Loading README.md +12 −12 Original line number Original line Diff line number Diff line # nested # nested #### Introduction ## Introduction *nested* (now also called *TE-greedy*) is software to analyze nested LTR transposable elements *nested* (now also called *TE-greedy*) is software to analyze nested LTR transposable elements in DNA sequences, such as reference genomes. It is made of two components: *nested-generator* in DNA sequences, such as reference genomes. It is made of two components: *nested-generator* Loading @@ -10,7 +10,7 @@ in the input. Unlike other similar software, *TE-greedy-nester* is structure-bas de-novo retrotransposon identification software *LTR Finder*, relying on sequence information de-novo retrotransposon identification software *LTR Finder*, relying on sequence information only secondarily. only secondarily. #### External tools ## External tools Program is using other external tools. Before usage make sure you have the following tools installed: Program is using other external tools. Before usage make sure you have the following tools installed: - LTR finder (v 1.05+) - - LTR finder (v 1.05+) - Loading @@ -20,7 +20,7 @@ https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Do - genometools (v 1.5.8) with gt sketch - - genometools (v 1.5.8) with gt sketch - https://github.com/genometools/genometools https://github.com/genometools/genometools #### Installation - a step-by-step guide ## Installation - a step-by-step guide ``` ``` chmod +x setup.sh chmod +x setup.sh Loading @@ -29,13 +29,13 @@ sudo ./setup.sh ### Prerequisites ### Prerequisites ## ncbi blast+ #### ncbi blast+ ``` ``` sudo apt install blast2 sudo apt install blast2 ``` ``` ## LTR_finder #### LTR_finder ``` ``` git clone https://github.com/xzhub/LTR_Finder.git git clone https://github.com/xzhub/LTR_Finder.git Loading @@ -43,14 +43,14 @@ cd source make make ``` ``` ## genome tools #### genome tools ``` ``` sudo apt-get install genometools sudo apt-get install genometools sudo apt-get install libgenometools0 libgenometools0-dev sudo apt-get install libgenometools0 libgenometools0-dev ``` ``` ## python requirements using pip3 #### python requirements using pip3 ``` ``` pip3 install bcbio-gff==0.6.4 click==6.7 decorator==4.2.1 networkx==2.1 numpy==1.14.2 pip3 install bcbio-gff==0.6.4 click==6.7 decorator==4.2.1 networkx==2.1 numpy==1.14.2 Loading @@ -59,22 +59,22 @@ PyYAML==3.12 six==1.11. --no-cache-dir ### TE-greedy-nester ### TE-greedy-nester ## clone whole directory from gitlab: #### clone whole directory from gitlab: ``` ``` git clone https://gitlab.fi.muni.cz/lexa/nested.git git clone https://gitlab.fi.muni.cz/lexa/nested.git cd nested cd nested ``` ``` ## modify respective paths in 'config_template.yml' save as 'config.yml' and call: #### modify respective paths in 'config_template.yml' save as 'config.yml' and call: ``` ``` sudo ./setup.sh sudo ./setup.sh ``` ``` ## that’s all! #### that’s all! #### Setting up the config ## Setting up the config Before usage, **config.yml** needs to be set up: Before usage, **config.yml** needs to be set up: - ltr finder paths - executable, prosite and tRNAdb - ltr finder paths - executable, prosite and tRNAdb Loading @@ -86,7 +86,7 @@ Before usage, **config.yml** needs to be set up: **Note**: `config.yml` is located by default in directory `/etc/nested/.` **Note**: `config.yml` is located by default in directory `/etc/nested/.` #### Usage ## Usage ``` ``` Usage: nested-nester [OPTIONS] INPUT_FASTA Usage: nested-nester [OPTIONS] INPUT_FASTA Loading Loading
README.md +12 −12 Original line number Original line Diff line number Diff line # nested # nested #### Introduction ## Introduction *nested* (now also called *TE-greedy*) is software to analyze nested LTR transposable elements *nested* (now also called *TE-greedy*) is software to analyze nested LTR transposable elements in DNA sequences, such as reference genomes. It is made of two components: *nested-generator* in DNA sequences, such as reference genomes. It is made of two components: *nested-generator* Loading @@ -10,7 +10,7 @@ in the input. Unlike other similar software, *TE-greedy-nester* is structure-bas de-novo retrotransposon identification software *LTR Finder*, relying on sequence information de-novo retrotransposon identification software *LTR Finder*, relying on sequence information only secondarily. only secondarily. #### External tools ## External tools Program is using other external tools. Before usage make sure you have the following tools installed: Program is using other external tools. Before usage make sure you have the following tools installed: - LTR finder (v 1.05+) - - LTR finder (v 1.05+) - Loading @@ -20,7 +20,7 @@ https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Do - genometools (v 1.5.8) with gt sketch - - genometools (v 1.5.8) with gt sketch - https://github.com/genometools/genometools https://github.com/genometools/genometools #### Installation - a step-by-step guide ## Installation - a step-by-step guide ``` ``` chmod +x setup.sh chmod +x setup.sh Loading @@ -29,13 +29,13 @@ sudo ./setup.sh ### Prerequisites ### Prerequisites ## ncbi blast+ #### ncbi blast+ ``` ``` sudo apt install blast2 sudo apt install blast2 ``` ``` ## LTR_finder #### LTR_finder ``` ``` git clone https://github.com/xzhub/LTR_Finder.git git clone https://github.com/xzhub/LTR_Finder.git Loading @@ -43,14 +43,14 @@ cd source make make ``` ``` ## genome tools #### genome tools ``` ``` sudo apt-get install genometools sudo apt-get install genometools sudo apt-get install libgenometools0 libgenometools0-dev sudo apt-get install libgenometools0 libgenometools0-dev ``` ``` ## python requirements using pip3 #### python requirements using pip3 ``` ``` pip3 install bcbio-gff==0.6.4 click==6.7 decorator==4.2.1 networkx==2.1 numpy==1.14.2 pip3 install bcbio-gff==0.6.4 click==6.7 decorator==4.2.1 networkx==2.1 numpy==1.14.2 Loading @@ -59,22 +59,22 @@ PyYAML==3.12 six==1.11. --no-cache-dir ### TE-greedy-nester ### TE-greedy-nester ## clone whole directory from gitlab: #### clone whole directory from gitlab: ``` ``` git clone https://gitlab.fi.muni.cz/lexa/nested.git git clone https://gitlab.fi.muni.cz/lexa/nested.git cd nested cd nested ``` ``` ## modify respective paths in 'config_template.yml' save as 'config.yml' and call: #### modify respective paths in 'config_template.yml' save as 'config.yml' and call: ``` ``` sudo ./setup.sh sudo ./setup.sh ``` ``` ## that’s all! #### that’s all! #### Setting up the config ## Setting up the config Before usage, **config.yml** needs to be set up: Before usage, **config.yml** needs to be set up: - ltr finder paths - executable, prosite and tRNAdb - ltr finder paths - executable, prosite and tRNAdb Loading @@ -86,7 +86,7 @@ Before usage, **config.yml** needs to be set up: **Note**: `config.yml` is located by default in directory `/etc/nested/.` **Note**: `config.yml` is located by default in directory `/etc/nested/.` #### Usage ## Usage ``` ``` Usage: nested-nester [OPTIONS] INPUT_FASTA Usage: nested-nester [OPTIONS] INPUT_FASTA Loading
