<commit_before>
.. _conda:

Conda mediated Installation
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

I'd really like to build a bioconda installation package, but would need some help.  You can however install quite a few of the dependencies with conda.


**If you are on LINUX -- start here:**

.. code-block:: none
    
    #If you do not have conda, install: download miniconda2 or miniconda3, miniconda3 shown
    wget --quiet https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh
    /bin/bash ~/miniconda.sh -b -p /conda/installation/path
    
    #setup bioconda repository
    conda config --add channels defaults
    conda config --add channels etetoolkit
    conda config --add channels bioconda
    conda config --add channels conda-forge
    
    #now create a conda environment and install dependencies
    conda create -y -n funannotate python=2.7 numpy pandas scipy matplotlib seaborn \
        natsort scikit-learn psutil biopython requests blast rmblast goatools fisher \
        bamtools augustus bedtools hmmer exonerate diamond>=0.9 tbl2asn ucsc-pslcdnafilter \
        samtools raxml trimal mafft>=7 iqtree kallisto bowtie2 infernal mummer minimap2 blat \
        trinity>=2.6.6 evidencemodeler pasa>=2.3 codingquarry stringtie gmap=2017.11.15 \
        ete3 salmon>=0.9 jellyfish>=2.2 htslib trnascan-se repeatmasker repeatmodeler hisat2 \
        trf perl-threaded perl-db-file perl-bioperl perl-dbd-mysql perl-dbd-sqlite \
        perl-text-soundex perl-scalar-util-numeric perl-data-dumper perl-dbi perl-clone \
        perl-json perl-logger-simple perl-hash-merge perl-yaml perl-pod-usage perl-getopt-long \
        perl-parallel-forkmanager perl-carp perl-soap-lite perl-class-inspector perl-app-cpanminus
    
    #if you are going to use remote search also need LWP module (not on conda)
    cpanm LWP
    
**If you are on MacOS X -- start here:**

.. code-block:: none
    
    #If you do not have conda, install: download miniconda2 or miniconda3, miniconda3 shown
    wget --quiet https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh
    /bin/bash ~/miniconda.sh -b -p /conda/installation/path
    
    #setup bioconda repository
    conda config --add channels defaults
    conda config --add channels etetoolkit
    conda config --add channels bioconda
    conda config --add channels conda-forge
    
    #now create a conda environment and install dependencies
    conda create -y -n funannotate python=2.7 numpy pandas scipy matplotlib seaborn \
        natsort scikit-learn psutil biopython requests blast rmblast goatools fisher \
        bedtools hmmer exonerate diamond>=0.9 tbl2asn ucsc-pslcdnafilter \
        samtools raxml trimal mafft>=7 iqtree kallisto bowtie2 infernal mummer \
        evidencemodeler  gmap=2017.11.15 hisat2 blat minimap2 \
        ete3 salmon>=0.9 jellyfish>=2.2 htslib trnascan-se repeatmasker repeatmodeler  \
        trf perl-threaded perl-db-file perl-bioperl perl-dbd-mysql perl-dbd-sqlite \
        perl-text-soundex perl-scalar-util-numeric perl-data-dumper perl-dbi perl-clone \
        perl-json perl-logger-simple perl-hash-merge perl-yaml perl-pod-usage perl-getopt-long \
        perl-parallel-forkmanager perl-carp perl-soap-lite perl-class-inspector perl-app-cpanminus
    
    #if you are going to use remote search also need LWP module (not on conda)
    cpanm LWP
    
    #need to install bamtools/augustus/trinity/pasa manually
    Install bamtools/Augustus here: https://github.com/nextgenusfs/augustus
    Trinity: https://github.com/trinityrnaseq/trinityrnaseq
    PASA: https://github.com/PASApipeline/PASApipeline
    
    
The above will automatically install most of the dependencies, below there are a few manual steps.
        
    1.  Download/install GeneMark-ES/ET: (gmes_petap.pl must be in PATH)
        http://exon.gatech.edu/GeneMark/license_download.cgi
        
        * make sure to activate the license and move into proper location. you can test proper installation by running `gmes_petap.pl` in the terminal -- you should see help menu. Be careful of the shebang line, default is `/usr/bin/perl` which most likely is not what you want, more appropriate is `/usr/bin/env perl`
        
    2.  Install RepeatMasker/RepeatModeler  http://www.repeatmasker.org
    
     
    2b. Download Repbase RepeatMasker Libraries if you have not done so already.

    .. code-block:: none 
      
        wget --user name --password pass http://www.girinst.org/server/RepBase/protected/repeatmaskerlibraries/RepBaseRepeatMaskerEdition-20170127.tar.gz
        tar zxvf RepBaseRepeatMaskerEdition-20170127.tar.gz -C /path/to/repeatmasker/location<commit_msg>update conda install docs<commit_after>
.. _conda:

Conda mediated Installation
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

I'd really like to build a bioconda installation package, but would need some help.  You can however install quite a few of the dependencies with conda.


