Hi there, I would like to submit this little ebuild for a simple program (clover) useful in finding profiles and functional sites into DNA sequences. Writing to the author, about the license, emerges that it *should* be public-domain: [...] I am afraid Clover has no official, specific license. The reason is that I would like it to be totally free in the public domain, but Boston University would probably disagree. The best fudge I could come up with was to put the source code on the web, so it is de-facto public domain. [...] As you use this software you always have to specify the path to a certain file (motif database). I've suggested a patch to the author so that this file can be specified either as environmental variable or command line option.
Created attachment 93118 [details] the ebuild for clover this is the *raw* ebuild, without patching instructions.
Created attachment 93119 [details, diff] this is the patch to have motif file in env variable In a multiuser environment this patch can be useful, so that you don't have to tell each time where the motif file is to every user, biologist like me tend to forget quite soon this kind of things ;-) Actually clover author doesn't think it is that useful, and he haven't released a patched version. Since there is no license except a public-domain one, I don't really know if the patch can be distributed, you should know this better than me ;-)
Created attachment 113365 [details] clover-2006.07.17.ebuild Edit to simplify and conform to Gentoo standards
The latest version will be available at http://www.gentoo-sunrise.org/sunrise/browser/sunrise/sci-biology/clover
NB: Because sci-biology/transfac is now available, and this package can use TRANSFAC data, it should be integrated and a use flag predicated dependency put in. However, I'm not clear on how the transfac files can be translated into clover readable PSSMs, or even whether sci-biology/transfac contains the needed data.
/usr/share/transfac-3/matrix.dat is the data file needed, and conversion seems to be trivial. I'll provide an update later.
>>> Emerging (2 of 4) sci-biology/clover-2006.07.17 * jaspar2005core RMD160 SHA1 SHA256 size ;-) ... [ ok ] * clover-2006-07-17.tar.gz RMD160 SHA1 SHA256 size ;-) ... [ ok ] * checking ebuild checksums ;-) ... [ ok ] * checking auxfile checksums ;-) ... [ ok ] * checking miscfile checksums ;-) ... [ ok ] >>> Unpacking source... >>> Unpacking clover-2006-07-17.tar.gz to /var/tmp/portage/sci-biology/clover-2006.07.17/work sed: can't read Makefile: No such file or directory * * ERROR: sci-biology/clover-2006.07.17 failed. * Call stack: * ebuild.sh, line 49: Called src_unpack * environment, line 988: Called die * The specific snippet of code: * sed -i "s:g++:$(tc-getCXX):; s:-Wall -O3:${CFLAGS}:" Makefile || die "sed failed" * The die message: * sed failed * * If you need support, post the topmost build error, and the call stack if relevant. * A complete build log is located at '/var/tmp/portage/sci-biology/clover-2006.07.17/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-biology/clover-2006.07.17/temp/environment'. * This ebuild is from an overlay: '/usr/local/portage/layman/sunrise/' * >>> Failed to emerge sci-biology/clover-2006.07.17, Log file: after adding one line to the ebuild into the src_unpack function I got a bit further: >>> Emerging (1 of 3) sci-biology/clover-2006.07.17 * jaspar2005core RMD160 SHA1 SHA256 size ;-) ... [ ok ] * clover-2006-07-17.tar.gz RMD160 SHA1 SHA256 size ;-) ... [ ok ] * checking ebuild checksums ;-) ... [ ok ] * checking auxfile checksums ;-) ... [ ok ] * checking miscfile checksums ;-) ... [ ok ] >>> Unpacking source... >>> Unpacking clover-2006-07-17.tar.gz to /var/tmp/portage/sci-biology/clover-2006.07.17/work >>> Source unpacked. >>> Compiling source in /var/tmp/portage/sci-biology/clover-2006.07.17/work/clover-2006-07-17 ... make i686-pc-linux-gnu-g++ -O2 -march=pentium4 -mmmx -msse -msse2 -fomit-frame-pointer -pipe -DNDEBUG -o clover *.cpp In file included from args.cpp:8: MCFgen.hpp: In function ‘void mcf::die(const std::string&)’: MCFgen.hpp:57: error: ‘EXIT_FAILURE’ was not declared in this scope MCFgen.hpp:57: error: ‘exit’ was not declared in this scope In file included from count_oligos.cpp:7: MCFgen.hpp: In function ‘void mcf::die(const std::string&)’: MCFgen.hpp:57: error: ‘EXIT_FAILURE’ was not declared in this scope MCFgen.hpp:57: error: ‘exit’ was not declared in this scope In file included from normalize_pssm.cpp:8: MCFgen.hpp: In function ‘void mcf::die(const std::string&)’: MCFgen.hpp:57: error: ‘EXIT_FAILURE’ was not declared in this scope MCFgen.hpp:57: error: ‘exit’ was not declared in this scope make: *** [clover] Error 1 * * ERROR: sci-biology/clover-2006.07.17 failed.
Created attachment 174464 [details] clover-2006.07.17.ebuild added just the "cd ${S}" line to the ebuild which is currently in sunrise
Created attachment 241027 [details] clover-2010.02.19.ebuild Version bump.
The ebuild is both in Sunrise and Science overlays. How shall we resolve this?
For sunrise it doesn't matter, it can remain in the sunrise overlay as long as it does not enter portage.
(In reply to comment #11) > For sunrise it doesn't matter, it can remain in the sunrise overlay as long as > it does not enter portage. > Too late, it's already gone. :)
Bumped in sci overlay.
You really aren't supposed to remove packages from Sunrise without prior masking unless they are moved to gx86. Otherwise, there is a risk that some users will end up with missing packages without a tip where to find a new one.
