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readme.txt
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Dependencies
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1. Chromosome3D is implemented to run in Linux environment.
It was tested in "x86_64 GNU/Linux" OS.
2. Perl v5.10.1 was used during development and testing;
But it should run with other versions of perl as well.
3. CNS suite
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Installation
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1. Install CNS suite
1.1. To download CNS suite, provide your academic profile related
information at http://cns-online.org/cns_request/. An email
with (a) link to download, (b) login, and (c) password
will be sent to you. Follow the link, possibly
http://cns-online.org/download/, and download
CNS suite "cns_solve_1.3_all_intel-mac_linux.tar.gz".
1.2. Unzip
$ tar xzvf cns_solve_1.3_all_intel-mac_linux.tar.gz
1.3. Change directory to cns_solve
$ cd cns_solve_1.3
1.4. Unhide the file '.cns_solve_env_sh'
$ mv .cns_solve_env_sh cns_solve_env.sh
1.5. Edit 'cns_solve_env.sh' and 'cns_solve_env' to replace
'_CNSsolve_location_' with CNS installation directory.
For instance, if your CNS installation path is
'/home/user/programs/cns_solve_1.3' replace
'_CNSsolve_location_' with this path
1.6. Increase the value for ‘nrestraints’ (maximum number of restraints it can take)
Change the code at line 60 of the module ‘cns_solve_1.3/modules/nmr/readdata’
$ vim cns_solve_1.3/modules/nmr/readdata
- change 20000 to 200000 (by adding a zero)
1.7. Test CNS installation
$ source cns_solve_env.sh
$ cd test
$ ../bin/run_tests -tidy *.inp
2. Download chromosome3D_v1.0.tar.gz
3.1 Download chromosome3D_v1.0.tar.gz if you don't have it.
3.2 Untar
$ tar zxvf chromosome3D_v1.0.tar.gz
3.3 Change directory to chromosome3D_v1.0
$ cd chromosome3D_v1.0
3. Change variable values in the chromosome3D.pl file
3.1 Change the path of the variable $cns_suite
to CNS installation directory
3.2 Make it executable
$chmod +x chromosome3D.pl
4. Test Chromosome3D
4.1 Execute "perl ./chromosome3D.pl" or "./chromosome3D.pl"
It should print the usage information.
4.2 Test using an example
$ ./chromosome3D.pl -if "./input/chr22_1mb_matrix.txt" -o "./output/chr22_1mb"
4.3 Test by building structures for all the chromosomes at 1MB and 500KB
$ ./test.sh
-----------------------------------------------------------
Please cite:
"Chromosome3D: reconstructing three-dimensional chromosomal structures from Hi-C interaction frequency data using distance geometry simulated annealing". B. Adhikari, T. Trieu, J. Cheng. BMC Genomics, 2016.
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chengji@missouri.edu (PI)