SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Mira assembly jmpi Bioinformatics 12 02-16-2015 07:47 PM
Mira Error robelb4 Bioinformatics 4 07-08-2013 08:45 PM
Running Mira coldturkey General 2 09-05-2011 04:59 AM
PyroNoise on Mac OS X? mbakker 454 Pyrosequencing 4 07-06-2010 02:32 PM
MIRA question kmkocot Bioinformatics 2 11-09-2009 06:54 AM

Reply
 
Thread Tools
Old 03-16-2010, 08:44 AM   #1
ondovb
Member
 
Location: Maryland

Join Date: Jan 2010
Posts: 20
Unhappy MIRA on Mac OS X

Has anyone gotten MIRA to work on OS X?

I found this post that implies that it should work.

However, I'm having trouble with the Boost library. I tried staging the latest version (1.4.2) and setting $BOOST_ROOT, but MIRA's configure script couldn't find it. I would have installed it, as recommended, but I can't figure out how to. Boost 1.4.2 has no makefile or configure script, and the docs just say "often, there's nothing to build". They list some libraries (such as thread, which MIRA needs) that have to be built, but they don't say how to build them. I tried going back to Boost 1.35 (the minimum required for MIRA). This version at least has a configure script, but it throws a bunch of errors when making, and then MIRA's configure script says "BOOST thread lib must be available".

Anyone have better luck?
ondovb is offline   Reply With Quote
Old 03-16-2010, 09:14 AM   #2
maubp
Peter (Biopython etc)
 
Location: Dundee, Scotland, UK

Join Date: Jul 2009
Posts: 1,543
Default

Which Mac OS X are you using? Snow Leopard?

A while back under Leopard (Mac OS X 10.5) I installed BOOST 1.4.0 (the latest at the time) and managed to compile and run the then latest pre-release MIRA v3rc4. But only in 32bit mode

I'm now on Snow Leopard (which is more 64bit than Leopard was) and plan to try the latest MIRA shortly...

Last edited by maubp; 03-16-2010 at 09:41 AM.
maubp is offline   Reply With Quote
Old 03-16-2010, 09:53 AM   #3
ondovb
Member
 
Location: Maryland

Join Date: Jan 2010
Posts: 20
Default

Yeah, it's Snow Leopard. I finally figured out how to build Boost 1.4.2 (you have to use their tool, BJam), but that failed on a bunch of libraries, including thread. The errors were all "ld: unknown option: -R".
ondovb is offline   Reply With Quote
Old 03-16-2010, 10:25 AM   #4
maubp
Peter (Biopython etc)
 
Location: Dundee, Scotland, UK

Join Date: Jul 2009
Posts: 1,543
Default

Quote:
Originally Posted by ondovb View Post
Yeah, it's Snow Leopard. I finally figured out how to build Boost 1.4.2 (you have to use their tool, BJam), but that failed on a bunch of libraries, including thread. The errors were all "ld: unknown option: -R".
They do document the fact you have to use bjam (even if it could be much clearer). What I used was just:

Code:
cd boost_1_42_0
./bootstrap.sh
./bjam
./bjam install --prefix=/Users/myusername/
However, I had a problem with the Python bindings (which I think is a 64bit issue as the error message was about the Apple provided Python 2.5 not their 64-bit capable Python 2.6):

Code:
...failed updating 56 targets...
...skipped 5 targets...
...updated 7743 targets...
I don't think we need to worry about the Boost Python stuff for MIRA.

