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: 19
Popularity: 0.000881
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

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 ;)

hobbypunk commented on 2015-10-21 19:57 (UTC)

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 (UTC)

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 (UTC)

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.

commented on 2012-09-05 08:14 (UTC)

There is a new version available: pkgver=6.5.7 md5sums=('6a2cb3f93d5e9415c74ab0f6b1ede5f0') But makepkg still fails with this error message: configure: error: Java OS include directory /usr/lib/jvm/java-7-openjdk/include/linux does not exist ==> ERROR: A failure occurred in build(). Aborting...

mschu commented on 2012-06-29 16:48 (UTC)

Thank you for the message, install seems to have changed its location. Updated.

benwbooth commented on 2012-06-29 15:28 (UTC)

The install tool is located at /usr/bin/install instead of /bin/install. I had to delete the last line of the build() function to get this package to build correctly.

commented on 2011-12-20 23:55 (UTC)

I can adopt it :)

commented on 2011-10-18 18:02 (UTC)

Adopted (but I do not use this program, so if someone who uses it is interested, I'd orphan).

commented on 2011-10-18 17:41 (UTC)

Adopted (but I do not use this program, so if someone who uses it is interested, I'd orphan).

commented on 2011-08-01 14:28 (UTC)

So I answer to myself after an email I got from @duca After downloading EMBOSS-6.4.0.tar.gz I did a md5sum name_of_emboss_version and replaced the md5sum in the pkbuild by the one I got from the command, after that pkbuild worked... anyways, please update the pkbuild here this is the md5sum 54993a22064222b01bd4fc8086f7684d

commented on 2011-07-25 21:39 (UTC)

this is out of date, new emboss out is 6.4 and can be found here ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-6.4.0.tar.gz My doubt is, where do I get the md5sum number? cheers

commented on 2011-01-11 14:06 (UTC)

updated to v.6.3.1

duca commented on 2010-12-16 00:55 (UTC)

guys, since this program is not of use for me anymore, i would like to hand it over. You are free to adopt it.

commented on 2010-11-07 21:39 (UTC)

@rent0n: theres is a new version online (since 7/19) and you have to edit the PKGUILD. Here is my edited PKGBUILD for version 3.6.1: http://aur.pastebin.com/bzReXLBB

commented on 2010-10-23 17:56 (UTC)

Emboss can't be downloaded: ┌─[enrico@aspire][~] └─[$] aurget -S emboss resolving dependencies... searching AUR... Targets (1): emboss-6.2.0-2 Proceed with installation? [Y/n] :: Retrieving source tarball from AUR... --2010-10-23 15:50:15-- http://aur.archlinux.org/packages/emboss/emboss.tar.gz Resolving aur.archlinux.org... 208.92.232.29 Connecting to aur.archlinux.org|208.92.232.29|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 620 [application/x-tgz] Saving to: `/home/enrico/.aur/emboss.tar.gz' 100%[===============================================================>] 620 --.-K/s in 0s 2010-10-23 15:50:16 (55.7 MB/s) - `/home/enrico/.aur/emboss.tar.gz' saved [620/620] :: Extracting source tarball... :: Building package... ==> Making package: emboss 6.2.0-2 (Sat Oct 23 15:50:16 BST 2010) ==> Checking Runtime Dependencies... ==> Checking Buildtime Dependencies... ==> Retrieving Sources... -> Downloading EMBOSS-6.2.0.tar.gz... --2010-10-23 15:50:16-- ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-6.2.0.tar.gz => `EMBOSS-6.2.0.tar.gz.part' Resolving emboss.open-bio.org... 208.94.50.58 Connecting to emboss.open-bio.org|208.94.50.58|:21... connected. Logging in as anonymous ... Logged in! ==> SYST ... done. ==> PWD ... done. ==> TYPE I ... done. ==> CWD (1) /pub/EMBOSS ... done. ==> SIZE EMBOSS-6.2.0.tar.gz ... done. ==> PASV ... done. ==> RETR EMBOSS-6.2.0.tar.gz ... No such file `EMBOSS-6.2.0.tar.gz'. ==> ERROR: Failure while downloading EMBOSS-6.2.0.tar.gz Aborting... Also, please update the package. Any news about Jemboss? Thank you!

commented on 2010-09-29 11:57 (UTC)

Hi here's an up to date PKGBUILD (with sun jdk) : http://aur.pastebin.com/D9XKwneL Many thanks for the original PKGBUILD

duca commented on 2010-05-22 21:08 (UTC)

sorry for not answering you before, i will try to come up with one as soon as possible.

commented on 2010-05-02 11:46 (UTC)

any chances for a Jemboss PKGBUILD?