The Mac OSX image contains the run scripts wrapped in the jar file under Artemis.app/Contents/artemis-8/lib. If you go to that directory and type
jar vtf artemis.jar | grep run_
They will be listed.
However, with the Mac distribution the ‘Readme.txt’ (in the image) gives you information on setting up databases and BLAST and FASTA tools:
Searching and Using Local Databases (Optional)
==============================================
BLAST and FASTA search tools need to be downloaded:
http://ncbi.nih.gov/BLAST/download.shtml
ftp://ftp.ebi.ac.uk/pub/software/unix/fasta/
and installed into:
Artemis.app/Contents/blast
Artemis.app/Contents/fasta
respectively.
Databases can be set-up and installed for BLAST and fasta. This
should be done from a UNIX window and going into the directory:
Artemis.app/Contents/blast-data/
The image is a fairly new way we are distributing Artemis for MacOSX (as of the current release), but you can always use the UNIX download with the scripts located in the ‘etc’ directory if you need more flexibility in the set up e.g. database location.
Regards
Tim Carver
On 17/8/06 19:08, "Andrew Stewart" <[EMAIL PROTECTED]> wrote:
Hello,
I have a short series of questions generally regarding the customization of Artemis. Rather than bombard the list with all my questions, I'll take them one at a time, as I expect they may be fairly involved. To note, I'm a bioinformatics guy and competent with both unix systems (I'm using Mac OS X), programming, and such. To begin, my ultimate aim here is to customize Artemis as a graphical, interactive front end (which it already is) for manually annotating in-house-generated genomic sequences stored in a remotely hosted relational database (what I'm hoping it can become :P)
Ok, Question #1: Configuring the items in the Run menu. I've already read through http://www.sanger.ac.uk/Software/Artemis/v8/manual/runmenu.html, though I am confused by the apparent absence of any run_blastp or run_fasta scripts either within the Artemis container package (Mac OS X distribution, remember) or anywhere else on my machine. I did find a script called setup_dbs.sh within the package contents, which I initially thought might generate these run_ scripts, though which I am now guessing only create a local set of databases.
*Should scripts such as run_blastp and run_fasta be generated during installation of Artemis, or are they generated during some sort of configuration step?
*Is it possible that the Mac OS X distribution of Artemis lacks these scripts (and thus this functionality)?
*Am I missing something obvious here?
Any help would be appreciated.
-Andrew Stewart
--
Andrew Stewart
Research Assistant, Genomics Team
Navy Medical Research Center (NMRC)
Biological Defense Research Directorate (BDRD)
BDRD Annex
12300 Washington Avenue, 2nd Floor
Rockville, MD 20852
email: [EMAIL PROTECTED]
phone: 301-231-6700 Ext 270
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