$ clustalw --help CLUSTAL W (1.83) Multiple Sequence Alignments Error: unknown option --help mokrejs@vrapenec$ clustalw -help CLUSTAL W (1.83) Multiple Sequence Alignments ERROR: Cannot open help file [/usr/share/doc/clustalw-1.83-r1/clustalw_help] $ $ equery files =sci-biology/clustalw-2.0.11 * Searching for clustalw in =sci-biology ... * Contents of sci-biology/clustalw-2.0.11: /usr /usr/bin /usr/bin/clustalw2 /usr/share /usr/share/aclocal $ which clustalw /usr/bin/clustalw $ ls -la /usr/bin/clustalw* -rwxr-xr-x 1 root root 190344 Dec 22 2005 /usr/bin/clustalw -rwxr-xr-x 1 root root 566849 Jul 16 16:25 /usr/bin/clustalw-mpi -rwxr-xr-x 1 root root 5438290 May 6 16:37 /usr/bin/clustalw2 $ It looks I have some remnant on my system from 1.83-r1 ebuild. How about others?
clustalw2 is for clustalw-2* clustalw is for slot one. please upgrade the clustalw SLOT 1 and report back if this issue still happens.
# emerge --unmerge clustalw sci-biology/clustalw selected: 1.83-r1 2.0.11 protected: none omitted: none >>> 'Selected' packages are slated for removal. >>> 'Protected' and 'omitted' packages will not be removed. >>> Waiting 5 seconds before starting... >>> (Control-C to abort)... >>> Unmerging in: 5 ^C Exiting on signal 2 # emerge -uN =sci-biology/clustalw-1.83-r1 * IMPORTANT: 1 news items need reading for repository 'gentoo'. * Use eselect news to read news items. Calculating dependencies... done! >>> Auto-cleaning packages... >>> No outdated packages were found on your system. * IMPORTANT: 1 news items need reading for repository 'gentoo'. * Use eselect news to read news items. # Looks my skills are only up to something like "emerge --unmerge =sci-biology/clustalw-1.83-r1". That's not what you wanted, right? ;-)
sci-biology/clustalw-1.83-r1 isn't in the tree anymore, means it isn't supported anymore. If you want to have help for clustalw version 2*, do clustalw2 -help for version 1*, make sure you have either 1.83-r2 or r3 emerged and than use clustalw -help.
