[kman42]

I'm getting really frustrated with Fink. I think it stems from my own ignorance, so I come loaded with a few questions.

I'm trying to install the EMBOSS package for bioinformatics. I used fink to install it and everything seems to have gone according to plan. My problem is that I don't entirely understand the directory structure that fink has set up and I can't edit any of the files I need to configure it. The EMBOSS instructions tell me to go edit $EMSBOSS_INSTALL/share/EMBOSS/jemboss/runjemboss.csh

I eventually found the file in /sw/share. I don't quite understand what this directory is, but I continued on since I found the file I was looking for. Easy enough to edit it, except it is owned by root and I can't even edit it with sudo. What's the deal here? Did something go wrong with my fink install. Should everything in the /sw/share folder be owned by root (as the folder itself seems to be)? How do I go about working with the files in this directory?

Any help would be most appreciated.

kman

[proton]

Originally posted by kman42:
I eventually found the file in /sw/share. I don't quite understand what this directory is, but I continued on since I found the file I was looking for. Easy enough to edit it, except it is owned by root and I can't even edit it with sudo. What's the deal here? Did something go wrong with my fink install. Should everything in the /sw/share folder be owned by root (as the folder itself seems to be)? How do I go about working with the files in this directory?

What error messages did you receive?

Using sudo the application runs as root so it doesn't sound like a permissions problem, could be that the file has the immutable or append-only flags set.

- proton

[suthercd]

kman-

There is a huge amount of documentation at the fink.sourceforge.net site. This question is answered there. The fink-beginners mailing list also is a good resource- the individual who maintains the fink FAQ directly answers many of the questions. You can also search the amiling list archives- most questions have been asked before.

I started at http://fink.sourceforge.net/faq/index.php. It takes some study and investigation, but it is all there.

HTH
Craig

[itai195]

FYI for those frustrated with fink, Gentoo is porting their platform to OS X. Portage is an excellent package manager. IMO, it's superior to fink.

[theory]

Originally posted by kman42:
I'm getting really frustrated with Fink. I think it stems from my own ignorance, so I come loaded with a few questions.

I'm trying to install the EMBOSS package for bioinformatics. I used fink to install it and everything seems to have gone according to plan. My problem is that I don't entirely understand the directory structure that fink has set up and I can't edit any of the files I need to configure it. The EMBOSS instructions tell me to go edit $EMSBOSS_INSTALL/share/EMBOSS/jemboss/runjemboss.csh

I eventually found the file in /sw/share. I don't quite understand what this directory is, but I continued on since I found the file I was looking for. Easy enough to edit it, except it is owned by root and I can't even edit it with sudo. What's the deal here? Did something go wrong with my fink install. Should everything in the /sw/share folder be owned by root (as the folder itself seems to be)? How do I go about working with the files in this directory?

Any help would be most appreciated.

kman

Simple answer is that install directory is usually /sw/ for all stuff installed by fink.

[kman42]

The app seems to be having a problem linking to apple x11. When I run the app from within xterm I get the following error:

Error in XCreatePixmap: BadDrawable (invalid Pixmap or Window parameter).


Any idea what that could be? Is there some environment variable that I am missing. The app mentions a setenv line for plplot, but it says it is already taken care of in the fink distribution and it is present in the config file that is mentioned in the readme.

kman

[drmbb2]

kman42, I use EMBOSS, with the JemBoss java interface all the time. My suggestion is to NOT install it via FINK. The source code installs just fine under OS X.

I would go to the EMBOSS home page and download the source package. The steps you would follow are:

tar xvzf EMBOSS-2.7.1 .tar.gz

Then cd into the EMBOSS-2.7.1 directory

Run the following
./configure --prefix=(install directory of your choice - mine is /usr/local/bin/emboss)
make
make install

Then, from within the /.../emboss/share/EMBOSS/jemboss/utils folder, run the script install-jemboss-server.sh and choose the standalone option. You will need to point it to your java installation, as mentioned in here

All you need do is make a symlink to the runJemboss.csh script in /.../emboss/bin and your are set, eg. in my usr/local/bin, I just entered

ln -s /usr/local/bin/emboss/bin/runJemboss.csh jemboss

[kman42]

Originally posted by drmbb2:
kman42, I use EMBOSS, with the JemBoss java interface all the time. My suggestion is to NOT install it via FINK. The source code installs just fine under OS X.