Last edited by maubp; 03-23-2010 at 07:53 AM. Reason: fixed typo
maubp is offline   Reply With Quote
Old 03-18-2010, 03:51 AM   #5
maubp
Peter (Biopython etc)
 
Location: Dundee, Scotland, UK

Join Date: Jul 2009
Posts: 1,543
Default

See also:
http://www.freelists.org/post/mira_t...6-Snow-Leopard
maubp is offline   Reply With Quote
Old 03-23-2010, 09:39 AM   #6
maubp
Peter (Biopython etc)
 
Location: Dundee, Scotland, UK

Join Date: Jul 2009
Posts: 1,543
Default

I ran into some issues with multiple copies of libexpat (apparently from Apple, BOOST and EMBOSS). I tried to get rid of my out of date EMBOSS, and removed the full BOOST install. I was able to simplify the BOOST installation to just this:

Code:
cd boost_1_42_0
./bootstrap.sh --with-libraries=thread
./bjam
./bjam install --prefix=/Users/myusername
I am now able to install a working MIRA 3.0.0 on Snow Leopard, but not 3.0.1, 3.0.2 or 3.0.3 (which all fail immediately with an abort trap). I'm still investigating (with Bastein etc).

Quote:
Originally Posted by Bastien
An error is occurring during static initialisation, before even the main()
starts. The code for this is new in 3.0.1 and works flawlessly on Linux and
other MacOS ... "This is not supposed to happen." [tm]

I'm not entirely sure, but I wouldn't search the cause for this in libraries.
looks like a weird compiler or linker bug.

I'll send you some files this evening to try out a few things, but let's take
this discussion offline now (and post a summary later), it's probably not
interesting for most of the subscribers.
Other uses on the MIRA talk mailing list report MIRA 3.0.0 though 3.0.3 all building and working fine on Snow Leopard - so this isn't a general issue.

Last edited by maubp; 03-23-2010 at 09:42 AM. Reason: Added quote
maubp is offline   Reply With Quote
Old 03-29-2010, 02:15 AM   #7
maubp
Peter (Biopython etc)
 
Location: Dundee, Scotland, UK

Join Date: Jul 2009
Posts: 1,543
Default

Quote:
Originally Posted by maubp View Post
Other uses on the MIRA talk mailing list report MIRA 3.0.0 though 3.0.3 all building and working fine on Snow Leopard - so this isn't a general issue.
That turned out to be a miss-communication. To summarise:
  • MIRA 3.0.0 works on Mac OS 10.6 Snow Leopard (but has some known issues fixed in the later point releases).
  • MIRA 3.0.1, 3.0.2 and 3.0.3 all fail on the Mac (they compile but when run immediately abort).
  • Bastien has tracked down the cause of the problem, and seems to have fixed it on the development branch.

In order to compile MIRA on Mac OS 10.6 Snow Leopard you can use the Apple provided libexpat (which will be detected automatically if there are no other versions present). You don't need all of BOOST, install just the threading library. I choose to install this under my home directory rather than at the system level:

Code:
cd boost_1_42_0
./bootstrap.sh --with-libraries=thread
./bjam
./bjam install --prefix=/Users/myusername
Then to compile MIRA,

Code:
cd mira-3.0.0
./configure --with-boost=/Users/myusername
make
make check
Peter

Last edited by maubp; 03-29-2010 at 02:22 AM. Reason: Adding instructions
maubp is offline   Reply With Quote
Old 03-29-2010, 07:36 AM   #8
ondovb
Member
 
Location: Maryland

Join Date: Jan 2010
Posts: 20
Default

Thanks for the help. I now have 3.0.0 running an assembly.
ondovb is offline   Reply With Quote
Old 04-19-2010, 08:46 AM   #9
maubp
Peter (Biopython etc)
 
Location: Dundee, Scotland, UK

Join Date: Jul 2009
Posts: 1,543
Default

Quote:
Originally Posted by maubp View Post
To summarise:
  • MIRA 3.0.0 works on Mac OS 10.6 Snow Leopard (but has some known issues fixed in the later point releases).
  • MIRA 3.0.1, 3.0.2 and 3.0.3 all fail on the Mac (they compile but when run immediately abort).
  • Bastien has tracked down the cause of the problem, and seems to have fixed it on the development branch.
I've just compiled the just released MIRA 3.0.5 (using the method described earlier on this thread), and it seems to work
maubp is offline   Reply With Quote
Old 11-10-2010, 03:17 AM   #10
carcalas
Member
 
Location: Cádiz

Join Date: Nov 2010
Posts: 11
Default Need help, please!!!!!!

