artemis_sqlmap/CvTerm.xml
  10. artemis-17.0.1.11/artemis_sqlmap/Db.xml
  11. artemis-17.0.1.11/artemis_sqlmap/DbXRef.xml
  12. artemis-17.0.1.11/artemis_sqlmap/Feature.xml
  13. artemis-17.0.1.11/artemis_sqlmap/FeatureCvTerm.xml
  14. artemis-17.0.1.11/artemis_sqlmap/FeatureCvTermDbXRef.xml
  15. artemis-17.0.1.11/artemis_sqlmap/FeatureCvTermProp.xml
  16. artemis-17.0.1.11/artemis_sqlmap/FeatureCvTermPub.xml
  17. artemis-17.0.1.11/artemis_sqlmap/FeatureDbXRef.xml
  18. artemis-17.0.1.11/artemis_sqlmap/FeatureLoc.xml
  19. artemis-17.0.1.11/artemis_sqlmap/FeatureProp.xml
  20. artemis-17.0.1.11/artemis_sqlmap/FeaturePub.xml
  21. artemis-17.0.1.11/artemis_sqlmap/FeatureRelationship.xml
  22. artemis-17.0.1.11/artemis_sqlmap/FeatureSynonym.xml
  23. artemis-17.0.1.11/artemis_sqlmap/Graph.xml
  24. artemis-17.0.1.11/artemis_sqlmap/Organism.xml
  25. artemis-17.0.1.11/artemis_sqlmap/OrganismProp.xml
  26. artemis-17.0.1.11/artemis_sqlmap/Pub.xml
  27. artemis-17.0.1.11/artemis_sqlmap/PubDbXRef.xml
  28. artemis-17.0.1.11/artemis_sqlmap/Synonym.xml
  29. artemis-17.0.1.11/artemis_sqlmap/chado_iBatis_config.properties
  30. artemis-17.0.1.11/artemis_sqlmap/chado_iBatis_config.xml
  31. artemis-17.0.1.11/bamview
  32. artemis-17.0.1.11/dnaplotter
  33. artemis-17.0.1.11/etc/af063097.embl
  34. artemis-17.0.1.11/etc/af063097.fasta
  35. artemis-17.0.1.11/etc/af063097_v_b132222.crunch
  36. artemis-17.0.1.11/etc/b132222.embl
  37. artemis-17.0.1.11/etc/b132222.fasta
  38. artemis-17.0.1.11/etc/c1215.blastn.crunch
  39. artemis-17.0.1.11/etc/c1215.blastn.tab
  40. artemis-17.0.1.11/etc/c1215.embl
  41. artemis-17.0.1.11/etc/c1215.genbank
  42. artemis-17.0.1.11/etc/c1215.seq
  43. artemis-17.0.1.11/etc/chado_extra.sql
  44. artemis-17.0.1.11/etc/feature_keys
  45. artemis-17.0.1.11/etc/feature_keys_gff
  46. artemis-17.0.1.11/etc/go_associations.pl
  47. artemis-17.0.1.11/etc/key_mapping
  48. artemis-17.0.1.11/etc/log4j.properties
  49. artemis-17.0.1.11/etc/log4j.properties.txt
  50. artemis-17.0.1.11/etc/options
  51. artemis-17.0.1.11/etc/pombe.usage
  52. artemis-17.0.1.11/etc/project.properties
  53. artemis-17.0.1.11/etc/qualifier_mapping
  54. artemis-17.0.1.11/etc/qualifier_types
  55. artemis-17.0.1.11/etc/qualifier_types_gff
  56. artemis-17.0.1.11/etc/readmeDNADraw.html
  57. artemis-17.0.1.11/etc/results_to_netscape
  58. artemis-17.0.1.11/etc/run_blastn
  59. artemis-17.0.1.11/etc/run_blastn.sanger
  60. artemis-17.0.1.11/etc/run_blastp
  61. artemis-17.0.1.11/etc/run_blastp.sanger
  62. artemis-17.0.1.11/etc/run_blastp.sanger.linux
  63. artemis-17.0.1.11/etc/run_blastx
  64. artemis-17.0.1.11/etc/run_blastx.sanger
  65. artemis-17.0.1.11/etc/run_clustalx
  66. artemis-17.0.1.11/etc/run_clustalx.sanger
