[BiO BB] Need installation of Bio software on Mac
Dr. Christoph Gille
christoph.gille at charite.de
Wed Jun 15 04:14:16 EDT 2005
many thanks for taking the time to try this out.
I generally append the suffix dot exe to binaries because this allows me
to have the same documentation for DOS and UNIX.
A symbolic link (ln -s ...) of the clustalW or dialign-t binarie to the
specified directory is only recognized when it gets the ending dot exe.
Most binaries like clustalW come in an JAR archive because some require
more than one file. Even though the clustalW version is the ordinary
C-version and not a java-version.
I am a bit disappointed that the installation of dialign-t fails on Mac.
Theroetically, STRAP should go to the directory
Subsequently the command make
should be executed
finally the binary should be renamed
mv dialign-t dialign-t.exe
Do you know which of these steps failed ?
Supposed it would work, how do you like the concept of distributing the
source rather than executables ?
> À 12:38 +0200 le 06/10/05, Dr. Christoph Gille a écrit:
>> Instead of CLUSTALW you select MUSCLE or DIALIGN-t. An automated
>> installing process is started and "make" is run.
>> I guess that Mac (though it is some sort of UNIX) has no C-compiler
>> and probably this installation process will fail until Gnu C-compiler is
> I have gcc 3 and 4 on my Mac (Part of X-Code 2.1
> on MacOS X 10.4). When I tried to install DIALIGN-t, the app downloaded the
> sources then warned me that it had failed to launch dialign-t. The same
> warning asked me to copy the dialign-t.exe binary to a specific location
> on my drive.
> If I take the precompiled binaries available on
> the dialign-t website and place them where Strap asks em to, I still get
> the same error warning if I try to align using dialign-t (a problem with
> the name of the binary that sure doesn't have the .exe ??)
> PS: I also noticed that your app installs the
> java version of CLUSTALW instead of using the regular compiled binaries
> which are much much faster. It actually doesn't even tries to launch
> CLUSTALW on the Mac. I have it installed in
> /usr/local/bin (which is in my $PATH) but Strap
> still downloaded and built the Java version.
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