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Package Details: emboss 6.6.0-2
| Git Clone URL: | https://aur.archlinux.org/emboss.git (read-only) |
|---|---|
| Package Base: | emboss |
| Description: | A collection of molecular biology applications |
| Upstream URL: | http://emboss.sourceforge.net/ |
| Licenses: | |
| Submitter: | Allan |
| Maintainer: | mschu |
| Last Packager: | mschu |
| Votes: | 17 |
| Popularity: | 0.381616 |
| First Submitted: | 2008-12-28 12:20 |
| Last Updated: | 2019-01-09 20:14 |
Dependencies (8)
- gd
- java-runtime (server-jre, jdk5, zulu-jdk, jdk9-openj9-bin, jdk7, jre7, jre6, tuxjdk, jre7-openjdk-infinality, java-8-openjdk-shenandoah, jre8-openjdk-infinality, java-gcj-compat, jdk-dcevm, jdk10-openjdk-openj9-bin, jre8-openjdk-shenandoah, jdk9, jre9, jdk8-j9-bin, jre8-openjdk-jetbrains, jdk-devel, jdk8-openj9-bin, jdk11-openj9-bin, jre, jdk7-j9-bin, jdk7r1-j9-bin, jdk8-arm64, jdk10, jdk-arm, graal-bin, java-openjdk-ea-bin, jre10, jdk8, jdk6, jre8, intellij-jdk, jre-openjdk, jre10-openjdk, jre7-openjdk, jre8-openjdk)
- pcre (pcre-svn)
- java-environment (jdk5, zulu-jdk, jdk9-openj9-bin, jdk7, tuxjdk, jdk7-openjdk-infinality, java-8-openjdk-shenandoah, jdk8-openjdk-infinality, java-gcj-compat, jdk-dcevm, jdk10-openjdk-openj9-bin, jdk8-openjdk-shenandoah, jdk9, zulu-10-bin, jdk8-j9-bin, jdk8-openjdk-jetbrains, jdk-devel, zulu-11-bin, jdk8-openj9-bin, jdk11-openj9-bin, jdk7-j9-bin, jdk7r1-j9-bin, jdk, jdk8-arm64, jdk10, jdk-arm, graal-bin, java-openjdk-ea-bin, jdk8, jdk6, intellij-jdk, jdk-openjdk, jdk10-openjdk, jdk7-openjdk, jdk8-openjdk) (make)
- libmariadbclient (libmysqlclient, libmysqlclient57, libmysqlclient56, libmysqlclient55, libmariadbclient-mainline-noconflict, libmariadb-10.3, mariadb-libs) (make)
- postgresql-libs (postgresql-git, agensgraph-git, postgresql-9.5, postgresql-beta-libs, postgresql-src-beta-libs, postgresql-lts-libs, postgresql-9.3, postgresql-9.6, postgresql-libs-1c, postgresql-src-libs, postgresql-9.4, postgresql-libs-10) (make)
- libmariadbclient (libmysqlclient, libmysqlclient57, libmysqlclient56, libmysqlclient55, libmariadbclient-mainline-noconflict, libmariadb-10.3, mariadb-libs) (optional)
- postgresql-libs (postgresql-git, agensgraph-git, postgresql-9.5, postgresql-beta-libs, postgresql-src-beta-libs, postgresql-lts-libs, postgresql-9.3, postgresql-9.6, postgresql-libs-1c, postgresql-src-libs, postgresql-9.4, postgresql-libs-10) (optional)
Latest Comments
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anadon commented on 2018-04-30 22:24
There is a file conflict between this and 'texlive-latexextra' on '/usr/bin/wordcount' which needs to be addressed.
mschu commented on 2018-03-02 10:21
emboss now puts its .h files in /usr/include/emboss/*. This should solve all conflicting headers, and libs work on my machine.
anadon commented on 2018-02-28 18:29
@mschu Please merge in previous commenter's fixes for this package. But this doesn't fully fix the problem.
Rhinoceros commented on 2016-09-05 06:35
Like two previous commentators, install failed because installation of /usr/bin/showdb conflicts with sqlite. IMO there really shouldn't be conflicts with official packages, especially when it's something as common as sqlite.
I fixed it by just installing /usr/bin/showdb under a different name. IMO it shouldn't be in `/opt`, because there will still be problems with conflicting binaries in $PATH, although @antony's suggestion is not bad.
--- emboss.orig/PKGBUILD 2016-04-25 19:10:09.000000000 +1000
+++ emboss/PKGBUILD 2016-09-05 16:09:49.756095544 +1000
@@ -30,4 +30,5 @@
make DESTDIR="$pkgdir" install
rm -f "$pkgdir/usr/include/{pcre,pcreposix}.h"
+ mv "$pkgdir"/usr/bin/showdb{,-emboss}
}
slackalaxy commented on 2016-06-17 10:29
hobbypunk,
I maintain EMBOSS and EMBASSY for Slackware at SlackBuilds.org and I uploaded their sources to SF here:
https://sourceforge.net/projects/sboppetrov/files/EMBOSS/
The link you provided may not be active in the near future.
-Petar
anntzer commented on 2016-05-05 17:38
This currently conflicts with the widely used sqlite because of the presence of /usr/bin/showdb.
Because this package provides so many executables in /usr/bin, perhaps it would make sense to rename them as /usr/bin/emboss-*?
hobbypunk commented on 2015-12-09 22:53
please update the link to:
http://www.student.oulu.fi/~ppetrov/source/EMBOSS-6.6.0/EMBOSS-6.6.0.tar.gz
the md5sum is the same ;)
hobbypunk commented on 2015-10-21 19:57
Hey, there are 2 little problems with your PKGBUILD, the source is offline, here is one that works "http://science-annex.org/pub/emboss/" and you should switch from "/usr" to "/opt/emboss", without the showdb file conflicts with showdb from sqlite
anadon commented on 2013-10-17 17:17
The 6.5.7 package has moved to the old directory. The new one is located at this link:
ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-6.6.0.tar.gz
mschu commented on 2013-09-03 09:26
I don't see why this should be out of date. Download fails, but the EMBOSS webpage still links the same version, so this is an upstream fault and not one of the package.