Révision 5badc2fd doc/sphinx_doc/tuto.rst
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Working Directory Organisation |
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ |
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The working directory...
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After having install NucleoMiner2 environment (Previous section), go to the root working directory of the tutorial by typing the following command in a terminal:
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$$$ TODO: Explain how and where retrieve the workdir
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.. code:: bash
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cd doc/Chuffart_NM2_workdir/ |
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Retrieving Experimental Dataset |
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.. |
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.. |
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.. $$$ other python script to describe: |
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.. - libcoverage.py |
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.. - wf.py |
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.. |
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APPENDICE: Generate .c2c Files |
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------------------------------ |
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$$$ TODO make it works properly. |
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working directory. |
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The `.c2c` files is a simple table that describes how the genome sequence can be aligned. We generate it using NucleoMiner 1.0. |
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To install NucleoMiner 1.0 on your UNIX/LINUX computer you need first to install the Genetic Data analysis Library (GDL), which is a dynamic library of useful C functions derived from the GNU Scientific Library. |
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.. code:: bash |
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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 priviledges: |
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sudo make install |
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Installing NucleoMiner |
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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 dedicated directory. Go into this directory using the cd command, and then unfold the archive by typing: |
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tar -xvzf nucleominer-1.0.tar.gz |
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This creates a directory called nucleominer-1.0. You now need to go into this directory and compile the library, by typing: |
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.. code:: bash |
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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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.. code:: bash |
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mkdir dir_4_c2c |
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NMgxcomp Data/BY_S288c/Sequence/Genome.fasta \
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Data/RM_11-1a/Sequence/Genome.fasta \
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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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After execution, the directory dir_4_c2c will hold the .c2c files. |
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After execution, the directory `dir_4_c2c` will hold the .c2c files. |
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