  67. artemis-17.0.1.11/etc/run_fasta
  68. artemis-17.0.1.11/etc/run_fasta.sanger
  69. artemis-17.0.1.11/etc/run_fasta.sanger.linux
  70. artemis-17.0.1.11/etc/run_fastx
  71. artemis-17.0.1.11/etc/run_fastx.sanger
  72. artemis-17.0.1.11/etc/run_hth
  73. artemis-17.0.1.11/etc/run_jalview
  74. artemis-17.0.1.11/etc/run_netblastp
  75. artemis-17.0.1.11/etc/run_pepstats
  76. artemis-17.0.1.11/etc/run_sigcleave
  77. artemis-17.0.1.11/etc/run_smart
  78. artemis-17.0.1.11/etc/run_tblastn
  79. artemis-17.0.1.11/etc/run_tblastx
  80. artemis-17.0.1.11/etc/run_tblastx.sanger
  81. artemis-17.0.1.11/etc/versions
  82. artemis-17.0.1.11/etc/writedb_entry
  83. artemis-17.0.1.11/images/Wellcome_Sanger_Institute_Logo_Landscape_Digital_RGB_Full_Colour.jpg
  84. artemis-17.0.1.11/images/act.gif
  85. artemis-17.0.1.11/images/helix.gif
  86. artemis-17.0.1.11/images/icon.gif
  87. artemis-17.0.1.11/images/sanger-centre.gif
  88. artemis-17.0.1.11/jars/act.jar
  89. artemis-17.0.1.11/jars/artemis.jar
  90. artemis-17.0.1.11/jars/bamview.jar
  91. artemis-17.0.1.11/jars/dnaplotter.jar
  92. artemis-17.0.1.11/lib/LICENSE.Apache
  93. artemis-17.0.1.11/lib/LICENSE.JDBC
  94. artemis-17.0.1.11/lib/LICENSE.Picard
  95. artemis-17.0.1.11/lib/README
  96. artemis-17.0.1.11/lib/batik/batik-awt-util.jar
  97. artemis-17.0.1.11/lib/batik/batik-codec.jar
  98. artemis-17.0.1.11/lib/batik/batik-dom.jar
  99. artemis-17.0.1.11/lib/batik/batik-ext.jar
  100. artemis-17.0.1.11/lib/batik/batik-svggen.jar
  101. artemis-17.0.1.11/lib/batik/batik-util.jar
  102. artemis-17.0.1.11/lib/batik/batik-xml.jar
  103. artemis-17.0.1.11/lib/batik/version
  104. artemis-17.0.1.11/lib/biojava.jar
  105. artemis-17.0.1.11/lib/commons-lang-2.6.jar
  106. artemis-17.0.1.11/lib/commons-net-3.6.jar
  107. artemis-17.0.1.11/lib/ibatis/README
  108. artemis-17.0.1.11/lib/ibatis/cglib-nodep-2.2.jar
  109. artemis-17.0.1.11/lib/ibatis/ibatis-2.3.4.726.jar
  110. artemis-17.0.1.11/lib/ibatis/license.txt
  111. artemis-17.0.1.11/lib/ibatis/log4j-1.2.14.jar
  112. artemis-17.0.1.11/lib/j2ssh/COMMONS.LICENSE
  113. artemis-17.0.1.11/lib/j2ssh/J2SSH.LICENSE
  114. artemis-17.0.1.11/lib/j2ssh/README
  115. artemis-17.0.1.11/lib/j2ssh/commons-logging.jar
  116. artemis-17.0.1.11/lib/j2ssh/j2ssh-artemis-plugin.jar
  117. artemis-17.0.1.11/lib/j2ssh/j2ssh-core.jar
  118. artemis-17.0.1.11/lib/j2ssh/j2ssh.properties
  119. artemis-17.0.1.11/lib/jakarta-regexp-1.2.jar
  120. artemis-17.0.1.11/lib/jemAlign.jar
  121. artemis-17.0.1.11/lib/picard/VERSION.txt
  122. artemis-17.0.1.11/lib/picard/picard.jar
  123. artemis-17.0.1.11/lib/postgresql-8.4-701.jdbc3.jar
  124. bin/act
  125. bin/art
  126. bin/bamview
  127. bin/dnaplotter
  128. Collapse this list.

