Multiple alignment of large DNA sequences
Created attachment 141697 [details] mavid-2.0.4.ebuild
requires out-of-tree dependency sci-biology/fastdnaml, still working on that license "UC" text follows in its entirety _______ Copyright B)2003. The Regents of the University of California (Regents). All Rights Reserved. Created by Nicolas Bray and Lior Pachter, Department of Mathematics, University of California, Berkeley. Permission is hereby granted to use, copy, modify, display and distribute this software and documentation for educational, academic and nonprofit purposes only, provided that the above copyright notice, this paragraph, and the following two paragraphs appear in all copies, modifications, displays and distributions. For use of this software and documentation for purposes other than educational purposes, contact the Office of Technology Licensing, UC Berkeley, 2150 Shattuck Avenue, Suite 510, Berkeley, CA 94720-1620; (510) 643-7201. IN NO EVENT SHALL REGENTS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF REGENTS HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. REGENTS SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE SOFTWARE AND ACCOMPANYING DOCUMENTATION, IF ANY, PROVIDED HEREUNDER IS PROVIDED "AS IS". REGENTS HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR MODIFICATIONS.
Now available in the science overlay.
Tested on x86. The source compiles fine, but it seems that the ebuild doesn't respect my CXXFLAGS. I include build log.
Created attachment 159905 [details] /var/log/portage/sci-biology:mavid-2.0.4:20080708-203009.log
Created attachment 159906 [details] /emerge-info
I see file collision with sci-libs/io_lib-1.12.2 because sci-biology/mavid-2.0.4 also installs /usr/bin/extract_seq file. # /var/tmp/portage/sci-biology/mavid-2.0.4/work/mavid-package-2.0.4/utils/extract_seq/extract_seq --help Usage: extract_seq [-i] <sequence file> region1 [region2 ... ] Extracts the specified regions of the sequences in the given file. A region is of the form "label", "label[start,end]", or "label[start,-1]" (in the latter case, the end position is taken to be the end of the sequence). If the -i option is specified then any sequence which does not have a region listed will be included in its entirety. And the behavior of the utility from io_lib: # /usr/bin/extract_seq --help Usage: extract_seq [-r] [-(abi|alf|scf|exp|pln|ctf|ztr)] [-good_only] [-clip_cosmid] [-fasta_out] [-output output_name] [input_name] ... #
