[EMBOSS] emboss-explorer post installation
Sumit Middha
smiddha at indiana.edu
Sun Aug 21 05:12:21 UTC 2005
Hello Andrew,
Thanks so much for your response. Probably I did not focus my question properly.
Yes I did manage to install using the script, and specified the paths.
However, I could not figure out, what my server should point to (I guess the
index page in html). Also I am unsure of how the emboss installation gets linked
to the explorer (I dont think I mentioned it anywhere during the installation of
this emboss-explorer).
And do you have or know of any comparisons, betwween emboss interfaces from w2h,
pise and emboss-explorer ?
Cheers,
Sumit
Quoting Andrew.Mather at dpi.vic.gov.au:
> Hi Sumit,
>
> No, I don't really have any notes, because the installation is very
> straightforward.
>
> The only thing I had to do was to edit the install script to point to my
> perl binary, which is in /usr/local/bin, not /usr/bin. Once I did that
> and ran the script, everything 'just worked', except for the clustal and
> primer3_core issue.
>
> That was fixed by making a symbolic link in my Emboss bin directory to the
> clustalw and primer3_core executables. Other than that, there was no
> problem.
>
> When you run the script, it asks you where the various directories are and
> installs things wherever you tell it. The only thing I'm not sure of is
> if you need to have bioPerl installed beforehand.
>
> Because we have, it didn't ask about it, so I'm not sure.
>
> I did have quite a few problems with the previous version of
> Emboss-explorer, which was called Emboss::GUI, however upgrading to the
> current version removed all of those.
>
> Andrew
>
>
>
> Bioinformatics Advanced Scientific Computing,
> Animal Genetics and Genomics, PIRVic Attwood
> 475 Mickleham Road, Attwood, 3049
> ph +61 3 92174342
> mob 0413 009 761
>
>
> ----------------
> There are 10 kinds of people...those who understand binary and those who
> don't.
>
>
>
>
>
> smiddha at indiana.edu
> 20/08/05 02:20 PM
>
>
> To: Andrew.Mather at dpi.vic.gov.au
> cc:
> Subject: Re: [EMBOSS] emma/clustalw PATH problems
>
>
>
> Hello Andrew,
> Do you have notes on installation of Emboss-explorer? It would be great
> help to
> look at those for my installation.
>
> Thanks,
> Sumit
>
>
> Quoting Andrew.Mather at dpi.vic.gov.au:
>
> > Hi,
> >
> > You can also put a symlink in the directory with all the Emboss
> > executables.
> >
> > I had to do this to get Emboss Explorer to work, even though both
> clustalw
> > and primer3_core executables were in /usr/local/bin.
> >
> > I made a symlink in the Emboss-2.xxxx/bin directory and all was well.
> >
> > Andrew
> >
> >
> >
> > Bioinformatics Advanced Scientific Computing,
> > Animal Genetics and Genomics, PIRVic Attwood
> > 475 Mickleham Road, Attwood, 3049
> > ph +61 3 92174342
> > mob 0413 009 761
> >
> >
> > ----------------
> > There are 10 kinds of people...those who understand binary and those who
>
> > don't.
> >
> >
> >
> >
> >
> > Sean.Maceachern at dpi.vic.gov.au
> > Sent by: emboss-bounces at emboss.open-bio.org
> > 19/08/05 09:01 AM
> >
> >
> > To: anders.nister at lcb.uu.se
> > cc: emboss at emboss.open-bio.org
> > Subject: Re: [EMBOSS] emma/clustalw PATH problems
> >
> >
> >
> > I have had a simillar problem with eprimer3, a temporary fix will be to
> > modify your path so that it can find the clustalw binary
> >
> > eg)
> >
> > export PATH=$PATH:/home/sm82/primer3_1.0.0/src
> >
> >
> >
> >
> >
> >
> > anders.nister at lcb.uu.se
> > Sent by: To:
> > emboss at emboss.open-bio.org
> > emboss-bounces at emboss.o cc:
> > pen-bio.org Subject: [EMBOSS]
> > emma/clustalw PATH problems
> >
> >
> > 19/08/2005 12:46 AM
> >
> >
> >
> >
> >
> >
> > I am trying to run emma, and for certain reasons i don't have clustalw
> in
> > my
> > PATH.
> >
> > Running emma produces this error:
> >
> > EMBOSS An error in ajsys.c at line 398:
> > cannot find program 'clustalw'
> >
> >
> > Looking through the manual for emma there is a mention of
> EMBOSS_CLUSTALW:
> >
> > "cannot find program 'clustalw'" - means that the ClustalW program
> has
> > not been set up on your site or is not in your environment (i.e. is
> > not on your path). The solutions are to (1) install clustalw in the
> > path so that emma can find it with the command "clustalw", or (2)
> > define a variable (an environment variable of in emboss.defaults or
> > your .embossrc file) called EMBOSS_CLUSTALW containing the command
> > (program name or full path) to run clustalw if you have it elsewhere
> > on your system.
> >
> > So I'm supposed to be able to specify the full path to clustalw through
> > EMBOSS_CLUSTALW....
> >
> > Setting this variable to the full path of clustalw produces a similar
> > error
> > to the one before.
> >
> > EMBOSS An error in ajsys.c at line 398:
> > cannot find program '/usr/local/bin/clustalw'
> >
> > Looking through the emma source code I can see that ajSystemEnv is used
> to
> > execute clustalw, this function will always look through the PATH env
> > variable for the executable it is trying to run, so specifying a full
> path
> > does absolutely nothing to get around the problem.
> >
> > Is the documentation wrong or is this a bug ?
> > Has anyone got a workaround ?
> > Is there any emboss function for executing an external program directly,
> > without it being present in PATH ?
> >
> > /Anders Nistér
> >
> > _______________________________________________
> > EMBOSS mailing list
> > EMBOSS at emboss.open-bio.org
> > http://newportal.open-bio.org/mailman/listinfo/emboss
> >
> >
> >
> >
> >
> >
> > _______________________________________________
> > EMBOSS mailing list
> > EMBOSS at emboss.open-bio.org
> > http://newportal.open-bio.org/mailman/listinfo/emboss
> >
> >
> >
> > _______________________________________________
> > EMBOSS mailing list
> > EMBOSS at emboss.open-bio.org
> > http://newportal.open-bio.org/mailman/listinfo/emboss
> >
>
>
>
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