Samtools has been successfully installed on my prefixed Gentoo system. Requesting keywords and minor ebuild modification. Reproducible: Always Steps to Reproduce: 1. ecopy sci-biology/samtools 2. apply patch (attached) 3. emerge samtools kowarsky@mac1684 ~ $ emerge --info Portage 2.2.01.17901-prefix (prefix/darwin/macos/10.5/x64, gcc-4.2.1, unavailable, 9.8.0 i386) ================================================================= System uname: Darwin-9.8.0-i386-64bit Timestamp of tree: Mon, 14 Feb 2011 22:12:50 +0000 distcc 2.18.5-Apple.1 powerpc-apple-darwin9.0 (protocols 1 and 2) (default port 3632) [disabled] app-shells/bash: 4.1_p7 dev-lang/python: 2.7.1-r00.1 sys-devel/autoconf: 2.68 sys-devel/automake: 1.11.1 sys-devel/gcc-config: 1.4.1-r00.2 sys-devel/libtool: 2.4-r1 sys-devel/make: 3.82 Repositories: gentoo_prefix local-overlay Installed sets: ACCEPT_KEYWORDS="~x64-macos" ACCEPT_LICENSE="* -@EULA" CBUILD="x86_64-apple-darwin9" CFLAGS="-O2 -pipe -march=nocona" CHOST="x86_64-apple-darwin9" CONFIG_PROTECT="/etc" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/gconf /etc/portage /etc/revdep-rebuild /etc/terminfo" CXXFLAGS="-O2 -pipe -march=nocona" DISTDIR="/Users/kowarsky/Gentoo/usr/portage/distfiles" FEATURES="assume-digests binpkg-logs collision-protect distlocks fixlafiles fixpackages news nostrip parallel-fetch preserve-libs protect-owned sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch" FFLAGS="" GENTOO_MIRRORS="http://distfiles.gentoo.org" LANG="en_AU.UTF-8" LDFLAGS="-Wl,-dead_strip_dylibs" MAKEOPTS="-j4" PKGDIR="/Users/kowarsky/Gentoo/usr/portage/packages" PORTAGE_CONFIGROOT="/Users/kowarsky/Gentoo/" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages" PORTAGE_TMPDIR="/Users/kowarsky/Gentoo/var/tmp" PORTDIR="/Users/kowarsky/Gentoo/usr/portage" PORTDIR_OVERLAY="/Users/kowarsky/Gentoo/usr/local/portage" SYNC="rsync://rsync.prefix.freens.org/gentoo-portage-prefix" USE="aqua coreaudio cracklib cxx mmx mmxext modules ncurses nls objc objc++ prefix readline sse sse2 ssl unicode x64-macos zlib" 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 cgi cgid 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" CAMERAS="ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" ELIBC="Darwin" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf superstar2 timing tsip tripmate tnt ubx" INPUT_DEVICES="keyboard mouse" KERNEL="Darwin" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" PHP_TARGETS="php5-3" RUBY_TARGETS="ruby18" USERLAND="GNU" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq steal rawnat logmark ipmark dhcpmac delude chaos account" Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, LINGUAS, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
Created attachment 262549 [details, diff] sed call in ebuild needed to fix shebang Should be self explanatory, the shebang in the python file distributed had the nonsense line executable "/software/bin/python", fixed it to something sane.
(In reply to comment #1) > Created an attachment (id=262549) [details] > sed call in ebuild needed to fix shebang > > Should be self explanatory, the shebang in the python file distributed had the > nonsense line executable "/software/bin/python", fixed it to something sane. > Thanks for the patch! That would be a general bug, assigning to maintainer. (please add ~x64-macos when you commit this fix, thanks)
Fixed in samtools-0.1.12a, thanks