Hi friends,
I have a problem with MIRA-3.2.0rc2, and I would be very grateful to you if you can help me. I am a novel user of Unix, and so my knowledge is very very limited. I have a Mac with system 10.5.8. First of all, I had to install the Xcode tools because gcc was not available by default. But one solved this problem, I had the following error when executing ./configure:

checking whether the Boost::Thread library is available... no

+++++++++++++++++++++++++++++++++++++
BOOST_CPPFLAGS: -I/include/boost-0
BOOST LDFLAGS: -L/lib
ac_boost_path: /opt/local
ac_boost_lib_path:
BOOST_THREAD_LIB:
CFLAGS now: -O2
CXXFLAGS now: -O2
LDFLAGS now: -L/usr/lib
+++++++++++++++++++++++++++++++++++++
Automatic recognition of Boost thread lib failed? I have
////// BOOST_CPPFLAGS: -I/include/boost-0
////// BOOST LDFLAGS: -L/lib
////// ac_boost_path: /opt/local
////// ac_boost_lib_path:
////// BOOST_THREAD_LIB:
////// BOOST_ROOT:
Please give the configure script the location of your BOOST
libraries. Or, if needed, the name of your thread library (without
'lib' in front):
--with-boost=DIR
or --with-boost-libdir=LIB_DIR
or --with-boost-thread=special-lib

configure: error: Stopping here as BOOST thread lib must be available at this stage. Sorry.

I previouslly installed boost 1.44 thinking that with this application all was OK. Do you know the reason why I cannot configure MIRA? Can you help me?.
Please, try to explain with as much details as possible, as I have commented before, I have no experience with Unix.
Thanks a lot in advance.
carcalas is offline   Reply With Quote
Old 11-10-2010, 03:21 AM   #11
maubp
Peter (Biopython etc)
 
Location: Dundee, Scotland, UK

Join Date: Jul 2009
Posts: 1,543
Default

Quote:
Originally Posted by carcalas View Post
Hi friends,
I have a problem with MIRA-3.2.0rc2, ... the following error when executing ./configure:

checking whether the Boost::Thread library is available... no
...

I previouslly installed boost 1.44 thinking that with this application all was OK.
Where did you install BOOST? Since MIRA can't find it, you will have to tell MIRA where to look using the --with-boost argument to configure.
maubp is offline   Reply With Quote
Old 11-10-2010, 03:24 AM   #12
carcalas
Member
 
Location: Cádiz

Join Date: Nov 2010
Posts: 11
Default

I located the folder in the desktop. May be this is the problem?. Where do I have to put the folder, inside the mira folder?.
Thanks a lot again
carcalas is offline   Reply With Quote
Old 11-10-2010, 03:31 AM   #13
maubp
Peter (Biopython etc)
 
Location: Dundee, Scotland, UK

Join Date: Jul 2009
Posts: 1,543
Default

You don't just unzip the BOOST files into a folder - it has to be compiled. Have you tried the method I gave earlier in this thread? See post 7:
http://seqanswers.com/forums/showpos...81&postcount=7
maubp is offline   Reply With Quote
Old 11-10-2010, 03:36 AM   #14
carcalas
Member
 
Location: Cádiz

Join Date: Nov 2010
Posts: 11
Default

Thanks a lot for your fast reponse. I compiled Boost following the instructions I found in a forum:

