reassign 476626 emboss retitle 476626 emboss: emma does not work with clustalw > 2.0 thanks
Le Fri, Apr 18, 2008 at 10:48:04AM +0900, Charles Plessy a écrit : > Severity: important > > User report on EMBOSS mailing list ( > http://lists.open-bio.org/pipermail/emboss/2008-April/003253.html ) > prompted me to check the situation of our packaged version of clustalw. > > Indeed the 'emma' wrapper does not work with clustalw 2.04 or 2.05. I > quickly found out that the -outfile option of clustalw is broken. I > think that this causes the problem and will report the bug in upstream's > bugzilla. After checking clustalw 1.83, there is no obvious regression: -outfile works, but only for the alignment file, and I was fooled by the fact that in the absence of the -newtree option, clustalw was trying to write the .dnd file in the read-only directory from which I read the sequences to align. The problem is more probably with emma, the EMBOSS wrapper for clustalw. -- Charles Plessy http://charles.plessy.org Wakō, Saitama, Japan
