NOTE: The version numbers for everything are given specifically because aspects of the installation process may change with different versions and, in the event, I will not necessarily know the answer to subsequent problems if major version changes include major changes to the below (and that should clear up the â€œqualificationsâ€ section).
The UNAFold (UNified Nucleic Acid Fold(ing)) nucleic acid folding and hybridization prediction program set (here using version 3.8) can by itself be built with few (and not important) errors in OSX with Xcode Tools 3. The actual running of UNAFold.pl produces several errors that do not affect the run but do affect the amount/format of the output. It is my assumption that any OS running a less-than â€œkitchen sinkâ€ installation of Linux/Unix (Ubuntu, gentoo and Damn Small Linux come to mind) will have these errors and will require subsequent installations of programs/libraries that pieces of UNAFold rely on for processing output into, specifically, images and PDF files. OSX has the same issue that is easy to handle using Fink (and less so trying to install otherwise completely unrelated programs to make these â€œdependenciesâ€ (programs and libraries) available to UNAFold). Once Fink is installed, it is a few-step process to build UNAFold, move the Mfold Utilities contents to their proper folders (and there is a small trick here as well), and generate a UNAFold-complete install for all your DNA/RNA needs.
1. UNAFold 3.8 Installation
To begin, download (currently at mfold.rna.albany.edu/?q=DINAMelt/software), extract, open a terminal, cd into the unafold_3.8 directory (likely ~/Downloads/unafold_3.8), and run ./configure.
[prompt]$ cd ~/Downloads/unafold_3.8 [prompt]$ ./configure
On my machine (MacBook Pro, 10.6.x OSX + XCode Tools 3), this produces the output found in the local file 2011june_unafold_configure_output.txt.
You will likely note two sets of errors in the ./configure output:
./configure: line 8579: sort: No such file or directory ./configure: line 8576: sed: No such file or directory
./configure: line 10077: sort: No such file or directory ./configure: line 10074: sed: No such file or directory
The 10077 and 10074 errors are a bit odd because there are only 10039 lines in the configure file.
Are these errors important? No, you can build UNAFold just fine. I have run into these two â€œsortâ€ and â€œsedâ€ problems with a few other build attempts in OSX but have no good answer as to how to get around them (in case youâ€™re wondering, sort and sed are most certainly installed on the machine. The â€œsortâ€ error can be removed by specifying the path explicitly in the configure file (in line 8579, change â€œsortâ€ the â€œ/usr/bin/sortâ€), but the sed error persists in the few attempts I tried to work around it. It doesnâ€™t appear to be a simple PATH issue. Iâ€™m not yet interested enough in finding a proper solution but, if you know, please post a comment or send a message. Is it just a character issue as discussed at itmercenary.livejournal.com/1585.html?).
running â€œmakeâ€ produces the output found in the local file 2011june_unafold_make_output.txt.
No issues. To install UNAFold, which will default to putting components into /usr/local/bin and /usr/local/share/, run sudo make install, which produces the output found in the local file 2011june_unafold_sudo_make_install_output.txt.
[prompt]$ sudo make install
Again, no issues. You will now have a populated /usr/local/bin folder.
2. MFold Utilities 4.5 (and, currently, the source for 4.6)
The next (optional) step is the inclusion of the mfold_util-4.5-Mac binaries (currently available at mfold.rna.albany.edu/?q=mfold/download-mfold), which Iâ€™ve also placed into the /usr/local/bin folder by extracting the contents of this file, them performing a cp * /usr/local/bin from within the MacBin directory.
[prompt]$ cd ~/Downloads/MacBin/ [prompt]$ sudo cp * /usr/local/bin
The processing of the data into plots with these programs requires that a set of *.col files be placed in the folder /usr/local/shared/mfold_util. Furthermore, these *.col are NOT provided in the mfold_util-4.5-Mac binary package. To get these files, you need only download the mfold_util-4.6.tar.gz file (currently at mfold.rna.albany.edu/?q=mfold/download-mfold), cd your way into src, make the /usr/local/shared/mfold_util folder, and copy the *.col files to /usr/local/shared/mfold_util.
[prompt]$ sudo mkdir /usr/local/shared/mfold_util [prompt]$ cd Downloads/mfold_util-4.6/src [prompt]$ sudo cp *.col /usr/local/shared/mfold_util
3. Fink 0.29.21 Install From Scratch
The first indication that other work was required came from trying to run mutplot randomly, which produced the following error:
dyld: Library not loaded: /sw/lib/libpng12.0.dylib Referenced from: /usr/local/bin/mutplot Reason: image not found Trace/BPT trap
As digging around for libraries is not as straightforward as it would be for a Linux distro, I chose instead to solve the many problems by installing dependencies through the Fink program (currently fink-0.29.21). As 10.6.x users will find that there is no available Fink binary, you must build this from the source (which, with Xcode Tools 3 installed, occurs without error. If you don’t have Xcode Tools 3 installed, the new mechanism for buying a copy of XCode Tools 4 is less than ideal (to me, anyway. $4.99?) but now occurs through the App Store).
Download the fink source (fink 0.29.21), extract, cd into the fink-0.29.21 directory, and run bootstrap. Upon completion, you run pathsetup.sh, source your .profile, and update fink.
[prompt]$ cd ~/Downloads/fink-0.29.21 [prompt]$ ./bootstrap [prompt]$ . /sw/bin/pathsetup.sh [prompt]$ cd ~/ [prompt]$ source .profile [prompt]$ fink selfupdate-rsync [prompt]$ fink update-all
The output for my installation can be found in 2011june_fink_install_output.txt. The rsync output can be found in 2011june_fink_selfupdate_rsync_output.txt. NOTE: You will be asked several questions about the installation process. Be prepared to blindly select the default settings with [enter], but don’t just walk away from the screen.
This completes the UNAFold install, MacBin install, and Fink install, meaning now we can walk through the dependencies.
4. Installing UNAFold (well, MFold Utils) Dependencies
First dependency-free UNAFold.pl run attempt produces the following error:
[prompt]$ UNAFold.pl seqtest.txt Checking for boxplot_ng... dyld: Library not loaded: /sw/lib/libpng12.0.dylib Referenced from: /usr/local/bin/boxplot_ng Reason: image not found found, supports Postscript Checking for hybrid-plot-ng... found, supports Postscript Checking for sir_graph_ng or sir_graph... dyld: Library not loaded: /sw/lib/libpng12.0.dylib Referenced from: /usr/local/bin/sir_graph Reason: image not found found, supports Postscript Checking for ps2pdfwr... not found Calculating for seqtest.txt, t = 37
As the UNAFold install page states, you need glut, the GD library, and gnuplot installed (and all of the many libraries therein).
[prompt]$ fink install libjpeg tetex gd2 gnuplot
For gnuplot, you will be required to make a few selections during the build process (blindly hitting the enter key at these questions will do, but this is not just a “type and go” install process. And it took about two hours on a MBP).
A final working error-free run looks as below, leaving you to process the data with the MFold Utilities as you like:
[prompt]$ UNAFold.pl seqtest.txt Checking for boxplot_ng... found, supports Postscript Checking for hybrid-plot-ng... found, supports Postscript Checking for sir_graph_ng or sir_graph... found, supports Postscript Checking for ps2pdfwr... found Calculating for seqtest.txt, t = 37