"sci-biology/t-coffee-2.66" should be stabilised on supporting arches.
Could you provide some sort of test to preform? I must admit I've got no clue what this package does, and the description just loses me more :) Can you give a testcase for functionality checks?
Links to a random sample of .fasta and .aln files would be nice. Preferably ones that are know to be of correct Syntax and format, and play nice with the available online servers. We can Read the manual to get the execution sequence. Also, after completion, how do we know it is correct. (For all us "ribosome is a thing in a Cell Right" kinda people)
Created attachment 70497 [details] sample_seq1.aln - Sample sequence alignment for testing Sure :) After compiling t-coffee, copy the "sample_seq1.fasta" file from "/usr/share/t-coffee/example" to your home directory. This file contains the amino acid sequences for four homologs of a protein in different species. Run "t_coffee sample_seq1.fasta" to have t-coffee align the sequences, calculate the alignment scores, construct a dendrogram, etc. Output files are created in the working directory. At the end, file "t_coffee.log" should contain only the names of the aligned proteins, no error or warning message. You can check the validity of the calculations by comparing the file "sample_seq1.aln" with the file I am attaching. (This output file is also available in the example directory, but it was created with an old version of the program, and the formatting is a bit different so you would have to compare the files manually. With the provided file, a diff should suffice.) The only difference between the files should be the CPU time used for the calculations. (And even this may not differ since small calculations like those require almost 0 CPU time.) Thanks,
Thanks :) Working fine for me here... no difference at all between the two, and no errors/warnings when running any of the tests here Portage 2.0.53_rc5 (default-linux/x86/2005.1, gcc-3.3.6, glibc-2.3.5-r1, 2.6.12-9-386 i686) ================================================================= System uname: 2.6.12-9-386 i686 AMD Athlon(tm) XP 2500+ Gentoo Base System version 1.6.13 dev-lang/python: 2.3.5-r2, 2.4.1-r1 sys-apps/sandbox: 1.2.12 sys-devel/autoconf: 2.13, 2.59-r6 sys-devel/automake: 1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r1 sys-devel/binutils: 2.15.92.0.2-r10 sys-devel/libtool: 1.5.18-r1 virtual/os-headers: 2.6.11-r2 ACCEPT_KEYWORDS="x86" AUTOCLEAN="yes" CBUILD="i686-pc-linux-gnu" CFLAGS="-O2 -march=athlon-xp -pipe" CHOST="i686-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/kde/2/share/config /usr/kde/3/share/config /usr/share/config /var/qmail/control" CONFIG_PROTECT_MASK="/etc/gconf /etc/env.d" CXXFLAGS="-O2 -march=athlon-xp -pipe" DISTDIR="/usr/portage/distfiles" FEATURES="autoconfig distlocks maketest sandbox sfperms strict test" GENTOO_MIRRORS="http://gentoo.mirrors.pair.com http://gentoo.mirrors.tds.net" LANG="en_US.UTF-8" PKGDIR="/usr/portage/packages" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="x86 X alsa apache2 apm arts avi berkdb bitmap-fonts crypt curl eds emboss encode fam flac foomaticdb fortran gd gdbm gif gnome gpm gstreamer gtk gtk2 imlib ipv6 jpeg kde libg++ libwww mad mikmod motif mp3 mpeg mysql ncurses nls ogg oggvorbis opengl oss pam pdflib perl png python qt quicktime readline sdl spell ssl tcpd truetype truetype-fonts type1-fonts vorbis xine xml2 xmms xv zlib userland_GNU kernel_linux elibc_glibc" Unset: ASFLAGS, CTARGET, LC_ALL, LDFLAGS, LINGUAS, MAKEOPTS, PORTDIR_OVERLAY
For the sake of completeness, Oliver could you provide a more taxing sequence to 'stress test' t_coffee, Perhaps one that would take 15min of cpu time. Completed simple test as per Oliver. No Errors, compiled without issue. Portage 2.0.51.22-r3 (default-linux/x86/2005.0, gcc-3.3.6, glibc-2.3.5-r2, 2.6.11-hardened-r15 i686) ================================================================= System uname: 2.6.11-hardened-r15 i686 AMD Athlon(tm) XP 2200+ Gentoo Base System version 1.6.13 distcc 2.18.3 i686-pc-linux-gnu (protocols 1 and 2) (default port 3632) [disabled] ccache version 2.3 [disabled] dev-lang/python: 2.3.5-r2, 2.4.1-r1 sys-apps/sandbox: 1.2.12 sys-devel/autoconf: 2.13, 2.59-r6 sys-devel/automake: 1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r1 sys-devel/binutils: 2.15.92.0.2-r10 sys-devel/libtool: 1.5.18-r1 virtual/os-headers: 2.6.11-r2 ACCEPT_KEYWORDS="x86" AUTOCLEAN="yes" CBUILD="i686-pc-linux-gnu" CFLAGS="-O2 -mcpu=athlon-xp -march=athlon-xp -pipe -fomit-frame-pointer" CHOST="i686-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/kde/2/share/config /usr/kde/3/share/config /usr/share/config /var/bind /var/qmail/control" CONFIG_PROTECT_MASK="/etc/gconf /etc/terminfo /etc/env.d" CXXFLAGS="-O2 -mcpu=athlon-xp -march=athlon-xp -pipe -fomit-frame-pointer" DISTDIR="/usr/portage/distfiles" FEATURES="autoconfig distlocks sandbox sfperms strict" GENTOO_MIRRORS="http://distfiles.gentoo.org http://distro.ibiblio.org/pub/Linux/distributions/gentoo" PKGDIR="/usr/portage/packages" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="x86 alsa apache2 apm arts avi berkdb bitmap-fonts crypt cups curl doc eds emboss encode foomatic foomaticdb fortran gd gdbm gif gpm gstreamer imagemagick imlib innodb ipv6 jpeg libg++ libwww mad mikmod motif mp3 mpeg mysql ncurses nls ogg oggvorbis opengl oss pam pdflib perl png postgres ppds python pyton quicktime readline samba sdl spell ssl tcpd tiff truetype truetype-fonts type1-fonts vorbis xml2 xmms xv zlib userland_GNU kernel_linux elibc_glibc" Unset: ASFLAGS, CTARGET, LANG, LC_ALL, LDFLAGS, LINGUAS, MAKEOPTS, PORTDIR_OVERLAY
Created attachment 70521 [details] glxrs.fasta - Sample sequences for testing
Created attachment 70522 [details] glxrs.aln - Sample sequence alignment for testing Why not? Let us align 32 sequences, and iterate the process by extracting each sequence in turn and realigning it with the multiple sequence alignment (after the initial MSA is computed). Download the "glxrs.fasta" file and execute: "t_coffee -iterate -1 -seq glxrs.fasta". You can then compare the resulting alignment with the one I am attaching.
New Test completed. No Errors/warnings. Same emerge info as above. No need to restate. Recommend Stable.
x86 done
Thanks for the tests, Lares. (BTW, stabilise is the correct ortograph in British/European/Australian English. Stabilize is the American ortograph. ;-)
Seems to work alright on ppc too, thanks for giving us something to test with. :)
All arches are done.
