Package Details: emboss 6.6.0-3

Git Clone URL: https://aur.archlinux.org/emboss.git (read-only, click to copy)
Package Base: emboss
Description: A collection of molecular biology applications
Upstream URL: http://emboss.sourceforge.net/
Licenses: GPL2
Submitter: Allan
Maintainer: mschu
Last Packager: mschu
Votes: 20
Popularity: 0.003149
First Submitted: 2008-12-28 12:20 (UTC)
Last Updated: 2020-05-11 20:54 (UTC)

Dependencies (8)

Required by (0)

Sources (1)

Latest Comments

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slackalaxy commented on 2022-03-15 17:41 (UTC) (edited on 2022-03-15 17:47 (UTC) by slackalaxy)

hi guys, to avoid emboss installing binaries that conflict with something else, you can always install them to a custom location, e.g. /usr/lib/emboss/bin, by passing this at compile time:

--bindir=/usr/lib/emboss/bin

Simply renaming them will make them lost for wossname and jEmboss. To make jEmboss aware of it, you should sed a few lines in jemboss/resources/jemboss.properties after compilation is done. I use Crux at the moment, and I do this:

# Make jEmboss find the binaries
sed -i "s|/usr/bin/|/usr/lib/emboss/bin/|g" \
$PKG/usr/share/EMBOSS/jemboss/resources/jemboss.properties

sed -i "s|/usr/bin:|/usr/lib/emboss/bin:/usr/bin:|g" \
$PKG/usr/share/EMBOSS/jemboss/resources/jemboss.properties

for more info, here's my Pkgfile: https://github.com/slackalaxy/crux-ports/blob/main/scientific/emboss/Pkgfile

hope this is useful

-petar

Rhinoceros commented on 2020-05-11 07:57 (UTC)

I feel like history is repeating itself, but…

Like the two previous commentators (from over two years ago now!), install failed because installation of /usr/bin/wordcount conflicts with texlive-latexextra. IMO there really shouldn't be conflicts with official packages, especially when it's something as common as this.

I fixed it by just installing /usr/bin/wordcount under a different name:

mv "$pkgdir"/usr/bin/{,emboss_}wordcount

ironcyborg commented on 2020-02-10 14:35 (UTC)

The file conflict between this and 'texlive-latexextra' on '/usr/bin/wordcount' is unfortunately still present. Any suggestion?

anadon commented on 2018-04-30 22:24 (UTC)

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 (UTC)

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 (UTC) (edited on 2018-02-28 19:34 (UTC) by anadon)

@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 (UTC)

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 (UTC)

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 (UTC)

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 (UTC)

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 ;)

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