**If you are on LINUX -- start here:**

.. code-block:: none
    
    #If you do not have conda, install: download miniconda2 or miniconda3, miniconda3 shown
    wget --quiet https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh
    /bin/bash ~/miniconda.sh -b -p /conda/installation/path
    
    #setup bioconda repository
    conda config --add channels defaults
    conda config --add channels etetoolkit
    conda config --add channels bioconda
    conda config --add channels conda-forge
    
    #now create a conda environment and install dependencies
    conda create -y -n funannotate python=2.7 numpy pandas scipy matplotlib seaborn \
        natsort scikit-learn psutil biopython requests blast rmblast goatools fisher \
        bamtools augustus bedtools hmmer exonerate diamond>=0.9 tbl2asn ucsc-pslcdnafilter \
        samtools raxml trimal mafft>=7 iqtree kallisto bowtie2 infernal mummer minimap2 blat \
        trinity>=2.6.6 evidencemodeler pasa>=2.3 codingquarry stringtie gmap=2017.11.15 \
        ete3 salmon>=0.9 jellyfish>=2.2 htslib trnascan-se repeatmasker repeatmodeler hisat2 \
        trf perl-threaded perl-db-file perl-bioperl perl-dbd-mysql perl-dbd-sqlite \
        perl-text-soundex perl-scalar-util-numeric perl-data-dumper perl-dbi perl-clone \
        perl-json perl-logger-simple perl-hash-merge perl-yaml perl-pod-usage perl-getopt-long \
        perl-parallel-forkmanager perl-carp perl-soap-lite perl-class-inspector perl-app-cpanminus
    
    #if you are going to use remote search also need LWP module (not on conda)
    cpanm LWP
    
**If you are on MacOS X -- start here:**

.. code-block:: none
    
    #If you do not have conda, install: download miniconda2 or miniconda3, miniconda3 shown
    wget --quiet https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh
    /bin/bash ~/miniconda.sh -b -p /conda/installation/path
    
    #setup bioconda repository
    conda config --add channels defaults
    conda config --add channels etetoolkit
    conda config --add channels bioconda
    conda config --add channels conda-forge
    
    #now create a conda environment and install dependencies
    conda create -y -n funannotate python=2.7 numpy pandas scipy matplotlib seaborn \
        natsort scikit-learn psutil biopython requests blast rmblast goatools fisher \
        bedtools hmmer exonerate diamond>=0.9 tbl2asn ucsc-pslcdnafilter \
        samtools raxml trimal mafft>=7 iqtree kallisto bowtie2 infernal mummer \
        evidencemodeler  gmap=2017.11.15 hisat2 blat minimap2 \
        ete3 salmon>=0.9 jellyfish>=2.2 htslib trnascan-se repeatmasker repeatmodeler  \
        trf perl-threaded perl-db-file perl-bioperl perl-dbd-mysql perl-dbd-sqlite \
        perl-text-soundex perl-scalar-util-numeric perl-data-dumper perl-dbi perl-clone \
        perl-json perl-logger-simple perl-hash-merge perl-yaml perl-pod-usage perl-getopt-long \
        perl-parallel-forkmanager perl-carp perl-soap-lite perl-class-inspector perl-app-cpanminus
    
    #if you are going to use remote search also need LWP module (not on conda)
    cpanm LWP

    
Need to install bamtools/augustus/trinity/pasa manually:

Install bamtools/Augustus from here: https://github.com/nextgenusfs/augustus
Trinity: https://github.com/trinityrnaseq/trinityrnaseq
PASA: https://github.com/PASApipeline/PASApipeline
    
    
**The above will automatically install most of the dependencies, below there are a few manual steps.**
        
    1.  Download/install GeneMark-ES/ET: (gmes_petap.pl must be in PATH)
        http://exon.gatech.edu/GeneMark/license_download.cgi
        
        * make sure to activate the license and move into proper location. you can test proper installation by running `gmes_petap.pl` in the terminal -- you should see help menu. Be careful of the shebang line, default is `/usr/bin/perl` which most likely is not what you want, more appropriate is `/usr/bin/env perl`
        
    2.  Install RepeatMasker/RepeatModeler  http://www.repeatmasker.org
    
     
    2b. Download Repbase RepeatMasker Libraries if you have not done so already.

    .. code-block:: none 
      
        wget --user name --password pass http://www.girinst.org/server/RepBase/protected/repeatmaskerlibraries/RepBaseRepeatMaskerEdition-20170127.tar.gz
        tar zxvf RepBaseRepeatMaskerEdition-20170127.tar.gz -C /path/to/repeatmasker/location
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