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

PKGNAME: artemis

distinfo:

TIMESTAMP = 1528734532
SHA256 (sanger-pathogens-artemis-v17.0.1-11-g3e43d27e_GH0.tar.gz) = a490d4b76bfdd8a531d22f2e0495e8c2c6e8efad18e6a9a0043ac425c7ab16dc
SIZE (sanger-pathogens-artemis-v17.0.1-11-g3e43d27e_GH0.tar.gz) = 77195529


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

Build dependencies:
  1. java : java/openjdk8
  2. gmake : devel/gmake
Runtime dependencies:
  1. bash : shells/bash
  2. java : java/openjdk8
There are no ports dependent upon this port

Configuration Options
     No options to configure

USES:
gmake shebangfix

Master Sites:
  1. https://codeload.github.com/sanger-pathogens/artemis/tar.gz/v17.0.1-11-g3e43d27e?dummy=/

Number of commits found: 24

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
11 Jun 2018 17:45:57
Original commit files touched by this commit  17.0.1.11
Revision:472197
yuri search for other commits by this committer
biology/artemis: Update 9 -> 17.0.1-11

Port changes:
* Take maintainership
* Change to github
* Change to DISTVERSION
* Add LICENSE
* Depends on bash
* Add USES=gmake
* Remove NO_BUILD: needs to build jars from java files
* Update the post-extract target
* Change do-install to do minimal installation
* Update WWW
13 Oct 2017 11:14:32
Original commit files touched by this commit  9_2
Revision:451981
bapt search for other commits by this committer
Remove dead master sites
21 Apr 2017 16:28:25
Original commit files touched by this commit  9_2
Revision:439093
amdmi3 search for other commits by this committer
- Fix shebangs
- Add NO_ARCH
- Switch to relative links
21 Oct 2016 12:51:41
Original commit files touched by this commit  9_1
Revision:424411  Sanity Test Failure
mat search for other commits by this committer
${RM} already has -f.

PR:		213570
Submitted by:	mat
Exp-run by:	antoine
Sponsored by:	Absolight
11 Mar 2015 14:41:54
Original commit files touched by this commit  9_1
Revision:380989
amdmi3 search for other commits by this committer
- Add empty directory to plist
20 Oct 2014 07:10:48
Original commit files touched by this commit  9_1
Revision:371237
bapt search for other commits by this committer
Cleanup plist
20 Jan 2014 23:06:48
Original commit files touched by this commit  9_1
Revision:340486
bapt search for other commits by this committer
Support stage
20 Sep 2013 15:55:44
Original commit files touched by this commit  9_1
Revision:327709
bapt search for other commits by this committer
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology)
10 Dec 2012 11:25:28
Original commit files touched by this commit  9_1
Revision:308600
bapt search for other commits by this committer
Decommissioning java 1.5 (EOLed since October 2009):
suppress any reference to USE_JAVA=	1.5+ (part1)
01 Oct 2012 14:45:17
Original commit files touched by this commit  9_1
Revision:305130
tabthorpe search for other commits by this committer
- Reassign to the heap at maintainer's request
21 Jul 2011 05:03:02
Original commit files touched by this commit  9_1
linimon search for other commits by this committer
Now that the Java 1.3 and Java 1.4 ports are deprecated and will expire soon,
remove support for them from bsd.java.mk.  As Jikes is not available in Java 1.5
or higher, remove it from bsd.java.mk too (suggested by hq@) and from the ports
which used it (only occurences were USE_JIKES=no).  Support for the Blackdown VM
is also removed, as it is not available in Java 1.5 and higher.

