Révision c25275e2 README
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APPENDICE: Generate .c2c Files |
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============================== |
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$$$ TODO make it works properly. working directory. |
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The *.c2c* files is a simple table that describes how the genome |
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sequence can be aligned. We generate it using NucleoMiner 1.0. |
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sequence can be aligned. We generate it using some NucleoMiner 1.0 |
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scripts. |
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To install NucleoMiner 1.0 on your UNIX/LINUX computer you need first
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to install the Genetic Data analysis Library (GDL), which is a dynamic
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library of useful C functions derived from the GNU Scientific Library.
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To use NucleoMiner 1.0 scripts on your UNIX/LINUX computer you need
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first to install MUMmer which is a system for rapidly aligning entire
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genomes, whether in complete or draft form.
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Installing the GDL library
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-------------------------- |
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Installing the MUMmer library
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-----------------------------
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Get the gdl-1.0.tar.gz archive on your computer (in the directory deps
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of your working directory). Copy it in a dedicated directory. Go into
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this directory using the cd command, and then unfold the archive by
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typing:
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Get the last version of MUMmer archive on your computer
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(MUMmer3.23.tar.gz distributed in the directory deps of your working
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directory). Copy it in a dedicated directory. Install it locally into
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the src folder of you working directory by typing (working directory):
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tar -xvzf gdl-1.0.tar.gz |
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This creates a directory called gdl-1.0. You now need to go into this |
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directory and compile the library, by typing: |
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mkdir tmp_c2c_workdir |
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cd tmp_c2c_workdir |
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cp ../deps/gdl-1.0.tar.gz . |
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tar -xvzf gdl-1.0.tar.gz |
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cd gdl-1.0 |
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./configure |
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make |
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cd .. |
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Now you need to install the library on your system. This needs root |
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priviledges: |
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cd src |
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tar xfvz ../deps/MUMmer3.23.tar.gz |
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cd MUMmer3.23 |
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make check |
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make install |
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sudo make install |
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Installing NucleoMiner 1.0 scripts |
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---------------------------------- |
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Installing NucleoMiner 1.0 |
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-------------------------- |
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Get the nucleominer-1.0.tar.gz archive on your computer. Copy it in a |
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dedicated directory. Go into this directory using the cd command, and |
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then unfold the archive by typing: |
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This creates a directory called nucleominer-1.0. You now need to go |
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into this directory and compile the library, by typing: |
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cp ../deps/nucleominer-1.0.tar.gz . |
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tar -xvzf nucleominer-1.0.tar.gz |
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cd nucleominer-1.0 |
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ln -s ../gdl-1.0/gdl |
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./configure |
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make |
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Get the nucleominer-1.0.tar.gz archive on your computer (distributed |
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in the directory deps of your working directory). Install it locally |
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into the src folder of you working directory by typing (working |
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directory): |
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You can then use the binaries dircetly from this folder (best then is |
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to add the path to this folder in your PATH environment variable). If |
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you want to install nucleominer at the system's level (useful if |
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mutiple users will need it) then type, with root priviledges: |
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cd src |
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tar xfvz ../deps/nucleominer-1.0.tar.gz |
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cd .. |
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sudo make install |
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This creates a directory called that contains NucleoMiner 1.0 scripts |
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(src/nucleominer-1.0/scripts). |
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Generate .c2c Files |
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To generate .c2c files you need to type the following command in a |
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terminal: |
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mkdir dir_4_c2c |
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NMgxcomp ../data/saccharomyces_cerevisiae_BY_S288c_chromosomes.fasta\ |
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../data/saccharomyces_cerevisiae_rm11-1a_1_supercontigs.fasta\ |
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dir_4_c2c/BY_RM 2>dir_4_c2c/BY_RM.log |
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export PATH=$PATH:src/MUMmer3.23:src/nucleominer-1.0/scripts |
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export PERL5LIB=$PERL5LIB:src/nucleominer-1.0/scripts/ |
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NMgxcomp data/saccharomyces_cerevisiae_BY_S288c_chromosomes.fasta \ |
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data/saccharomyces_cerevisiae_rm11-1a_1_supercontigs.fasta \ |
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data/byxrm 2>NMgxcomp.log |
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After execution, the directory *dir_4_c2c* will hold the .c2c files. |
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After execution, the directory *data* will hold the .c2c files. |
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