I would go to the EMBOSS home page and download the source package. The steps you would follow are:

tar xvzf EMBOSS-2.7.1 .tar.gz

Then cd into the EMBOSS-2.7.1 directory

Run the following
./configure --prefix=(install directory of your choice - mine is /usr/local/bin/emboss)
make
make install

Then, from within the /.../emboss/share/EMBOSS/jemboss/utils folder, run the script install-jemboss-server.sh and choose the standalone option. You will need to point it to your java installation, as mentioned in here

All you need do is make a symlink to the runJemboss.csh script in /.../emboss/bin and your are set, eg. in my usr/local/bin, I just entered

ln -s /usr/local/bin/emboss/bin/runJemboss.csh jemboss

Thanks! I thought fink would make it easier with all of the dependencies, but I guess not. Did you have to install qd (I think that's what it is called) or anything like that as well?

kman

[drmbb2]

Originally posted by kman42:
Thanks! I thought fink would make it easier with all of the dependencies, but I guess not. Did you have to install qd (I think that's what it is called) or anything like that as well?

kman

All you need is an X install - I use XDarwin, installed via the packages from sourceforge (I used fink though to get rxvt and blackbox).

JemBoss will work with either Java 1.3.1 or 1.4.1 - the "Home" path is specific for each, but the "Headers" is the same.

Oh, also, before you try to run runjemBoss.csh, be sure to edit the last line ("(cd /usr/local/bin/emboss-2.7.1/share/EMBOSS/jemboss; java org/emboss/jemboss/Jemboss &") and add the word "local" between the "Jemboss" and the "&", and be sure to use and editor that WILL NOT wrap the existing lines by default (they are quite long, but need to be unbroken).

If you want any of the EMBASSY packages, you'll need to install each one separately. They don't integrate with JemBoss well though, so I didn't bother with them. PHYLIP, HMMER, etc are also available in ready to compile/install versions for OS X, and the native packages are usually superior to work with anyway.

[kman42]

Is there a website dedicated to bioinformatics on OSX? That would really be helpful. So much has become available recently and it seems that each package has it's own unique quirks. Some are easy with fink, some are easier to install from source. There are lots of people with way less experience than me who would really benefit from these tools, but just don't have a good starting point. Most bio labs have lots of Macs capable of running osx and if they could get some of these open source packages up and running it would really help to keep macs humming along in bio.

kman

[drmbb2]

Originally posted by kman42:
Is there a website dedicated to bioinformatics on OSX? That would really be helpful. So much has become available recently and it seems that each package has it's own unique quirks. Some are easy with fink, some are easier to install from source. There are lots of people with way less experience than me who would really benefit from these tools, but just don't have a good starting point. Most bio labs have lots of Macs capable of running osx and if they could get some of these open source packages up and running it would really help to keep macs humming along in bio.

kman

I hear you - my job is to provide molecular computing support, mostly for medical researchers, and about half of which use Mac's as their main machines. However, I do not know of any such site like you wish for. Basically you need to track down information by program or application type. Most popular and commonly used applications either compile nicely on OS X, or have even been ported to full binary install packages (FASTA, BLAST, CLUSTAL, PHYLIP, EMBOSS, HMMER, Se-Al, XCed, etc).

But you are correct, it's not easy for many people to find either the application they need, and/or the information needed to get it installed properly (part of the reasons positions like mine even exist).

some sites that might prove useful to you include:
the biolist

the IU bio archives

and the SAL site (strictly speaking, a Linux site, but much of the stuff there will compile under OS X with minimal effort).

Best of luck with EMBOSS.

[kman42]

I followed your instructions exactly. I had to do a chmod on the install-jemboss.server.sh file before it would run, but then it seemed to execute okay. After making the symlink and typing in 'jemboss' I get the following error:

Code:
n.jar:/usr/local/bin/emboss/share/EMBOSS/jemboss/lib/jakarta-regexp-1.2.jar:/usr/local/bin/embos
s/share/EMBOSS/jemboss/lib/jalview.jar:/usr/local/bin/emboss/share/EMBOSS/jemboss/lib/jcert.jar:
/usr/local/bin/emboss/share/EMBOSS/jemboss/lib/jnet.jar:/usr/lo: Command not found.
cal/bin/emboss/share/EMBOSS/jemboss/lib/jsse.jar:/usr/local/bin/emboss/share/EMBOSS/jemboss/lib/
axis/axis-ant.jar:/usr/local/bin/emboss/share/EMBOSS/jemboss/lib/axis/axis.jar:/usr/local/bin/em
boss/share/EMBOSS/jemboss/lib/axis/commons-discovery.jar:/usr/l: Command not found.
ocal/bin/emboss/share/EMBOSS/jemboss/lib/axis/commons-logging.jar:/usr/local/bin/emboss/share/EM
BOSS/jemboss/lib/axis/jaxrpc.jar:/usr/local/bin/emboss/share/EMBOSS/jemboss/lib/axis/log4j-1.2.4
.jar:/usr/local/bin/emboss/share/EMBOSS/jemboss/lib/axis/saaj.j: Command not found.
ar:/usr/local/bin/emboss/share/EMBOSS/jemboss/lib/axis/wsdl4j.jar:/usr/local/bin/emboss/share/EM
BOSS/jemboss/lib/axis/servlet.jar:/usr/local/bin/emboss/share/EMBOSS/jemboss: Command not found.
[Kurt-Mareks-Computer:/usr/local/bin] kmarek% Exception in thread "main" java.lang.NoClassDefFou
ndError: org/emboss/jemboss/Jemboss

