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Port details
erminej Analyses of gene sets such as gene expression profiling studies
3.2 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 Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2021-07-09 12:30:08
Last Update: 2022-09-07 21:58:51
Commit Hash: fb16dfe
Also Listed In: java
License: APACHE20
Description:
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb - no subversion history for this port
pkg-plist: as obtained via: make generate-plist
Expand this list (37 items)
Collapse this list.
  1. /usr/local/share/licenses/erminej-3.2/catalog.mk
  2. /usr/local/share/licenses/erminej-3.2/LICENSE
  3. /usr/local/share/licenses/erminej-3.2/APACHE20
  4. bin/ermineJ
  5. etc/forehead.conf
  6. share/java/classes/erminej/antlr.jar
  7. share/java/classes/erminej/baseCode.jar
  8. share/java/classes/erminej/colt.jar
  9. share/java/classes/erminej/commons-beanutils.jar
  10. share/java/classes/erminej/commons-cli.jar
  11. share/java/classes/erminej/commons-collections.jar
  12. share/java/classes/erminej/commons-configuration.jar
  13. share/java/classes/erminej/commons-io.jar
  14. share/java/classes/erminej/commons-lang3.jar
  15. share/java/classes/erminej/commons-logging.jar
  16. share/java/classes/erminej/commons-math3.jar
  17. share/java/classes/erminej/commons-net.jar
  18. share/java/classes/erminej/ermineJ.jar
  19. share/java/classes/erminej/forehead.jar
  20. share/java/classes/erminej/gemma-core.jar
  21. share/java/classes/erminej/gemma-gsec.jar
  22. share/java/classes/erminej/javax.activation-api.jar
  23. share/java/classes/erminej/jaxb-api.jar
  24. share/java/classes/erminej/jcl-over-slf4j.jar
  25. share/java/classes/erminej/jcommon.jar
  26. share/java/classes/erminej/jfreechart.jar
  27. share/java/classes/erminej/jsontools-core.jar
  28. share/java/classes/erminej/log4j.jar
  29. share/java/classes/erminej/mtj.jar
  30. share/java/classes/erminej/opencsv.jar
  31. share/java/classes/erminej/slf4j-api.jar
  32. share/java/classes/erminej/slf4j-log4j12.jar
  33. share/java/classes/erminej/xercesImpl.jar
  34. share/java/classes/erminej/xml-apis.jar
  35. @owner
  36. @group
  37. @mode
Collapse this list.
Dependency lines:
  • erminej>0:biology/erminej
To install the port:
cd /usr/ports/biology/erminej/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/erminej
  • pkg install erminej
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: erminej
Flavors: there is no flavor information for this port.
distinfo:

Packages (timestamps in pop-ups are UTC):
erminej
ABIlatestquarterly
FreeBSD:11:aarch64pkg-falloutpkg-fallout
FreeBSD:11:amd643.2pkg-fallout
FreeBSD:11:armv6pkg-falloutpkg-fallout
FreeBSD:11:i3863.2pkg-fallout
FreeBSD:11:mipspkg-falloutpkg-fallout
FreeBSD:11:mips64pkg-falloutpkg-fallout
FreeBSD:12:aarch64pkg-fallout3.2
FreeBSD:12:amd643.23.2
FreeBSD:12:armv6pkg-falloutpkg-fallout
FreeBSD:12:armv7pkg-falloutpkg-fallout
FreeBSD:12:i3863.23.2
FreeBSD:12:mipspkg-falloutpkg-fallout
FreeBSD:12:mips64pkg-falloutpkg-fallout
FreeBSD:12:powerpc64pkg-falloutpkg-fallout
FreeBSD:13:aarch643.23.2
FreeBSD:13:amd643.23.2
FreeBSD:13:armv6pkg-fallout3.2
FreeBSD:13:armv73.23.2
FreeBSD:13:i3863.23.2
FreeBSD:13:mipspkg-falloutpkg-fallout
FreeBSD:13:mips64pkg-falloutpkg-fallout
FreeBSD:13:powerpc64pkg-fallout3.2
FreeBSD:13:riscv64pkg-falloutpkg-fallout
FreeBSD:14:aarch643.2pkg-fallout
FreeBSD:14:amd643.2pkg-fallout
FreeBSD:14:armv63.2pkg-fallout
FreeBSD:14:armv73.2pkg-fallout
FreeBSD:14:i3863.2pkg-fallout
FreeBSD:14:mipspkg-falloutpkg-fallout
FreeBSD:14:mips64pkg-falloutpkg-fallout
FreeBSD:14:powerpc643.2pkg-fallout
FreeBSD:14:riscv64pkg-falloutpkg-fallout
 
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Runtime dependencies:
  1. java : java/openjdk8
This port is required by:
for Run
  1. biology/biostar-tools

Configuration Options:
Options name:
USES:
FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (1 items)
Collapse this list.
  1. http://home.pavlab.msl.ubc.ca/ermineJ/distributions/
Collapse this list.

Number of commits found: 3

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
07 Sep 2022 21:58:51
commit hash:fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash:fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash:fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash:fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Remove WWW entries moved into port Makefiles

Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.

This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.

Approved by:		portmgr (tcberner)
3.2
07 Sep 2022 21:10:59
commit hash:b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash:b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash:b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash:b7f05445c00f2625aa19b4154ebcbce5ed2daa52 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Add WWW entries to port Makefiles

It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.

Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.

There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.
(Only the first 15 lines of the commit message are shown above View all of this commit message)
3.2
09 Jul 2021 12:26:58
commit hash:e44f917e298a1f860fab0790aacd348cae60f74bcommit hash:e44f917e298a1f860fab0790aacd348cae60f74bcommit hash:e44f917e298a1f860fab0790aacd348cae60f74bcommit hash:e44f917e298a1f860fab0790aacd348cae60f74b files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/erminej: Analyses of gene sets, e.g. gene expression profiling

ErmineJ performs analyses of gene sets in high-throughput genomics data
such as gene expression profiling studies. A typical goal is to
determine whether particular biological pathways are "doing something
interesting" in an experiment that generates long lists of candidates.
The software is designed to be used by biologists with little or no
informatics background (but if you do, you might be interested in the
CLI or the R support).

Number of commits found: 3