Also remove the mapping from Java 1.1-1.4 to Java 1.5+ in bsd.java.mk to detect
old, broken ports; therefore bump the minimal value of JAVA_VERSION to 1.5.
While here, replace static values of JAVA_VERSION in files/*.in by
%%JAVA_VERSION%% .

PR:             ports/158969
Submitted by:   rene
Tested on:      pointyhat-west -exp
19 Mar 2011 12:38:54
Original commit files touched by this commit  9_1
miwi search for other commits by this committer
- Get Rid MD5 support
06 Jun 2008 13:08:29
Original commit files touched by this commit  9_1
edwin search for other commits by this committer
Bump portrevision due to upgrade of devel/gettext.

The affected ports are the ones with gettext as a run-dependency
according to ports/INDEX-7 (5007 of them) and the ones with USE_GETTEXT
in Makefile (29 of them).

PR:             ports/124340
Submitted by:   edwin@
Approved by:    portmgr (pav)
08 Jul 2007 11:47:58
Original commit files touched by this commit  9
rafan search for other commits by this committer
- Update to version 9
- Don't install CVS directories which are going to be removed
  in next release

PR:             ports/113831
Submitted by:   Thomas Abthorpe <thomas at goodking.ca>
Approved by:    maintainer timeout (20 days)
26 May 2007 21:03:05
Original commit files touched by this commit  7_2
kris search for other commits by this committer
BROKEN: Unfetchable
19 May 2007 20:32:57
Original commit files touched by this commit  7_2
flz search for other commits by this committer
- Welcome X.org 7.2 \o/.
- Set X11BASE to ${LOCALBASE} for recent ${OSVERSION}.
- Bump PORTREVISION for ports intalling files in ${X11BASE}.
05 Dec 2005 16:57:26
Original commit files touched by this commit  7_1
tdb search for other commits by this committer
- Fix fetch problems

PR:             89971
Submitted by:   Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
Approved by:    clement (mentor)
20 Sep 2005 14:59:28
Original commit files touched by this commit  7
hq search for other commits by this committer
Update to version 7

PR:             86196
Submitted by:   Tony Maher <anthony.maher@uts.edu.au>
Approved by:    maintainer
20 Mar 2005 14:43:55
Original commit files touched by this commit  6
hq search for other commits by this committer
- Add 'java' category
- Remove incorrect (and unneeded) JAVA_RUN statement

PR:             78761
Submitted by:   me
12 Mar 2005 08:01:19
Original commit files touched by this commit  6
sem search for other commits by this committer
- Update to version 6
- Pass maintainership to submitter

PR:             ports/76219
Submitted by:   Fernan Aguero <fernan@iib.unsam.edu.ar>
Approved by:    maintainer timeout (2 monthes)
31 Mar 2004 03:12:58
Original commit files touched by this commit  4.0_1
trevor search for other commits by this committer
SIZEify (maintainer timeout)
04 Feb 2004 05:21:48
Original commit files touched by this commit  4.0_1
marcus search for other commits by this committer
Bump PORTREVISION on all ports that depend on gettext to aid with upgrading.

(Part 2)
21 Feb 2003 11:01:38
Original commit files touched by this commit  4.0
knu search for other commits by this committer
De-pkg-comment.
22 Dec 2001 14:39:40
Original commit files touched by this commit
kevlo search for other commits by this committer
Initial import of artemis 4.0    

Number of commits found: 24

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