Bug 206521

Summary:	new ebuild: sci-biology/exonerate
Product:	Gentoo Linux	Reporter:	dawe <daweonline>
Component:	New packages	Assignee:	Default Assignee for New Packages <maintainer-wanted>
Status:	RESOLVED FIXED
Severity:	enhancement	CC:	daweonline, sci-biology
Priority:	High	Keywords:	EBUILD
Version:	unspecified
Hardware:	All
OS:	Linux
URL:	http://www.ebi.ac.uk/~guy/exonerate/
Whiteboard:
Package list:		Runtime testing required:	---
Attachments:	The ebuild for exonerate 1.4.0

Description dawe 2008-01-18 12:22:12 UTC

This is the ebuild for exonerate, a generic tool for pairwise sequence comparison.


Reproducible: Always




emerge --info
Portage 2.1.4_rc14 (default-linux/x86/no-nptl, gcc-4.2.2, glibc-2.5-r4, 2.6.19-gentoo-r4-smp i686)
=================================================================
System uname: 2.6.19-gentoo-r4-smp i686 Intel(R) Xeon(TM) CPU 3.06GHz
Timestamp of tree: Tue, 08 Jan 2008 10:16:01 +0000
app-shells/bash:     3.2_p33
dev-java/java-config: 1.3.7, 2.1.3
dev-lang/python:     2.4.4, 2.5.1-r5
dev-python/pycrypto: 2.0.1-r6
sys-apps/baselayout: 1.12.10-r5
sys-apps/sandbox:    1.2.18.1-r2
sys-devel/autoconf:  2.13, 2.61-r1
sys-devel/automake:  1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.9.6-r2, 1.10
sys-devel/binutils:  2.18-r1
sys-devel/gcc-config: 1.4.0-r4
sys-devel/libtool:   1.5.24
virtual/os-headers:  2.6.23-r3
ACCEPT_KEYWORDS="x86 ~x86"
CBUILD="i686-pc-linux-gnu"
CFLAGS="-march=pentium4 -O2 -fomit-frame-pointer -pipe"
CHOST="i686-pc-linux-gnu"
CONFIG_PROTECT="/etc"
CONFIG_PROTECT_MASK="/etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/revdep-rebuild /etc/terminfo /etc/texmf/web2c /etc/udev/rules.d"
CXXFLAGS="-march=pentium4 -O2 -fomit-frame-pointer -pipe"
DISTDIR="/usr/portage/distfiles"
FEATURES="distlocks metadata-transfer sandbox sfperms strict unmerge-orphans userfetch"
GENTOO_MIRRORS="http://mirror.switch.ch/ftp/mirror/gentoo http://distfiles.gentoo.org http://www.ibiblio.org/pub/Linux/distributions/gentoo"
MAKEOPTS="-j3"
PKGDIR="/usr/portage/packages"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --delete-after --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages --filter=H_**/files/digest-*"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/usr/local/portage"
SYNC="rsync://rsync.europe.gentoo.org/gentoo-portage"
USE="X apm arts berkdb bitmap-fonts cli cracklib crypt eds emboss encode foomaticdb fortran gdbm gif gpm gstreamer gtk gtk2 iconv imlib ipv6 isdnlog jpeg kde ldap libwww mad midi mikmod motif mp3 mpeg mudflap mysql ncurses nls ogg opengl openmp oss pam pcre perl png pppd python qt3 qt4 quicktime readline reflection session spell spl ssl tcpd threads truetype truetype-fonts type1-fonts vorbis x86 xml xorg xv zlib" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1 emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat linear meter mulaw multi null plug rate route share shm softvol" APACHE2_MODULES="actions alias auth_basic authn_alias authn_anon authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache dav dav_fs dav_lock deflate dir disk_cache env expires ext_filter file_cache filter headers include info log_config logio mem_cache mime mime_magic negotiation rewrite setenvif speling status unique_id userdir usertrack vhost_alias" ELIBC="glibc" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" USERLAND="GNU"
Unset:  CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, LDFLAGS, LINGUAS, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS

Comment 1 dawe 2008-01-18 12:23:34 UTC

Created attachment 141216 [details]
The ebuild for exonerate 1.4.0

I have keywords for alpha, x86, ia64 and amd64, although the emerge --info pasted is only for x86.

Comment 2 Jeffrey Gardner (RETIRED) gentoo-dev

2008-01-18 18:06:09 UTC

This looks like something I can use...
I'll put it in the science overlay for a couple of weeks of testing.

Comment 3 dawe 2008-01-19 19:16:20 UTC

(In reply to comment #2)
> This looks like something I can use...
> I'll put it in the science overlay for a couple of weeks of testing.
> 

Great! Please, note the emake -j1 in ebuild... it raises errors if you try parallel compiling!

d