BSD Ports

biology/erminej 3.2_2 FreeBSD

Analyses of gene sets such as gene expression profiling studies

System
FreeBSD
Repository
FreeBSD ports
Maintainer
[email protected]
Last update
Commit
2414383046
License
APACHE20
Categories
biology, java
Package size
13723.1 KiB, 15656.2 KiB installed

Description

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).

In the other systems

The newest version among them is 3.2, as upstream numbers it.

SystemPortVersionVulnerabilitiesStatusMaintainerLast update
FreeBSDbiology/erminej3.2_2 newestnone known-[email protected]2026-10-08
DragonFlybiology/erminej3.2 newestnone known-[email protected]-
HardenedBSDbiology/erminej3.2_2 newestno data-[email protected]-
GhostBSDbiology/erminej3.2_2 newestno data-[email protected]-

Install

Binary package:

pkg install erminej

From the ports tree:

cd /usr/ports/biology/erminej/ && make install clean

To depend on this port in another port's Makefile:

RUN_DEPENDS=	erminej>0:biology/erminej

Packages

The version each package repository carries. “-” means the repository builds no package of it, “n/a” that there is no such repository.

Repositoryaarch64amd64armv6armv7i386
FreeBSD:14:latest3.2_23.2_23.23.23.2_2
FreeBSD:14:quarterly3.2_23.2_2n/a3.23.2_2
FreeBSD:15:latest3.2_23.2_2n/a3.23.2
FreeBSD:15:quarterly3.2_23.2_2n/an/an/a
FreeBSD:16:latest3.2_23.2_2n/an/an/a
FreeBSD:16:quarterlyn/an/an/an/an/a

Dependencies

The Makefile names none itself; they come from USES and USE_*.

The full lists below include those, and their dependencies in turn.

Run dependencies 53
Required by 1

Configuration

No options to configure.

USES
java zip
Service scripts
none

Message after installing

===>   NOTICE:

The erminej port currently does not have a maintainer. As a result, it is
more likely to have unresolved issues, not be up-to-date, or even be removed in
the future. To volunteer to maintain this port, please create an issue at:

https://bugs.freebsd.org/bugzilla

More information about port maintainership is available at:

https://docs.freebsd.org/en/articles/contributing/#ports-contributing

Files

pkg-plist 31
  • bin/ermineJ
  • etc/forehead.conf
  • %%JAVAJARDIR%%/erminej/antlr.jar
  • %%JAVAJARDIR%%/erminej/baseCode.jar
  • %%JAVAJARDIR%%/erminej/colt.jar
  • %%JAVAJARDIR%%/erminej/commons-beanutils.jar
  • %%JAVAJARDIR%%/erminej/commons-cli.jar
  • %%JAVAJARDIR%%/erminej/commons-collections.jar
  • %%JAVAJARDIR%%/erminej/commons-configuration.jar
  • %%JAVAJARDIR%%/erminej/commons-io.jar
  • %%JAVAJARDIR%%/erminej/commons-lang3.jar
  • %%JAVAJARDIR%%/erminej/commons-logging.jar
  • %%JAVAJARDIR%%/erminej/commons-math3.jar
  • %%JAVAJARDIR%%/erminej/commons-net.jar
  • %%JAVAJARDIR%%/erminej/ermineJ.jar
  • %%JAVAJARDIR%%/erminej/forehead.jar
  • %%JAVAJARDIR%%/erminej/gemma-core.jar
  • %%JAVAJARDIR%%/erminej/gemma-gsec.jar
  • %%JAVAJARDIR%%/erminej/javax.activation-api.jar
  • %%JAVAJARDIR%%/erminej/jaxb-api.jar
  • %%JAVAJARDIR%%/erminej/jcl-over-slf4j.jar
  • %%JAVAJARDIR%%/erminej/jcommon.jar
  • %%JAVAJARDIR%%/erminej/jfreechart.jar
  • %%JAVAJARDIR%%/erminej/jsontools-core.jar
  • %%JAVAJARDIR%%/erminej/log4j.jar
  • %%JAVAJARDIR%%/erminej/mtj.jar
  • %%JAVAJARDIR%%/erminej/opencsv.jar
  • %%JAVAJARDIR%%/erminej/slf4j-api.jar
  • %%JAVAJARDIR%%/erminej/slf4j-log4j12.jar
  • %%JAVAJARDIR%%/erminej/xercesImpl.jar
  • %%JAVAJARDIR%%/erminej/xml-apis.jar
distinfo 1
FileSizeSHA256
ermineJ-3.2-generic-bundle.zip1.4314004e+076e711b100e7619863ad2730714cdfa466115b563c146cb20a30488780504d5ac
Master sites 1
  • http://home.pavlab.msl.ubc.ca/ermineJ/distributions/

Commit history 1

DateCommitCreditsLog message
2414383046 Jason W. Bacon Release numerous ports to ports@
I've been retired for a few years, and it is unlikely I will be doing any more scientific computing support in the future. I have continued to maintain ~160 ports to the best of my ability, mainly as a favor to the community, but I can no longer justify the time and effort required. I am therefore releasing most of my scientific ports, along with a few others, to ports@. I will continue to maintain ports I am actively using and those for which I am upstream.