I have no idea where things went wrong. Any ideas?

kman

[kman42]

Originally posted by drmbb2:

Oh, also, before you try to run runjemBoss.csh, be sure to edit the last line ("(cd /usr/local/bin/emboss-2.7.1/share/EMBOSS/jemboss; java org/emboss/jemboss/Jemboss &") and add the word "local" between the "Jemboss" and the "&", and be sure to use and editor that WILL NOT wrap the existing lines by default (they are quite long, but need to be unbroken).

I did notice that the last line of that file wasn't exactly as you described. Mine says (after adding 'local'):

(cd /usr/local/bin/emboss/share/EMBOSS/jemboss; java org/emboss/jemboss/Jemboss local &


Also, I didn't copy the unzipped emboss-2.7.1 folder to /usr/local/bin before installing it. Should I have done that?

kman

[drmbb2]

Originally posted by kman42:
I did notice that the last line of that file wasn't exactly as you described. Mine says (after adding 'local'):

(cd /usr/local/bin/emboss/share/EMBOSS/jemboss; java org/emboss/jemboss/Jemboss local &


Also, I didn't copy the unzipped emboss-2.7.1 folder to /usr/local/bin before installing it. Should I have done that?

kman

kman - be sure that /usr/local/bin is in your path, and also check the top lines in runjemBoss.csh (the setenv lines) and be sure that the "CLASSPATH" line is a single line. It looks like your's got wrapped.

<edit> Since you have X installed, a really nice editor is NEdit, installable via FINK - it will NOT wrap lines on you unwittingly, and, for sequence work, it has column select (hold down the "control" key while selecting). </edit>

The only reason my final line in that file is different is that, after seeing this thread, I did go out and get the current 2.7.1 release, but installed it in emboss-2.7.1 so I'd still have my old version if things went wrong.

[kman42]

I'm having trouble even running from the command line. When I try to use abiview, I get the following error:

Error in XCreatePixmap: BadDrawable (invalid Pixmap or Window parameter).

Seems like it is having trouble interfacing with x11. I'm running Apple's x11; is there some environment variable or something that I might have to change?

I think I get something similar when running through jemboss because it never displays the trace. I get analogous problems running any of the applications. They don't seem to ever display their output.

thanks,
kman

[kman42]

I'm still not able to get this working. I've tried just about everything I can think of. I do notice that the instructions you provided above are somewhat different than what is described here. The main difference being that the instructions on the Jemboss page don't mention actually isntalling emboss, as if the install-jemboss-server.sh script will take care of that. You were explicit about installing emboss prior to running that script.

Either way, I get the same result. I can run the jemboss interface, but things don't seem to work quite right. Whenever a result window opens it is blank. If I run the apps from the command line they seem to work okay with several of the output options, but not all. For instance, if I run abiview I can use xterm to see the trace, but if I enter x11 it fails.

I haven't installed png, gd, or zlib as is indicated in the emboss installation guide, but I'm not sure if that is necessary.

Any other ideas would be greatly appreciated as I'd really like to get this working.

kman

[kman42]

I did notice that it didn't find a useable png library:

checking if png driver is wanted... yes
checking for inflateEnd in -lz... yes
checking for png_destroy_read_struct in -lpng... no
No png driver will be made due to librarys missing/old.


Might that be a problem?

kman

[drmbb2]

Originally posted by kman42:
I did notice that it didn't find a useable png library:

checking if png driver is wanted... yes
checking for inflateEnd in -lz... yes
checking for png_destroy_read_struct in -lpng... no
No png driver will be made due to librarys missing/old.


Might that be a problem?

kman

I've not actually used the AbiView program, so I can't test it on my install (send me a small trace file though and I'll be happy to try things out) - I thought it used postscript for it's output, but maybe it needs the png drivers?

FINK should be able to install everything you'd need for png support - gd2, gd2-bin, and lippng3 - zlib is already an included OS X shared library. I can try to install these and see if thay makes a difference, but I'd need a sample trace file to test it (I don't work with things at that level, just the final sequence files).


<edit> Well, installing those packages via fink, then compiling EMBOSS with the "--with-pngdriver=/sw" option does give png driver support, at least. </edit>