> But I am not quite there yet. I have two other "problems" and one other > question. Part of my problem is my lack of familiarity with the GUI > interface. I have been using EMBOSS on the command line for quite some > time. Anyway with Jemboss when I run the runJemboss.sh script a little > box pops up asking for a username and password (it looks like a login > for a remote server). Do you have any idea what that is for? Do I have > to comment out something in the runJemboss.sh script to stop it running?
You might have "user.auth=true" in your jemboss.properties file which might be found in your share/EMBOSS/jemboss/resources/ directory under your jemboss installation folder or it might be in your home directory. Setting this property to false may help. > The other problem I am having is that when I use pepstats on the command > line on the file at this link: > https://webspace.uth.tmc.edu/rmackenzie/public/orf_trans_all_assembly_21 > .fasta > I get a result in about 2 seconds. But when I try doing this through > Jemboss it just sits there with the hourglass going. > I have also tried this using the windows XP version of Jemboss, running > on my dual core 2 Gb of RAM PC at my house. I ran it for 12 hours and > still go no output. If you have a Jemboss running there could you try > running the file through pepstats for me? I think it is a bug and if so > I should report it. By the way I tried stripping out the * for the stop > codons but it made no difference. I'm able to reproduce this problem and will return you tomorrow with more details. I initially thought giving more memory to Java may help to solve the problem but it doesn't. > And the final question. Do other users of this list normally post > replies to the list? I think it depends on the post. It is good to post to the list when you think others may also hit the same problem. Regards, Mahmut _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
