Could someone introduce ebuld for bjplot program? This package should be required by wemboss package (wemboss is cgi wrapper around emboss package, provided by gentoo already; wemboss and njplot are not). http://pbil.univ-lyon1.fr/software/njplot.html ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/njplot/ www.wemboss.org
please look at the EBUILD howto on http://www.gentoo.org/proj/en/devrel/handbook/handbook.xml and see if you can make one.
Hi Martin, I will try to have a look at wEMBOSS during the holidays. As Daniel said, things might go faster if you can provide an ebuild yourself. njplot is already available in Portage in the njplot-unrooted package. You can use the search function of emerge to find packages (for instance "emerge -s njplot").
dis anything happen with this: jut looking at wEmboss myself
wEMBOSS is an awfull mess. EMBOSS is not better. :( The configuration file for EMBOSS is not used by wEMBOSS, so you have to configure all your databases twice, if you wish to use both. Personally I configured only wEMBOSS, as it's enough for me. I needed a patch on SMP machine to fix child processes not returning to the parent, causing that no output was collected by wEMBOSS wrapper and browser was just waiting for data (empty screen). I'll attach the patch. wEMBOSS developers, emailed twice by me with the patch attach never bothered to respond. :( I'm attaching the patches and my "*answers" file (the way to install wEMBOSS without configure). ;)
Created attachment 56062 [details, diff] patch to install wEMBOSS easily
Created attachment 56063 [details] wEMBOSS-answers file used for installation of wEMBOSS
Created attachment 56064 [details] wrappers4EMBOSS-answers also used for installation
Created attachment 56066 [details, diff] patch to get around the bug when child processes do not return Was necessary on: linux 2.4.30-pre2-bk3 # perl -V Summary of my perl5 (revision 5 version 8 subversion 6) configuration: Platform: osname=linux, osvers=2.4.30-pre2-bk3, archname=i686-linux uname='linux oxygen 2.4.30-pre2-bk3 #3 smp mon mar 7 13:35:40 met 2005 i686 intel(r) xeon(tm) cpu 3.06ghz genuineintel gnulinux ' config_args='-des -Darchname=i686-linux -Dcccdlflags=-fPIC -Dccdlflags=-rdynamic -Dcc=gcc -Dprefix=/usr -Dvendorprefix=/usr -Dsiteprefix=/usr -Dlocincpth= -Doptimize=-march=pentium4 -mcpu=pentium4 -mmmx -msse -msse2 -msse3 -O3 -fomit-frame-pointer -funroll-loops -pipe -Duselargefiles -Dd_semctl_semun -Dscriptdir=/usr/bin -Dman1dir=/usr/share/man/man1 -Dman3dir=/usr/share/man/man3 -Dinstallman1dir=/usr/share/man/man1 -Dinstallman3dir=/var/tmp/portage/perl-5.8.6-r4/image//usr/share/man/man3 -Dman1ext=1 -Dman3ext=3pm -Dinc_version_list=5.8.0 5.8.0/i686-linux 5.8.2 5.8.2/i686-linux 5.8.4 5.8.4/i686-linux 5.8.5 5.8.5/i686-linux -Dcf_by=Gentoo -Ud_csh -Di_ndbm -Di_gdbm -Di_db' hint=recommended, useposix=true, d_sigaction=define usethreads=undef use5005threads=undef useithreads=undef usemultiplicity=undef useperlio=define d_sfio=undef uselargefiles=define usesocks=undef use64bitint=undef use64bitall=undef uselongdouble=undef usemymalloc=n, bincompat5005=undef Compiler: cc='gcc', ccflags ='-fno-strict-aliasing -pipe -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64', optimize='-march=pentium4 -mcpu=pentium4 -mmmx -msse -msse2 -msse3 -O3 -fomit-frame-pointer -funroll-loops -pipe', cppflags='-DPERL5 -fno-strict-aliasing -pipe' ccversion='', gccversion='3.3.4 20040623 (Gentoo Linux 3.3.4-r1, ssp-3.3.2-2, pie-8.7.6)', gccosandvers='' intsize=4, longsize=4, ptrsize=4, doublesize=8, byteorder=1234 d_longlong=define, longlongsize=8, d_longdbl=define, longdblsize=12 ivtype='long', ivsize=4, nvtype='double', nvsize=8, Off_t='off_t', lseeksize=8 alignbytes=4, prototype=define Linker and Libraries: ld='gcc', ldflags =' -L/usr/local/lib' libpth=/usr/local/lib /lib /usr/lib libs=-lpthread -lnsl -lndbm -lgdbm -ldb -ldl -lm -lcrypt -lutil -lc perllibs=-lpthread -lnsl -ldl -lm -lcrypt -lutil -lc libc=/lib/libc-2.3.4.so, so=so, useshrplib=false, libperl=libperl.a gnulibc_version='2.3.4' Dynamic Linking: dlsrc=dl_dlopen.xs, dlext=so, d_dlsymun=undef, ccdlflags='-rdynamic' cccdlflags='-fPIC', lddlflags='-shared -L/usr/local/lib' Characteristics of this binary (from libperl): Compile-time options: USE_LARGE_FILES Built under linux Compiled at Mar 16 2005 11:03:46 @INC: /etc/perl /usr/lib/perl5/site_perl/5.8.6/i686-linux /usr/lib/perl5/site_perl/5.8.6 /usr/lib/perl5/site_perl/5.8.2 /usr/lib/perl5/site_perl/5.8.2/i686-linux /usr/lib/perl5/site_perl/5.8.4 /usr/lib/perl5/site_perl/5.8.5 /usr/lib/perl5/site_perl/5.8.5/i686-linux /usr/lib/perl5/site_perl /usr/lib/perl5/vendor_perl/5.8.6/i686-linux /usr/lib/perl5/vendor_perl/5.8.6 /usr/lib/perl5/vendor_perl/5.8.2 /usr/lib/perl5/vendor_perl/5.8.2/i686-linux /usr/lib/perl5/vendor_perl /usr/lib/perl5/5.8.6/i686-linux /usr/lib/perl5/5.8.6 /usr/local/lib/site_perl /usr/lib/perl5/site_perl/5.8.2 /usr/lib/perl5/site_perl/5.8.2/i686-linux /usr/lib/perl5/site_perl/5.8.4 /usr/lib/perl5/site_perl/5.8.5 /usr/lib/perl5/site_perl/5.8.5/i686-linux . # emerge info Portage 2.0.51.19 (default-linux/x86/2004.0, gcc-3.3.4, glibc-2.3.4.20050125-r0, 2.4.30-pre2-bk3 i686) ================================================================= System uname: 2.4.30-pre2-bk3 i686 Intel(R) Xeon(TM) CPU 3.06GHz Gentoo Base System version 1.6.9 Python: dev-lang/python-2.3.5 [2.3.5 (#1, Feb 18 2005, 20:07:19)] dev-lang/python: 2.3.5 sys-devel/autoconf: 2.59-r6, 2.13 sys-devel/automake: 1.6.3, 1.7.9-r1, 1.5, 1.4_p6, 1.8.5-r3, 1.9.5 sys-devel/binutils: 2.15.92.0.2-r4 sys-devel/libtool: 1.5.14 virtual/os-headers: 2.4.22-r1 ACCEPT_KEYWORDS="x86 ~x86" AUTOCLEAN="yes" CFLAGS="-march=pentium4 -mcpu=pentium4 -mmmx -msse -msse2 -msse3 -O3 -fomit-frame-pointer -funroll-loops -pipe" CHOST="i686-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/kde/2/share/config /usr/kde/3/share/config /usr/lib/X11/xkb /usr/lib/mozilla/defaults/pref /usr/share/config /usr/share/texmf/dvipdfm/config/ /usr/share/texmf/dvips/config/ /usr/share/texmf/tex/generic/config/ /usr/share/texmf/tex/platex/config/ /usr/share/texmf/xdvi/ /var/bind /var/qmail/alias /var/qmail/control" CONFIG_PROTECT_MASK="/etc/afs/C /etc/afs/afsws /etc/gconf /etc/terminfo /etc/env.d" CXXFLAGS="-march=pentium4 -mcpu=pentium4 -mmmx -msse -msse2 -msse3 -O3 -fomit-frame-pointer -funroll-loops -pipe" DISTDIR="/usr/portage/distfiles" FEATURES="autoaddcvs autoconfig ccache distlocks sandbox sfperms" GENTOO_MIRRORS="http://gentoo.mirror.icd.hu/ http://ftp-stud.fht-esslingen.de/pub/Mirrors/gentoo/ http://gd.tuwien.ac.at/opsys/linux/gentoo/ ftp://ftp.tu-clausthal.de/pub/linux/gentoo/" MAKEOPTS="-j2" PKGDIR="/usr/portage/packages" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="x86 FFmpeg X Xaw3d aalib acpi afs alsa apache2 apm arts ati avi berkdb bidi bitmap-fonts caca cdparanoia cdr crypt cscope cups curl dba dga directfb divx divx4 divx4linux divx5 divx5linux doc dvb dvd dvdr dvdread emacs emacs-w3 emboss encode esd ethereal evo f77 faad faad2 fam fame fbcon ffmpeg flac flash font-server foomaticdb fortran fvwm fvwm2 g77 gb gcj gd gdbm ggi gif gphoto2 gpm gstreamer gtk gtk2 gtkhtml guile i8x0 icc imagemagick imlib imlib2 innodb java jpeg junit lcms leim libg++ libwww live lzo mad mcal mesa mikmod mmx mmx2 motif mozilla mp3 mpeg mule mysql ncurses network nls oggvorbis opengl oss pam pda pdflib perl php php4 plotutils png postgres ppds python qt qtx quicktime readline rtc samba sdl slang slp spell sse sse2 sse3 ssl svga tcltk tcpd tetex theora tiff truetype truetype-fonts type1-fonts unicode usb v4l v4l2 win32 winvidix wmf xml xml2 xmms xosd xv xvid xvmc zeo zlib video_cards_radeon" Unset: ASFLAGS, CBUILD, CTARGET, LANG, LC_ALL, LDFLAGS, PORTDIR_OVERLAY #
Created attachment 56067 [details] how I installed underlying EMBOSS Note that to relocate EMBOSS into different target $prefix (here set to /afs/.biomed.cas.cz/i386_linux24/bio/EMBOSS-2.9.0), you have to set the EMBOSSRC, otherwise EMBOSS cannot find itself (I believe this would be nice to append just for completeness and clarity to /etc/env.d/22emboss, when emboss get's installed). export EMBOSSRC=/afs/.biomed.cas.cz/i386_linux24/bio/EMBOSS-2.9.0/share/EMBOSS cd /afs/.biomed.cas.cz/i386_linux24/bio/EMBOSS-2.9.0/share/EMBOSS ln -s emboss.default .embossrc
I am not dead, but this slipped off my mind for a while, and then I was gone to the ENC. I will have a look at this soon, but if the installation is another Staden Package-like nightmare (why cannot we biologists come up with decent packaging for our software?), I am not sure I will want to invest the time required to make it work out-off-the-box on Gentoo. :(
Yes, it's a bit messy, but maybe easier to configure than EMBOSS itself. An I forgot to note you need to update apache config files to set webroot and cgi-root. But that is somewhat documented in the docs.