1. The first thing to do is to download the Boost distribution from the Boost downloads page.
2. Unpack the archive somewhere sensible, I’d suggest the desktop. Don’t do it where the absolute folder path will have any spaces in the name e.g. “/users/matt/code/bad folder/”, this will prevent the install script from working later. I found this out the hard way.
3. Next open a terminal window and navigate to the Boost root folder you just unpacked, it will be called “boost_1_39_0″ if you are using the current version. If it’s on your desktop you will need to use “cd /users/username/desktop/boost_1_39_0“. We refer to this path in future as the $BOOST_ROOT
4. Next run the bootstrap script by typing “./bootstrap.sh“. This configures the install tools for your environment. Check it for error messages, this is where I found out my path was bad.
5. If you run the “ls” command you should now have an executable called bjam.
6. To compile Boost, type “./bjam architecture=combined” and press enter, this will build Universal (x86 and PowerPC compatible) libraries.
7. Make a cup of coffee and wait while the libraries build.

Is this OK?. I did it exactly as indicated in these instructions, including point 7.
carcalas is offline   Reply With Quote
Old 11-10-2010, 03:42 AM   #15
maubp
Peter (Biopython etc)
 
Location: Dundee, Scotland, UK

Join Date: Jul 2009
Posts: 1,543
Default

OK. Were there any errors? Where did it put the files?

e.g. Can you find libboost_thread.dylib (and note that Spotlight may not check the system folders - try looking in /local/usr/lib as a guess).
maubp is offline   Reply With Quote
Old 11-10-2010, 03:49 AM   #16
carcalas
Member
 
Location: Cádiz

Join Date: Nov 2010
Posts: 11
Default

I had no errors during installation. The file libboost_thread.dylib is in:

desktop/boost_1_44_0/stage/lib

I can also find a file with the same name but in other location:

desktop/boost_1_44_0/binV.2/libs_/thread/build/darwin-4.0.1/release/architecture-combined/threading-multi

Any problem with this?
carcalas is offline   Reply With Quote
Old 11-10-2010, 03:56 AM   #17
maubp
Peter (Biopython etc)
 
Location: Dundee, Scotland, UK

Join Date: Jul 2009
Posts: 1,543
Default

I see now: Having reread your post, you never actually installed the boost library (just built it - i.e. compiled it). You could try pointing MIRA at this folder...

Or, you could try installing BOOST under your home directory (you won't need root access this way):

Code:
cd ~/desktop/boost_1_42_0
./bjam install --prefix=/Users/$USER

cd ~/where-ever-you-put-it/mira-3.2.0
./configure --with-boost=/Users/$USER
make
make check
maubp is offline   Reply With Quote
Old 11-10-2010, 04:03 AM   #18
carcalas
Member
 
Location: Cádiz

Join Date: Nov 2010
Posts: 11
Default

Ok. Many thanks, maubp. A silly question. When you say users and $User is just it, or I have to indicate a specifc name of the user in both sites. May be it is something obvious for you, but not for me. I will try it and contact you again when finished installing, if you have no troubles.
carcalas is offline   Reply With Quote
Old 11-10-2010, 04:18 AM   #19
maubp
Peter (Biopython etc)
 
Location: Dundee, Scotland, UK

Join Date: Jul 2009
Posts: 1,543
Default

At the Unix/Linux command line $XXX is shorthand for insert the environment variable XXX here. On Windows you'd use %XXX% instead. Try this:

Code:
echo $USER
echo $PATH
echo $HOME
Notice these are case sensitive! It is $USER not $User for example.

With hindsight, using $HOME would have been more elegant.
maubp is offline   Reply With Quote
Old 11-10-2010, 04:27 AM   #20
carcalas
Member
 
Location: Cádiz

Join Date: Nov 2010
Posts: 11
Default

Sorry maubp, but I did not understand your last reply. My knowledge of unix is very poor. I am currently following your instructions, compiling boost with the following:

./bjam install --prefix=/Users/$USER

It is running, and seems to be OK. Once finished, I will try to configure mira again typing:

./configure --with-boost=/Users/$USER

Do you think it should work?. Thanks a lot for your patience.
carcalas is offline   Reply With Quote
Reply

Tags
apple, leopard, mac, mira

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 04:04 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO