One of the tools necessary to convert genome assemblies between consed and gap4 are caftools. It is nicely summarized here: http://envgen.nox.ac.uk/envgen/software/archives/000581.html http://sarton.imb-jena.de/software/consed2gap/
No comments have been made on this bug report for some time. Is anyone still interested in integration of this package? If yes, please indicate that here in this bug report. Otherwise we'll resolve the bug in the near future, since sci(-*) has an extremely large number of pending package requests and we would like to focus...
Committed the new ebuild.
*** Bug 259847 has been marked as a duplicate of this bug. ***
Current problems. 1. >>> Completed installing caftools-2.0.2 into /mnt/1TB/var/tmp/portage/sci-biology/caftools-2.0.2/image/ * QA Notice: Package triggers severe warnings which indicate that it * may exhibit random runtime failures. * cl.c:650:4: warning: implicit declaration of function 'ctime' [-Wimplicit-function-declaration] * ncr.c:68:4: warning: implicit declaration of function 'exit' [-Wimplicit-function-declaration] * ncr.c:68:4: warning: incompatible implicit declaration of built-in function 'exit' * seq_dict.c:80:4: warning: implicit declaration of function 'qsort' [-Wimplicit-function-declaration] * seq_dict.c:102:4: warning: implicit declaration of function 'free' [-Wimplicit-function-declaration] * seq_dict.c:102:4: warning: incompatible implicit declaration of built-in function 'free' * seq_dict.c:146:4: warning: incompatible implicit declaration of built-in function 'free' * seq_dict.c:206:4: warning: implicit declaration of function 'exit' [-Wimplicit-function-declaration] * seq_dict.c:206:4: warning: incompatible implicit declaration of built-in function 'exit' * seq_dict.c:399:5: warning: incompatible implicit declaration of built-in function 'free' * Please do not file a Gentoo bug and instead report the above QA * issues directly to the upstream developers of this software. * Homepage: http://www.sanger.ac.uk/resources/software/caf/ 2. $ caf_depad Floating point exception (core dumped) $ 3. The 2.0.2 archive lacks manpages compared to 2.0. 4. The man/Makefile.in is screwed in 2.0.2 so we cannot use it to install the manpage files, not even copying over whole caftools-2.0/man/ to caftools-2.0.2/man does not help. One needs to do it "manually".
